WO2018191534A1 - Procédés, compositions et dispositifs permettant de séparer et/ou d'enrichir des cellules - Google Patents

Procédés, compositions et dispositifs permettant de séparer et/ou d'enrichir des cellules Download PDF

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Publication number
WO2018191534A1
WO2018191534A1 PCT/US2018/027358 US2018027358W WO2018191534A1 WO 2018191534 A1 WO2018191534 A1 WO 2018191534A1 US 2018027358 W US2018027358 W US 2018027358W WO 2018191534 A1 WO2018191534 A1 WO 2018191534A1
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Prior art keywords
filtration
filter
sample
housing
pluronic
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PCT/US2018/027358
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English (en)
Inventor
Antonio Guia
Michael J. BALACEK
Ky TRUONG
Alejandra RAMOS
Keith CANNON
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Aviva Biosciences Corporation
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Publication of WO2018191534A1 publication Critical patent/WO2018191534A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
    • C12M47/00—Means for after-treatment of the produced biomass or of the fermentation or metabolic products, e.g. storage of biomass
    • C12M47/02—Separating microorganisms from the culture medium; Concentration of biomass
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00—Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50—Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/502753—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip characterised by bulk separation arrangements on lab-on-a-chip devices, e.g. for filtration or centrifugation
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C1/00—Magnetic separation
    • B03C1/005—Pretreatment specially adapted for magnetic separation
    • B03C1/01—Pretreatment specially adapted for magnetic separation by addition of magnetic adjuvants
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C1/00—Magnetic separation
    • B03C1/02—Magnetic separation acting directly on the substance being separated
    • B03C1/025—High gradient magnetic separators
    • B03C1/031—Component parts; Auxiliary operations
    • B03C1/033—Component parts; Auxiliary operations characterised by the magnetic circuit
    • B03C1/0332—Component parts; Auxiliary operations characterised by the magnetic circuit using permanent magnets
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C1/00—Magnetic separation
    • B03C1/02—Magnetic separation acting directly on the substance being separated
    • B03C1/025—High gradient magnetic separators
    • B03C1/031—Component parts; Auxiliary operations
    • B03C1/033—Component parts; Auxiliary operations characterised by the magnetic circuit
    • B03C1/0335—Component parts; Auxiliary operations characterised by the magnetic circuit using coils
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C1/00—Magnetic separation
    • B03C1/02—Magnetic separation acting directly on the substance being separated
    • B03C1/28—Magnetic plugs and dipsticks
    • B03C1/288—Magnetic plugs and dipsticks disposed at the outer circumference of a recipient
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C5/00—Separating dispersed particles from liquids by electrostatic effect
    • B03C5/005—Dielectrophoresis, i.e. dielectric particles migrating towards the region of highest field strength
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C5/00—Separating dispersed particles from liquids by electrostatic effect
    • B03C5/02—Separators
    • B03C5/022—Non-uniform field separators
    • B03C5/026—Non-uniform field separators using open-gradient differential dielectric separation, i.e. using electrodes of special shapes for non-uniform field creation, e.g. Fluid Integrated Circuit [FIC]
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C5/00—Separating dispersed particles from liquids by electrostatic effect
    • B03C5/02—Separators
    • B03C5/022—Non-uniform field separators
    • B03C5/028—Non-uniform field separators using travelling electric fields, i.e. travelling wave dielectrophoresis [TWD]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
    • C12M33/00—Means for introduction, transport, positioning, extraction, harvesting, peeling or sampling of biological material in or from the apparatus
    • C12M33/14—Means for introduction, transport, positioning, extraction, harvesting, peeling or sampling of biological material in or from the apparatus with filters, sieves or membranes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N13/00—Treatment of microorganisms or enzymes with electrical or wave energy, e.g. magnetism, sonic waves
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00—Sampling; Preparing specimens for investigation
    • G01N1/28—Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/40—Concentrating samples
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/06—Auxiliary integrated devices, integrated components
    • B01L2300/0681—Filter
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0861—Configuration of multiple channels and/or chambers in a single devices
    • B01L2300/0864—Configuration of multiple channels and/or chambers in a single devices comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00—Additional constructional details
    • B01L2300/08—Geometry, shape and general structure
    • B01L2300/0861—Configuration of multiple channels and/or chambers in a single devices
    • B01L2300/0867—Multiple inlets and one sample wells, e.g. mixing, dilution
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2400/00—Moving or stopping fluids
    • B01L2400/06—Valves, specific forms thereof
    • B01L2400/0622—Valves, specific forms thereof distribution valves, valves having multiple inlets and/or outlets, e.g. metering valves, multi-way valves
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C2201/00—Details of magnetic or electrostatic separation
    • B03C2201/18—Magnetic separation whereby the particles are suspended in a liquid
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B03—SEPARATION OF SOLID MATERIALS USING LIQUIDS OR USING PNEUMATIC TABLES OR JIGS; MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C—MAGNETIC OR ELECTROSTATIC SEPARATION OF SOLID MATERIALS FROM SOLID MATERIALS OR FLUIDS; SEPARATION BY HIGH-VOLTAGE ELECTRIC FIELDS
    • B03C2201/00—Details of magnetic or electrostatic separation
    • B03C2201/26—Details of magnetic or electrostatic separation for use in medical applications
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N15/14—Optical investigation techniques, e.g. flow cytometry
    • G01N15/1456—Optical investigation techniques, e.g. flow cytometry without spatial resolution of the texture or inner structure of the particle, e.g. processing of pulse signals
    • G01N15/1459—Optical investigation techniques, e.g. flow cytometry without spatial resolution of the texture or inner structure of the particle, e.g. processing of pulse signals the analysis being performed on a sample stream
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N15/14—Optical investigation techniques, e.g. flow cytometry
    • G01N15/1468—Optical investigation techniques, e.g. flow cytometry with spatial resolution of the texture or inner structure of the particle
    • G01N15/147—Optical investigation techniques, e.g. flow cytometry with spatial resolution of the texture or inner structure of the particle the analysis being performed on a sample stream
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00—Sampling; Preparing specimens for investigation
    • G01N1/28—Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/40—Concentrating samples
    • G01N1/4077—Concentrating samples by other techniques involving separation of suspended solids
    • G01N2001/4088—Concentrating samples by other techniques involving separation of suspended solids filtration
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N2015/1006—Investigating individual particles for cytology
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/10—Devices for transferring samples or any liquids to, in, or from, the analysis apparatus, e.g. suction devices, injection devices

Definitions

  • the present invention relates generally to the field of bioseparation, and in particular to the field of biological sample processing. Methods, compositions, kits, and devices for separating and/or enriching cells, such as those in human blood, are disclosed. Background
  • Sample preparation is a necessary step for many genetic, biochemical, and biological analyses of biological and environmental samples.
  • Sample preparation frequently requires the separation of sample components of interest from the remaining components of the sample. Such separations are often labor intensive and difficult to automate.
  • a sample must be“debulked” to reduce its volume, and in addition subjected to separation techniques that can enrich the components of interest.
  • biological samples such as ascites fluid, lymph fluid, or blood, that can be harvested in large amounts, but that can contain minute percentages of target cells (such as virus-infected cells, anti-tumor T-cells, inflammatory cells, cancer cells, or fetal cells) whose separation is of critical importance for understanding the basis of disease states as well as for diagnosis and development of therapies.
  • Filtration has been used as a method of reducing the volume of samples and separating sample components based on their ability to flow through or be retained by the filter.
  • membrane filters are used in such applications in which the membrane filters have interconnected, fiber-like, structure distribution and the pores in the membrane are not discretely isolated; instead the pores are of irregular shapes and are connected to each other within the membrane.
  • the so-called“pore” size really depends on the random tortuosity of the fluid-flow spaces (e.g., pores) in the membrane. While the membrane filters can be used for a number of separation applications, the variation in the pore size and the irregular shapes of the pores prevent them being used for precise filtration based on particle size and other properties.
  • Microfabricated filters have been made for certain cellular or molecular separation applications. These microfabricated structures do not have pores, but rather include channels that are microetched into one or more chips, by using“bricks” (see, for example, U.S. Patent No.5,837,115 issued Nov.17, 1998 to Austin et al., incorporated by reference) or dams see, for example, U.S. Patent No.5,726,026 issued Mar.10, 1998 to Wilding et al., incorporated by reference) that are built onto the surface of a chip. While these microfabricated filters have precise geometries, a limitation is that the filtration area of the filter is small, limited by the geometries of these filters, so that these filters can process only small volumes of the fluid sample.
  • Blood samples provide special challenges for sample preparation and analysis. Blood samples are easily obtained from subjects, and can provide a wealth of metabolic, diagnostic, prognostic, and genetic information. However, the great abundance of non-nucleated red blood cells, and their major component hemoglobin, can be an impediment to genetic, metabolic, and diagnostic tests.
  • the debulking of red blood cells from peripheral blood has been accomplished using different layers of dense solutions (for example, see US patent 5,437,987 issued August 1, 1995 to Teng, Nelson N.H. et al). Long chain polymers such as dextran have been used to induce the aggregation of red blood cells resulting in the formation of long red blood cell chains (Sewchand LS, Canham PB.
  • Exfoliated cells in body fluids present a significant opportunity for detection of precancerous lesions and for eradication of cancer at early stages of neoplastic development.
  • urine cytology is universally accepted as the noninvasive test for the diagnosis and surveillance of transitional cell carcinoma (Larsson et al (2001) Molecular Diagnosis 6: 181-188).
  • the cytologic identification of abnormal exfoliated cells has been limited by the number of abnormal cells isolated. For routine urine cytology (Ahrendt et al. (1999) J. Natl.
  • the overall sensitivity is less than 50%, which varies with tumor grade, tumor stage, and urine collection and processing methods used.
  • Molecular analysis e.g. using in situ hybridization, PCR, microarrays, etc.
  • biomarkers can significantly improve the cytology sensitivity.
  • Both biomarker studies and use of biomarkers for clinical practice would require a relatively pure exfoliated cell population enriched from body fluids comprising not only exfoliated cells but also normal cells, bacteria, body fluids, body proteins and other cell debris.
  • Meye et al., Int. J. Oncol., 21(3):521-30 (2002) describes isolation and enrichment of urologic tumor cells in blood samples by a semi-automated CD45 depletion autoMACS protocol.
  • Iinuma et al., Int. J. Cancer, 89(4):337-44 (2000) describes detection of tumor cells in blood using CD45 magnetic cell separation followed by nested mutant allele-specific amplification of p53 and K-ras genes in patients with colorectal cancer.
  • tumor cells were mixed with mononuclear cells (MNCs) isolated by Ficoll gradient centrifugation from a blood sample. Tumor cells were then enriched from MNCs by negative depletion using an anti-CD45 antibody.
  • MNCs mononuclear cells
  • the present invention recognizes that diagnosis, prognosis, and treatment of many conditions can depend on the enrichment of target cells and/or cellular organelles from a complex fluid sample. Often, enrichment can be accomplished by one or more separation steps using a filtration device with slots that filter the cells according to the size, shape, deformability, binding affinity and/or binding specificity of the cells. For example, nucleated cells may be separated from non-nucleated red blood cells in peripheral blood samples using the filtration device.
  • the filtration device disclosed in the present application may deplete red blood cells based on their size, shape, deformability, binding affinity and/or binding specificity, and minimize loss of nucleated cells due to nonspecific lysis. Further, it may achieve minimal alteration to nucleated cell volume and make a centrifugation step unnecessary.
  • the separation of fetal cells from maternal blood samples can greatly aid in the detection of fetal abnormalities or a variety of genetic conditions.
  • the present invention recognizes that the enrichment or separation of rare malignant cells from patient samples, such as the isolation of cancerous cells from patient body fluid samples, can aid in the detection and typing of such malignant cells and therefore aid in diagnosis and prognosis, as well as in the development of therapeutic modalities for patients.
  • a filtration chamber comprising a microfabricated filter enclosed in a housing, wherein the surface of said filter and/or the inner surface of said housing are modified by vapor deposition, sublimation, vapor-phase surface reaction, or particle sputtering to produce a uniform coating; and a method for separating cells of a fluid sample, comprising: a) dispensing a fluid sample into the filtration chamber disclosed herein; and b) providing fluid flow of the fluid sample through the filtration chamber, wherein components of the fluid sample flow through or are retained by the filter based on the size, shape, or deformability of the components.
  • the present invention provides a filtration chamber comprising a
  • the filtration chamber comprises an antechamber and a post-filtration subchamber, and the fluid flow path in the antechamber is substantially opposite to the fluid flow path in the post-filtration subchamber.
  • each of the antechamber and the post- filtration subchamber has an inflow port and/or an outflow port.
  • the antechamber comprises at least two inflow ports.
  • the antechamber comprises a suprafilter thereby creating a suprachamber, wherein the suprafilter may be placed on the side opposing the microfabricated filter.
  • the suprafilter, between the antechamber and the suprachamber is sufficiently rigid to maintain its flatness under slow flow conditions.
  • the suprafilter comprises holes or slots with openings smaller than about 5 microns.
  • the inflow port and outflow port may be used interchangeably.
  • the microfabricated filter comprises one or more tapered slots. In some embodiments, the microfabricated filter comprises from about 100 to 5,000,000 tapered slots. In some embodiments, the thickness of the microfabricated filter is from about 20 to about 200 microns. In some embodiments, the thickness of the microfabricated filter is from about 40 to about 70 microns.
  • the tapered slots are from approximately 20 microns to 200 microns in length and from about 2 microns to about 16 microns in width, and the tapering of said slots is from about 0 degree to about 10 degrees, and the variation in slot size of said tapered slot is less than about 20%. In some embodiments, the size of the tapered slots varies by more than 20%. In some embodiments, the size of the tapered slots varies by more than 50%. In some embodiments, the size of the tapered slots varies by more than 100%. In some embodiments, the size of the tapered slots varies along the fluid flow path in the antechamber. In some embodiment, the post-filtration subchamber comprises at least two outflow ports.
  • the at least two outflow ports are arranged along the fluid flow path in the antechamber.
  • the filtration chamber comprises two or more electrodes.
  • the electrodes are placed on opposite sides of the microfabricated filter.
  • the electrodes are placed on the housing of the filtration chamber. In some embodiments, the electrodes are placed in the antechamber and/or the post-filtration subchamber. In some embodiments, the electrodes are incorporated or placed into one or more of the ports or connections that interact with the antechamber and/or the post-filtration subchamber. In some embodiments, the filtration chamber comprises at least one acoustic element. In some embodiments, the outflow port of the antechamber is connected to a collection chamber or collection well. In some embodiments, the housing comprises a top part and a bottom part, and the top part and the bottom part engage and may optionally bond together to form the filtration chamber.
  • the filtration chamber has a length of about 1 mm to about 10 cm, a width of about 1 mm to about 3 cm, and a depth of about 0.02 mm to about 20 mm. In some embodiments, the filtration chamber has a length of about 10 mm to about 50 mm, a width of about 5 mm to about 20 mm, and a depth of about 0.05 mm to about 2.5 mm. In some embodiments, the filtration chamber has a length of about 30 mm, a width of about 6 mm, and a depth of about 1 mm. In some embodiments, the housing containing it has a length of about 38 mm, a width of about 12 mm, and a depth of about 20 mm as outer dimensions.
  • the antechamber has a length of about 1 mm to about 10 cm, a width of about 1 mm to about 3 cm, and a depth of about 0.01 mm to about 10 mm. In some embodiments, the antechamber has a length of about 10 mm to about 50 mm, a width of about 5 mm to about 20 mm, and a depth of about 0.01 mm to about 1 mm. In some embodiments, the antechamber has a length of about 30 mm, a width of about 6 mm, and a depth of about 0.1-0.4 mm. In some embodiments, the volume of the antechamber is about 0.01 ⁇ L to about 5 mL.
  • the volume of the antechamber is about 1 ⁇ L to about 100 ⁇ L. In some embodiments, the volume of the antechamber is about 40-80 ⁇ L. In some embodiments, the post-filtration subchamber has a length of about 1 mm to about 10 cm, a width of about 1 mm to about 3 cm, and a depth of about 0.01 mm to about 1 cm. In some embodiments, the post-filtration subchamber has a length of about 10 mm to about 50 mm, a width of about 5 mm to about 20 mm, and a depth of about 0.2 mm to about 1.5 mm. In some embodiments, the post-filtration subchamber has a length of about 30 mm, a width of about 6.4 mm, and a depth of about 0.6-1 mm.
  • the present invention provides a filtration chamber comprising a
  • the filtration chamber comprises an antechamber and a post-filtration subchamber.
  • the antechamber comprises a suprafilter thereby creating a suprachamber.
  • the surface of the suprafilter is modified by vapor deposition, sublimation, vapor-phase surface reaction, or particle sputtering to produce a uniform coating.
  • the modification is by physical vapor deposition. In some embodiments, the modification is by plasma-enhanced chemical vapor deposition.
  • the vapor deposition is of a metal nitride or a metal halide.
  • the metal nitride is titanium nitride, silicon nitride, zinc nitride, indium nitride, and/or boron nitride.
  • the modification is by chemical vapor deposition.
  • the chemical vapor deposition is by Parylene or a derivative thereof.
  • the Parylene or derivative thereof is selected from the group consisting of Parylene, Parylene-N, Parylene-D, Parylene AF-4, Parylene SF, and Parylene HT.
  • the modification is by polytetrafluoroethylene (PTFE). In some embodiments, the modification is by amorphous Teflon or Teflon-AF. In some embodiments, the modification is by a perfluorocarbon. In some embodiments, the perfluorocarbon is 1H,1H,2H,2H-perfluorooctyltriethoxysilane, 1H,1H,2H,2H- perfluorodecyltriethoxysilane, trichloro(1H,1H,2H,2H-perfluorooctyl)silane or trichloro(octadecyl)silane and is in liquid form.
  • the filter and/or housing comprises silicon, silicon dioxide, glass, metal, carbon, ceramics, plastic, or a polymer. In some embodiments, the filter and/or housing comprises silicon nitride or boron nitride.
  • the present invention provides a filtration chamber comprising a
  • microfabricated filter enclosed in a housing, wherein the surface of said filter and/or the inner surface of said housing are modified by a metal nitride, a metal halide, a Parylene or derivative thereof, a
  • the filtration chamber comprises an antechamber and a post-filtration subchamber.
  • the antechamber comprises a suprafilter thereby creating a suprachamber.
  • the surface of the suprafilter is modified by a metal nitride, a metal halide, a Parylene or derivative thereof, a
  • the metal nitride is titanium nitride, silicon nitride, zinc nitride, indium nitride, and/or boron nitride.
  • the Parylene is selected from the group consisting of Parylene, Parylene-N, Parylene-D, Parylene AF-4, Parylene SF, and Parylene HT.
  • the perfluorocarbon is 1H,1H,2H,2H- perfluorooctyltriethoxysilane, 1H,1H,2H,2H-perfluorodecyltriethoxysilane, trichloro(1H,1H,2H,2H- perfluorooctyl)silane or trichloro(octadecyl)silane, and the perfluorocarbon covalently binds the surface.
  • the filter and/or housing comprises silicon, silicon dioxide, glass, metal, carbon, ceramics, plastic, or a polymer.
  • the filter and/or housing comprises silicon nitride or boron nitride.
  • a filtration chamber comprising a microfabricated filter enclosed in a housing, wherein the filtration chamber comprises an antechamber and a post-filtration subchamber, and the fluid flow path in the antechamber is substantially opposite to the fluid flow path in the post-filtration subchamber, wherein the surface of the filter and/or the inner surface of said housing are modified by vapor deposition, sublimation, vapor-phase surface reaction, or particle sputtering to produce a uniform coating.
  • a filtration chamber comprising a
  • the filtration chamber comprises an antechamber and a post-filtration subchamber, and the fluid flow path in the antechamber is substantially opposite to the fluid flow path in the post-filtration subchamber, wherein the surface of the filter and/or the inner surface of said housing are modified by a metal nitride, a metal halide, a Parylene, a polytetrafluoroethylene (PTFE), a Teflon-AF or a perfluorocarbon.
  • the filtration chamber provided herein may comprise at least two microfabricated filters. In some embodiments, the at least two microfabricated filters are arranged in tandem.
  • a filtration chamber comprising at least two filtration chambers disclosed herein arranged in tandem.
  • the antechambers of the at least two filtration chambers are in fluid connection.
  • the at least two filtration chambers share one microfabricated filter and/or suprafilter.
  • the slots of the filters within each filtration chamber are of different widths, and the filtration chambers are arranged in order of increasing slot widths.
  • the present invention provides a cartridge comprising a filtration chamber disclosed herein.
  • the cartridge comprises at least two filtration chambers.
  • the cartridge comprises eight filtration chambers.
  • the present invention provides an automated filtration unit for separating a target component in a fluid sample, comprising a filtration chamber disclosed herein.
  • the automated filtration unit comprises a control algorithm for controlling the fluid flow in the filtration chamber.
  • the automated filtration unit comprises at least two filtration chambers.
  • the at least two filtration chambers are arranged in tandem, and the filtration chambers comprise filters of increasing slot width.
  • the filters contain slot widths of increasing size along the fluidic path.
  • the filtration chamber comprises a suprachamber.
  • the post-filtration subchamber comprises multiple partitions each comprising an outflow port.
  • the outflow port from each partition of the post-filtration chamber is aligned with individual wells of a multi-well plate.
  • the wells are spaced about every 1-100 mm, e.g., about every 2.25 mm; about every 4.5 mm, or about every 9 mm or 18 mm.
  • the automated filtration unit comprises eight filtration chambers. In some embodiments, the automated filtration unit comprises a means for effecting fluid flow in the filtration chamber. In some embodiments, the means for effecting fluid flow is a fluidic pump. In some embodiments, the automated filtration unit comprises a means for collecting the separated target component.
  • the present invention provides an automated system for separating and analyzing a target component in a fluid sample, comprising an automated filtration unit disclosed herein and an analysis apparatus connected to the filtration unit.
  • the analysis apparatus is a cell sorting device.
  • the analysis apparatus is a flow cytometer.
  • the present invention provides a method for separating a target component in a fluid sample, comprising: a) dispensing a fluid sample into the filtration chamber disclosed herein; and b) providing a fluid flow of the fluid sample through the filtration chamber, wherein the target component of the fluid sample is retained by or passes through the filter.
  • the method comprises providing a fluid flow of the fluid sample through the antechamber of the filtration chamber and a fluid flow of a solution through the post-filtration subchamber of the filtration chamber, and optionally a fluid flow of a solution through the suprachamber of the filtration chamber.
  • the fluid sample is separated based on the size, shape, deformability, binding affinity and/or binding specificity of the components.
  • the fluid sample is dispensed through the inflow port of the antechamber.
  • the solution is introduced to the inflow port of the post-filtration subchamber.
  • the solution is introduced to the inflow port of the supra-filtration chamber.
  • the fluid sample is manipulated by a physical force effected via a structure that is external to the filter and/or a structure that is built-in on the filter.
  • the physical force is selected from the group consisting of a dielectrophoretic force, a traveling-wave dielectrophoretic force, a magnetic force, an acoustic force, an electrostatic force, a mechanical force, an optical radiation force and a thermal convection force.
  • the dielectrophoretic force or the traveling-wave dielectrophoretic force is effected via an electrical field produced by an electrode.
  • the acoustic force is effected via a standing-wave acoustic field or a traveling-wave acoustic field.
  • the acoustic force is effected via an acoustic field produced by piezoelectric material.
  • the acoustic force is effected via a voice coil or audio speaker.
  • the electrostatic force is effected via a direct current (DC) electric field.
  • the optical radiation force is effected via laser tweezers.
  • the sample is blood, an effusion, urine, a bone marrow sample, ascitic fluid, pelvic wash fluid, pleural fluid, spinal fluid, lymph, serum, mucus, sputum, saliva, semen, ocular fluid, extract of nasal, throat or genital swab, cell suspension from digested tissue, extract of fecal material, cultured cells of either mixed types and/or mixed sizes, or cells that contain contaminants or unbound reactants that need to be removed.
  • the fluid sample is a blood sample and the cells being separated are platelets and/or red blood cells (RBCs).
  • RBCs red blood cells
  • the fluid sample are cells that contain contaminants or unbound reactants that need to be removed, and the reactant is a labeling reagent for the cells.
  • the fluid sample is a blood sample and the cells being separated are non-hematopoietic cells, subpopulations of blood cells, fetal red blood cells, stem cells, or cancerous cells.
  • the fluid sample is an effusion or a urine sample and the cells being separated are cancerous cells or non-hematopoietic cells.
  • the present invention provides a method of separating a target component in a fluid sample using the automated filtration unit disclosed herein, comprising: a) dispensing the fluid sample into the filtration chamber; and b) providing a fluid flow of the fluid sample through the filtration chamber, wherein the target component of the fluid sample is retained by or flows through the filter.
  • the fluid sample is separated based on the size, shape, deformability, binding affinity and/or binding specificity of the components.
  • the fluid sample in the antechamber flows substantially anti-parallel to the solution in the post-filtration subchamber.
  • the filter rate is about 0-1 mL/min.
  • the filter rate is about 10-500 ⁇ L/min. In some embodiments, the filter rate is about 80-140 ⁇ L/min. In some embodiments, the feed rate is about 1-10 times the filter rate. [0024] In some embodiments, the method further comprises rinsing the retained components of the fluid sample with an additional sample-free rinsing reagent. In some embodiments, during the rinsing step the feed rate is less than or equal to the filter rate. In some embodiments, a rinsing reagent is introduced to the post-filtration subchamber. In some embodiments, the rinsing reagent is introduced to the antechamber and/or the suprachamber.
  • the method further comprises providing a labeling reagent to bind to the target component.
  • the labeling reagent is an antibody.
  • the labeling reagent is added to the collection chamber.
  • the labeling reagent is added to the antechamber and/or the suprachamber.
  • the method further comprises removing the unbound labeling reagent.
  • the method further comprises recovering the target component in the collection chamber. In some embodiments, during recovering the feed rate is about 5-20 mL/min.
  • the outflow rate equals the inflow rate in the post-filtration subchamber. In some embodiments, during the recovering step the outflow is paused for about 50 ms.
  • the fluid sample is a blood sample, which comprises removing at least one type of undesirable component using a specific binding member.
  • the at least one undesirable component are white blood cells (WBCs).
  • WBCs white blood cells
  • the specific binding member selectively binds to WBCs and is coupled to a solid support.
  • the specific binding member is an antibody or an antibody fragment that selectively binds to WBCs.
  • the specific binding member is an antibody that selectively binds to CD3, CD11b, CD14, CD17, CD31, CD45, CD50, CD53, CD63, CD69, CD81, CD84, CD102 or CD166.
  • the specific binding member is an antibody that selectively binds to CD35 and/or CD50.
  • the method further comprises contacting the blood sample with a secondary specific binding member.
  • the secondary specific binding member is an antibody that selectively binds to CD31, CD36, CD41, CD42 (a, b, or c), CD51, or CD51/61.
  • the present invention provides a method of enriching and analyzing a component in a fluid sample using the automated system disclosed herein, comprising: a) dispensing the fluid sample into the filtration chamber; b) providing a fluid flow of the fluid sample through the antechamber of the filtration chamber and a fluid flow of a solution through the post-filtration subchamber of the filtration chamber, wherein the target component of the fluid sample is retained in the antechamber and non-target components flow through the filter into the post-filtration subchamber; c) labeling the target component; and d) analyzing the labeled target component using the analysis apparatus.
  • the method comprises providing fluid flow into the suprachamber.
  • the target component is a cell or cellular organelle.
  • the cell is a nucleated cell.
  • the cell is a rare cell.
  • a method for separating a target component in a fluid sample comprises: a) passing a fluid sample that comprises or is suspected of comprising a target component and cell aggregates through a microfabricated filter so that said target component, if present in said fluid sample, is retained by or passes through said microfabricated filter, and b) prior to and/or concurrently with passing said fluid sample through said microfabricated filter, contacting said fluid sample with an emulsifying agent and/or a cellular cellular membrane charging agent to reduce, remove, and/or disaggregate said cell aggregates, if present in said fluid sample.
  • the fluid sample is a blood sample
  • the target components are nucleated cells
  • the cell aggregates to be reduced or disaggregated are rouleaux
  • the fluid sample is treated with a washing composition comprising one or more emulsifying agent(s) and/or one or more cellular membrane charging agent(s), e.g., DMSO and/or pluronic acid, before and/or during the filtration step (step a), the red blood cell, platelets and plasma pass through the microfabricated filter, and the target nucleated cells are retained by the microfabricated filter.
  • a washing composition comprising one or more emulsifying agent(s) and/or one or more cellular membrane charging agent(s), e.g., DMSO and/or pluronic acid
  • the fluid sample is a blood sample
  • the cell aggregates to be reduced or disaggregated are rouleaux
  • the fluid sample is treated with a washing composition comprising one or more emulsifying agent(s) and/or one or more cellular membrane charging agent(s), e.g., DMSO and/or pluronic acid, before and/or during the filtration step (step a), the blood sample passes a first part of the
  • the first filtrate then passes the second part of the microfabricated filter that allows the nucleated cells or other smaller cells, e.g., lymphocytes and monocytes, to pass through, while retaining larger cells or cell aggregates, e.g., doublets of cells.
  • the nucleated cells or other smaller cells that pass through the second part of the microfabricated filter are collected via a separate pathway.
  • the fluid sample is a blood sample
  • the cell aggregates to be reduced or disaggregated are rouleaux
  • the fluid sample is treated with a washing composition comprising one or more emulsifying agent(s) and/or one or more cellular membrane charging agent (s), e.g., DMSO and/or pluronic acid, before and/or during the filtration step (step a)
  • a filtration device comprising a first and a second microfabricated filters, a sample feed channel and a recovery chamber is used, the first microfabricated filter being located above the sample feed channel, having a non-stick surface and having a pore size smaller than about 5 ⁇ m, and the second microfabricated filter being located below the sample feed channel, the first microfabricated filter being used to maintain a continuous current of flow of a wash buffer across both microfabricated filters such that when the blood sample is fed through the feed channel and into the recovery chamber, all smaller particles, e.g., RBC, are caught in the cross current and removed from the blood sample.
  • a washing composition
  • the method can further comprise before the steps a) and/or b), passing the fluid sample through a prefilter that retains aggregated cells and microclots, and allows single cells and smaller particles with a diameter smaller than about 20 ⁇ m to pass through to generate a pre- treated fluid sample that is subject to the steps a) and/or b) subsequently.
  • the method further comprises before passing the fluid sample through the prefilter, treating the fluid sample with a cell aggregation agent to aggregate red blood cells, and removing the aggregated red blood cells.
  • the cell aggregation agent is a dextran, dextran sulfate, dextran or dextran sulfate with a molecular weight less than about 15kD, hetastarch, gelatin, pentastarch, poly ethylene glycol (PEG), fibrinogen, gamma globulin, hespan, pentaspan, hepastarch, ficoll, gum arabic, poyvinylpyrrolidone, or any combination thereof.
  • the aggregated red blood cells are removed via sedimentation or laminar flow or a combination thereof.
  • the fluid sample can be separated based on the size, shape, deformability, binding affinity and/or binding specificity of the components, e.g., the target component, cells and cell aggregates, in the fluid sample.
  • the fluid sample can be manipulated by a physical force effected via a structure that is external to the microfabricated filter and/or a structure that is built-in on the microfabricated filter.
  • the physical force is selected from the group consisting of a dielectrophoretic force, a traveling-wave dielectrophoretic force, a magnetic force, an acoustic force, an electrostatic force, a mechanical force, an optical radiation force and a thermal convection force.
  • the dielectrophoretic force or the traveling-wave dielectrophoretic force is effected via an electrical field produced by an electrode.
  • the acoustic force is effected via a standing-wave acoustic field or a traveling-wave acoustic field, via an acoustic field produced by piezoelectric material, and/or via a voice coil or audio speaker, or a combination thereof.
  • the electrostatic force is effected via a direct current (DC) electric field.
  • the optical radiation force is effected via laser tweezers.
  • the target component can be a cell, a sub-cellular structure or a virus in the fluid sample.
  • the fluid sample can comprise blood, effusion, urine, bone marrow sample, ascitic fluid, pelvic wash fluid, pleural fluid, spinal fluid, lymph, serum, mucus, sputum, saliva, semen, ocular fluid, extract of nasal, throat or genital swab, cell suspension from digested tissue, extract of fecal material, cultured cells of either mixed types and/or mixed sizes, or cells that contain contaminants or unbound reactants that need to be removed.
  • the fluid sample is a blood sample and the component being removed is a plasma, a platelet and/or a red blood cell (RBC).
  • the fluid sample comprises cells that contain contaminants or unbound reactants that need to be removed.
  • the reactant is a labeling reagent for the cells.
  • the reactant is a soluble or dissolved antigen or molecule that may compete for or interfere with downstream analyses.
  • the fluid sample is a blood sample and the target component is a nucleated cell.
  • the nucleated cell is a non-hematopoietic cell, a subpopulation of blood cells, a fetal red blood cell, a stem cell, or a cancerous cell.
  • the fluid sample is an effusion or a urine sample and the target component is a nucleated cell.
  • the nucleated cell is a cancerous cell or a non-hematopoietic cell.
  • the fluid sample can be blood and the cell aggregates to be reduced, removed, and/or disaggregated can be rouleaux, i.e., stacks or aggregates of red blood cells.
  • the target component can be retained by the target component
  • the target component can pass through the microfabricated filter.
  • the method can comprise, prior to passing the fluid sample through the microfabricated filter, contacting the fluid sample with an emulsifying agent and/or a cellular membrane charging agent.
  • the method can comprise, concurrently with passing the fluid sample through the microfabricated filter, contacting the fluid sample with an emulsifying agent and/or a cellular membrane charging agent.
  • the method can comprise, prior to and concurrently with passing the fluid sample through the microfabricated filter, contacting the fluid sample with an emulsifying agent and/or a cellular membrane charging agent.
  • the emulsifying agent and/or a cellular membrane charging agent is used at a first level
  • the emulsifying agent and/or a cellular membrane charging agent is used at a second level, and the first level is higher than the second level.
  • the emulsifying agent and/or a cellular membrane charging agent can be used at a level ranging from about 1 mg/mL to about 300 mg/mL, or from about 0.01% (v/v) to about 15% (v/v).
  • the emulsifying agent can be a synthetic emulsifier, a natural emulsifier, a finely divided or finely dispersed solid particle emulsifier, an auxiliary emulsifier, a monomolecular emulsifier, a multimolecular emulsifier, or a solid particle film emulsifier.
  • the synthetic emulsifier is a cationic, an anionic or a nonionic agent.
  • the cationic emulsifier is benzalkonium chloride or benzethonium chloride.
  • the anionic emulsifier is an alkali soap, e.g., sodium or potassium oleate, an amine soap, e.g., triethanolamine stearate, or a detergent, e.g., sodium lauryl sulfate, sodium dioctyl sulfosuccinate, or sodium docusate.
  • the nonionic emulsifier can be a sorbitan ester, e.g., Spans®, a polyoxyethylene derivative of sorbitan ester, e.g., Tweens®, or a glyceryl ester.
  • the natural emulsifier is a vegetable derivative, an animal derivative, a semi-synthetic agent or a synthetic agent.
  • the vegetable derivative is acacia, tragacanth, agar, pectin, carrageenan, or lecithin.
  • the animal derivative is gelatin, lanolin, or cholesterol.
  • the semi-synthetic agent is methylcellulose or carboxymethylcellulose.
  • the synthetic agent is Carbopols®.
  • the finely divided or finely dispersed solid particle emulsifier is bentonite, veegum, hectorite, magnesium hydroxide, aluminum hydroxide or magnesium trisilicate.
  • the auxiliary emulsifier is a fatty acid, e.g., stearic acid, a fatty alcohol, e.g., stearyl or cetyl alcohol, or a fatty ester, e.g., glyceryl monostearate.
  • the emulsifying agent can have a hydrophile-lipophile balance (HLB) value from about 1 to about 40.
  • HLB hydrophile-lipophile balance
  • the emulsifying agent can be selected from the group consisting of PEG 400 Monoleate (polyoxyethylene monooleate), PEG 400 Monostearate (polyoxyethylene monostearate), PEG 400 Monolaurate (polyoxyethylene monolaurate), potassium oleate, sodium lauryl sulfate, sodium oleate, Span® 20 (sorbitan monolaurate), Span® 40 (sorbitan monopalmitate), Span® 60 (sorbitan monostearate), Span® 65 (sorbitan tristearate), Span® 80 (sorbitan monooleate), Span® 85 (sorbitan trioleate), triethanolamine oleate, Tween® 20 (polyoxyethylene sorbitan monolaurate), Tween® 21 (polyoxyethylene sorbitan monolaurate), Tween® 40 (polyoxyethylene sorbitan monopalmitate), Tween® 60 (polyoxyethylene sorbititan sorbit
  • the emulsifying agent can be a pluronic acid or an organosulfur compound.
  • the pluronic acid is Pluronic® 10R5, Pluronic® 17R2, Pluronic® 17R4, Pluronic® 25R2, Pluronic® 25R4, Pluronic® 31R1, Pluronic® F-108, Pluronic® F-108NF, Pluronic® F-108 Pastille, Pluronic® F-108NF Prill Poloxamer 338, Pluronic® F-127 NF, Pluronic® F- 127NF 500 BHT Prill, Pluronic® F-127NF Prill Poloxamer 407, Pluronic® F 38, Pluronic® F 38 Pastille, Pluronic® F 68, Pluronic® F 68 NF, Pluronic® F 68 NF Prill Poloxamer 188, Pluronic® F 68 Pastille, Pluronic® F 77, Pluronic® F 77
  • the pluronic acid is used at a level ranging from about 1 mg/mL to about 300 mg/mL, from about 1 mg/mL to about 200 mg/mL, from about 5 mg/mL to about 50 mg/mL, from about 5 mg/mL to about 15 mg/mL, or from about 15 mg/mL to about 50 mg/mL.
  • the pluronic acid is used at about 15 mg/mL.
  • the organosulfur compound is dimethyl sulfoxide (DMSO).
  • the DMSO is used at a level ranging from about 0.01% (v/v) to about 15% (v/v), from about 0.02% (v/v) to about 0.4% (v/v), or from about 0.01% (v/v) to about 0.5% (v/v). In one embodiment, the DMSO is used at about 0.1% (v/v). In another embodiment, the DMSO is used at about 0.5% (v/v).
  • At least two different emulsifying agents can be used, or at least two cellular membrane charging agents can be used, or at least one emulsifying agent and at least one cellular membrane charging agent can be used.
  • a pluronic acid and DMSO are used.
  • the method can further comprise: c) rinsing the retained target component of the fluid sample with an additional sample-free rinsing reagent.
  • the method can further comprise: d) providing a labeling reagent to bind to the target component.
  • the labeling reagent is an antibody.
  • the method can further comprise: e) removing the unbound labeling reagent.
  • the method can further comprise: f) recovering the target component in a collection device.
  • the method can further comprise removing at least one type of undesirable component using a specific binding member from the fluid sample.
  • the fluid sample is a blood sample.
  • the at least one undesirable component are white blood cells (WBCs).
  • WBCs white blood cells
  • the specific binding member selectively binds to WBCs and is coupled to a solid support.
  • the specific binding member is an antibody or an antibody fragment that selectively binds to WBCs.
  • the specific binding member can be an antibody that selectively binds to CD3, CD11b, CD14, CD17, CD31, CD35, CD45, CD50, CD53, CD63, CD69, CD81, CD84, CD102, and/or CD166.
  • the specific binding member is an antibody that selectively binds to CD35 and/or CD50.
  • the method can further comprise contacting the blood sample with a secondary specific binding member.
  • the secondary specific binding member is an antibody that selectively binds to CD31, CD36, CD41, CD42 (a, b or c), CD51, and/or CD51/61.
  • the fluid sample can be a blood sample
  • the target components can be nucleated cells
  • the cell aggregates to be reduced, removed, and/or disaggregated can be rouleaux
  • the fluid sample can be treated with a washing composition comprising one or more emulsifying agent(s) and/or one or more cellular membrane charging agent(s), e.g., DMSO and/or pluronic acid, before and/or during the filtration step (step a)
  • the red blood cell, platelets and plasma can pass through the microfabricated filter
  • the target nucleated cells can be retained by the microfabricated filter.
  • the fluid sample can be a blood sample, the cell aggregates to be reduced, removed, and/or disaggregated can be rouleaux, the fluid sample can be treated with a washing composition comprising one or more emulsifying agent(s) and/or one or more cellular membrane charging agent(s), e.g., DMSO and/or pluronic acid, before and/or during the filtration step (step a), the blood sample can pass a first part of the microfabricated filter to produce a first filtrate that is substantially cleared of the red blood cell, platelets and plasma, the first filtrate can then pass the second part of the microfabricated filter that allows the nucleated cells or other smaller cells, e.g., lymphocytes and monocytes, to pass through, while retaining larger cells or cell aggregates, e.g., doublets of cells.
  • the nucleated cells or other smaller cells that pass through the second part of the microfabricated filter are collected via a separate pathway.
  • the fluid sample can be a blood sample, the cell aggregates to be reduced, removed, and/or disaggregated can be rouleaux, the fluid sample can be treated with a washing composition comprising one or more emulsifying agent(s) and/or one or more cellular membrane charging agent(s), e.g., DMSO and/or pluronic acid, before and/or during the filtration step (step a), a filtration device comprising a first and a second microfabricated filters, a sample feed channel and a recovery chamber can be used, the first microfabricated filter being located above the sample feed channel, having a non-stick surface and having a pore size smaller than about 5 ⁇ m, and the second microfabricated filter being located below the sample feed channel, the first microfabricated filter being used to maintain a continuous current of flow of a wash buffer across both microfabricated filters such that when the blood sample is fed through the feed channel and into the recovery chamber, all smaller particles, e.g., RBC, are caught
  • a washing composition comprising one or more
  • the method can further comprise before the steps a) and/or b), passing the fluid sample through a prefilter that retains aggregated cells and microclots, and allows single cells and smaller particles with a diameter smaller than about 20 ⁇ m to pass through to generate a pre- treated fluid sample that is subject to the steps a) and/or b) subsequently.
  • the method further comprises before passing the fluid sample through the prefilter, treating the fluid sample with a cell aggregation agent to aggregate red blood cells, and removing the aggregated red blood cells.
  • the cell aggregation agent is a dextran, dextran sulfate, dextran or dextran sulfate with a molecular weight less than about 15kD, hetastarch, gelatin, pentastarch, poly ethylene glycol (PEG), fibrinogen, gamma globulin, hespan, pentaspan, hepastarch, ficoll, gum arabic, poyvinylpyrrolidone, or any combination thereof.
  • the aggregated red blood cells are removed via sedimentation or laminar flow or a combination thereof.
  • the fluid sample can be separated based on the size, shape, deformability, binding affinity and/or binding specificity of the components, e.g., the target component, cells and cell aggregates, in the fluid sample.
  • a housing for a filter array comprising:
  • a first (e.g., upper) surface a second (e.g., lower) surface, and a periphery, which are configured to house (e.g., enclose) a filter array comprising a plurality of filters; for each filter of the array, at least two pre-filtration ports on the first surface which are connected to a pre-filtration chamber of the filter, and at least two post-filtration ports on the second surface which are connected to a post-filtration chamber of the filter,
  • center-to-center distance between any two adjacent pre-filtration ports, one of each for two adjacent filters, and/or the center-to-center distance between any two adjacent post- filtration ports, one of each for two adjacent filters is between about 2.00 mm and about 2.50 mm (e.g., about 2.25 mm) or a multiple thereof, and/or
  • one or both of the two post-filtration ports are each configured to fittingly and/or sealingly engage an o-ring structure, or wherein one or both of the two post-filtration ports comprise a needle configured to insert into and form a sealed fluidic path with an outside port, or wherein one or both of the two post-filtration ports are configured to form a sealed fluidic path with a needle inserted therein, or wherein one or both of the two post-filtration ports comprise a fluidic tube configured to fittingly and/or sealingly engage an outside port, or wherein one or both of the two post-filtration ports are configured to fittingly and/or sealingly engage a fluidic tube connected to an outside port.
  • the center-to-center distance between any two adjacent pre- filtration ports, one of each for two adjacent filters, and/or the center-to-center distance between any two adjacent post-filtration ports, one of each for two adjacent filters is about 2.25 mm, about 4.5 mm, about 9 mm, about 13.5 mm, about 18 mm, about 24 mm, or about 36 mm.
  • the center-to-center distance between the two post- filtration ports and/or between the two pre-filtration ports for the same filter can be between about 18.9 mm and about 36 mm, such as between about 18.9 mm and about 29.5 mm, between about 19 mm and about 35 mm, between about 29.0 mm and about 29.2 mm, for example, about 29.1 mm.
  • the housing can be configured to house (e.g., enclose) a filter array comprising 2, 3, 4, 6, 8, 12, 16, 24, 32, or 48 filters arranged in parallel.
  • one of the two pre-filtration ports for each filter of the array can be configured to fittingly and/or sealingly engage a dispensing end of a receptacle.
  • the receptacle is a pipette tip, a syringe, or a fluid delivery pipe.
  • the other of the two pre-filtration ports can be connected to a reservoir or well, and optionally the reservoir or well is formed by said housing itself.
  • one or both of the two post-filtration ports each can be configured to fittingly and/or sealingly engage an o-ring structure.
  • the o- ring structure is configured to fittingly and/or sealingly engage an outside port, e.g., an outside port of a seating for the housing.
  • the periphery of the housing can comprise a standoff for each o-ring structure, e.g., to control compression of the o-ring structure.
  • the housing can further comprise one or more through holes connecting the first surface and the second surface.
  • the housing can be molded as one piece, or molded as a first piece and a second piece which are irreversibly or reversibly assembled to enclose a filter array.
  • the housing can be irreversibly or reversibly assembled from a plurality of individual housings each for one or more filters, and each individual housing is molded as one piece, or molded as a first piece and a second piece which are irreversibly or reversibly assembled to enclose a filter.
  • a seat for the housing of the preceding embodiments comprising:
  • At least two interface ports on the interface which are configured to engage the at least two post-filtration ports on the second surface of the housing,
  • center-to-center distance between any two adjacent interface ports, one of each for two adjacent filters is between about 2.00 mm and about 2.50 mm (e.g., about 2.25 mm) or a multiple thereof, and/or
  • one or both of the two interface ports each comprises an o-ring structure, or wherein one or both of the two interface ports each comprises a needle configured to insert into or onto and form a sealed fluidic path with the post-filtration port, or wherein one or both of the two interface ports are configured to form a sealed fluidic path with a needle inserted therein or thereupon, or wherein one or both of the two interface ports comprise a fluidic tube configured to fittingly and/or sealingly engage the post-filtration port, or wherein one or both of the two interface ports are configured to fittingly and/or sealingly engage a fluidic tube connected to the post-filtration port.
  • the center-to-center distance between any two adjacent interface ports, one of each for two adjacent filters is about 2.25 mm, about 4.5 mm, about 9 mm, about 13.5 mm, about 18 mm, about 24 mm, or about 36 mm.
  • the center-to-center distance between the two interface ports for the same filter can be between about 18.9 mm and about 36 mm, such as between about 18.9 mm and about 29.5 mm, between about 19 mm and about 35 mm, between about 29.0 mm and about 29.2 mm, for example, about 29.1 mm.
  • the seat can be configured to engage a housing enclosing a filter array comprising 2, 3, 4, 6, 8, 12, 16, 24, 32, or 48 filters arranged in parallel.
  • At least one of the two interface ports can comprise a fluidic tube configured to fittingly and/or sealingly engage the post-filtration port.
  • the seat can further comprise a means for securing the housing onto the interface, such as a hole for a screw, or a cam-operated key or a screw-down key which is optionally motorized and/or automated.
  • the seat can further comprise tubing connected to the two interface ports, e.g., for each filter in the array.
  • the seat can further comprise a fluidics system priming port or sink for each of the filters.
  • the seat can further comprise a valve connected to one or both of the two interface ports, such as a three-way valve or a rotary valve; and/or further comprising a series of pumps (e.g., one-way miniaturized pumps) connected to one or both of the two interface ports.
  • a valve connected to one or both of the two interface ports, such as a three-way valve or a rotary valve; and/or further comprising a series of pumps (e.g., one-way miniaturized pumps) connected to one or both of the two interface ports.
  • one of the two interface ports is connected to a three-way valve, and the other interface port is connected to a first pump (e.g., syringe pump) for removing waste.
  • the three-way valve is configured to control flow between the interface port and the fluidics system priming port or sink, and flow between the interface port and a second pump (e.g., syringe pump).
  • the seat can comprise one or more holes each for receiving a screw.
  • a tube holder rack comprising a plurality of tube holders each configured to receive and hold a tube, and optionally wherein the center-to-center distance between any two adjacent tube holders is between about 2.00 mm and about 2.50 mm (e.g., about 2.25 mm) or a multiple thereof.
  • the center-to-center distance between any two adjacent tube holders is about 2.25 mm, about 4.5 mm, about 9 mm, about 13.5 mm, about 18 mm, about 24 mm, or about 36 mm.
  • the tube holders can be separated from each other, or some or all of the tube holders can be connected.
  • the tube holder rack can further comprise one or more magnetic or magnetizable element, e.g., a permanent magnet or an electromagnet.
  • the tube holder rack can comprise 2, 3, 4, 6, 8, 12, 16, 24, 32, or 48 tube holders.
  • a tube holder rack set comprising at least two of the tube holder rack of any of the preceding embodiments, in which one is a sample tube holder rack and one is a product tube holder rack.
  • the product tube holder rack is
  • the product tube holder rack is distinguishable by the color, the shape, and/or the presence or absence of a letter, number, symbol, notch, or structure on the product tube holder rack.
  • one or both of the product tube holder rack and the sample tube holder rack can comprise one or more magnetic or magnetizable element.
  • the product tube holder rack comprises one or more magnetic or magnetizable element while the sample tube holder rack does not.
  • the sample tube holder rack comprises one or more magnetic or magnetizable element while the product tube holder rack does not.
  • an assembly comprising the housing of any of the preceding embodiments and the housing seat of any of the preceding embodiments.
  • the assembly further comprises a securing means for fastening the housing to the seat, and the securing means optionally comprises one or more screws and optionally one or more clamps straddling the housing.
  • the assembly can further comprise a filter array enclosed in the housing, and each filter is optionally a microfabricated filter comprising a filter substrate and a plurality of slots extending through the filter substrate.
  • a plurality of the housings can be assembled together to form an array of the filter array.
  • kits comprising the housing of any of the preceding embodiments, the housing seat of any of the preceding embodiments, the tube holder rack of any of the preceding embodiments, and/or the tube holder rack set of any of the preceding embodiments.
  • the kit further comprises a securing means for fastening the housing to the seat.
  • a chute e.g., a pipette tip ejection chute
  • a receiving section comprising a first (e.g., vertical) surface and an adjoining second (e.g., horizontal) surface
  • the receiving section comprises a plurality of slits each spanning the first surface and the adjoining second surface, and optionally the slits are substantially parallel to each other, and/or optionally the angle between the first and second surfaces is between about 0 and 180 degrees, such as about 90 degrees; and/or a sliding section comprising an inclined sliding surface.
  • the length of the slit on the first surface is longer than the length of a pipette tip.
  • the slit can comprise an enlarged section near the top of the first surface, and/or the slit of the first surface can taper to narrow toward the bottom of the first surface.
  • the center-to-center distance between any two adjacent slits can be between about 2.00 mm and about 2.50 mm (e.g., about 2.25 mm) or a multiple thereof. In one embodiment, the center-to-center distance between any two adjacent slits about 2.25 mm, about 4.5 mm, about 9 mm, about 13.5 mm, about 18 mm, about 24 mm, or about 36 mm.
  • the chute can comprise 2, 3, 4, 6, 8, 12, 16, 24, 32, or 48 parallel slits.
  • a base plate comprising the housing seat of any of the preceding embodiments mounted to the base plate, a recess for the tube holder rack of any of the preceding embodiments or the tube holder rack set of any of the preceding embodiments, the tube holder rack of any of the preceding embodiments or the tube holder rack set of any of the preceding embodiments, and/or the chute of any of the preceding embodiments.
  • the base plate further comprises a recess configured to hold a pipette tip rack, and/or the pipette tip rack.
  • the pipette tip rack holds 3 ⁇ 2 pipette tips (e.g., for a 6-well plate), 6 ⁇ 2 pipette tips (e.g., for a 12-well plate), 6 ⁇ 4 pipette tips (e.g., for a 24-well plate), 12 ⁇ 4 pipette tips (e.g., for a 48-well plate), 12 ⁇ 8 pipette tips (e.g., for a 96-well plate, at 9 mm spacing between wells), 24 ⁇ 16 pipette tips (e.g., for a 384-well plate, at 4.5mm spacing between wells), or 48 ⁇ 32 pipette tips (e.g., for a 1536-well plate, at 2.25 mm spacing between wells).
  • 3 ⁇ 2 pipette tips e.g., for a 6-well plate
  • 6 ⁇ 2 pipette tips e.g., for a 12-well plate
  • the base plate can further comprise the housing of any one of the preceding embodiments seated onto the housing seat.
  • the base plate further comprises one or more transporting means for transporting a pipette tip to or from the tube holder rack, to or from the housing, to or from the pipette tip rack, to or from the pipette tip rack, and/or between or among any of these locations.
  • the transporting means comprises an automated or robotic arm, and/or a gantry, and optionally the gantry comprises a screen (e.g., a touch screen) for operating the device.
  • the base plate can further comprise an outflow manifold attached to the housing seat.
  • a device comprising the base plate of any of the preceding embodiments, and one or more pumps (e.g., syringe pumps) configured to control flow in and/or out of the filters.
  • the device comprises three or four syringe pumps.
  • the device can further comprise an inflow manifold connected to the one or more pumps, optionally wherein at least three pumps work in concert while engaged to at least three ports of the housing to control simultaneously the filtration rate and rate of flow at the port of the housing that is left open to ambient.
  • the device can further comprise a controller, a processor, a port for accessing the controller and/or processor (such as a USB port), a means for wired or wireless connection such as internet and/or Bluetooth, and/or a power supply.
  • the device can further comprise a dust cover, a front panel, a back panel, a bottom panel, and/or two side panels, defining a working chamber of the device.
  • the dust cover is transparent and/or comprises a magnetic interlock configured to sense whether the dust cover is closed.
  • the front panel or top panel can comprise a screen for operating the device, wherein the screen is optionally a touch screen.
  • a panel of the device can comprise an air filter, one or more fans configured to blow air out of the device through the air filter, and/or a vent hole.
  • the air filter is a HEPA or HEPA-like or HEPA-type filter.
  • a panel of the device can further comprise a waste receptacle connected to the chute, or aligned with or engaged under the chute.
  • a panel of the device can further comprise an interface of the inflow manifold.
  • a panel of the device optionally the back panel, can further comprise a pass through grommet for a vacuum line.
  • a panel of the device can comprise an inflow ventilation port and a dust filter.
  • the outward air flow through the air filter is faster than the inward air flow through the inflow ventilation port.
  • the two side panels of the device can be removable.
  • the working chamber of the device can be a contained chamber during operation, with a net negative air pressure relative to ambient air pressure.
  • a method of filtering a liquid sample comprising:
  • a liquid sample e.g., in a pipette tip or a syringe
  • a sample tube optionally wherein the top portion of the pipette tip or syringe is filled with a filtration solution and the bottom portion is filled with the sample;
  • the method further comprises a step of priming the device before step 1) for one or more times with the filtration solution, wherein the filtration solution optionally comprises a standard biological buffer or saline such as PBS (phosphate-buffered saline), an anticoagulant such as heparin, a mild chelating agent such as citrate, and/or a protein.
  • the filtration solution optionally comprises a standard biological buffer or saline such as PBS (phosphate-buffered saline), an anticoagulant such as heparin, a mild chelating agent such as citrate, and/or a protein.
  • the method further comprises:
  • the method can further comprise drawing the larger components into the pipette tip or syringe, optionally wherein the larger components are the desired component and are recovered from the pre-filtration chamber and/or wherein the smaller components are the desired component and are flushed from the post-filtration chamber.
  • the method further comprises delivering the larger components and/or the smaller components into a product tube.
  • the method further comprises ejecting the pipette tip into the chute.
  • the fluid sample can be a blood, effusion, urine, bone marrow sample, fine needle aspirate, core-needle biopsy, dissociated solid tissue, ascitic fluid, pelvic wash fluid, pleural fluid, spinal fluid, lymph, serum, mucus, sputum, saliva, semen, ocular fluid, extract of nasal, throat or genital swab, cell suspension from digested tissue, extract of fecal material, cultured cells of either mixed types and/or mixed sizes, cells that contain contaminants or unbound reactants that need to be removed, or fibers or particles to be sorted by size and/or shape and/or conformity.
  • the fluid sample is a blood sample and the undesired component being removed is a plasma component, a platelet and/or a red blood cell (RBC).
  • RBC red blood cell
  • the fluid sample can be a blood sample and the desired component being enriched is a cell or a cluster of cells, such as a nucleated cell, e.g., a non-hematopoietic cell, a subpopulation of blood cells, a fetal red blood cell, a stem cell, or a cancerous cell, or a cluster of these cells.
  • a nucleated cell e.g., a non-hematopoietic cell, a subpopulation of blood cells, a fetal red blood cell, a stem cell, or a cancerous cell, or a cluster of these cells.
  • the filtration rate across the filter can be between about 1 ⁇ L/s and about 100 ⁇ L/s. In one embodiment, the filtration rate across the filter is between about 1 ⁇ L/s and about 60 ⁇ L/s. In another embodiment, the filtration rate across the filter is between about 15 ⁇ L/s and about 40 ⁇ L/s. In one other embodiment, the filtration rate across the filter is between about 10 ⁇ L/s and about 40 ⁇ L/s. In another embodiment, the filtration rate across the filter is between about 20 ⁇ L/s and about 40 ⁇ L/s, such as 25 ⁇ L/s.
  • the method can further comprise diluting the sample, such as a blood sample, prior to filtration, with a pre-filtration solution, optionally wherein the pre-filtration solution comprises an emulsifying agent and/or a cellular membrane charging agent, and/or the pre-filtration solution is a hyperosmotic saline solution between about 320 mOsm and about 1000 mOsm, such as between about 350 mOsm and about 600 mOsm, between about 360 mOsm and about 390 mOsm, or between about 400 mOsm and about 450 mOsm.
  • the pre-filtration solution reduces or disaggregates a cell aggregate in the liquid sample.
  • the liquid sample is blood and the cell aggregate to be reduced or disaggregated is rouleaux (stacks or aggregates of red blood cells).
  • the emulsifying agent can be used at a level ranging from about 1 mg/mL to about 300 mg/mL, or from about 0.01% (v/v) to about 15% (v/v).
  • the emulsifying agent can be a synthetic emulsifier, a natural emulsifier, a finely divided or finely dispersed solid particle emulsifier, an auxiliary emulsifier, a monomolecular emulsifier, a
  • the cellular membrane charging agent is a negatively charged polysaccharide or heteropolysaccharide, for example, heparin, heparan sulfate, dextran, dextran sulfate, or chondroitin-4- and 6-sulphate, keratan sulfate, dermatan sulfate, hirudin, or hyaluronic acid, or a low molecular weight (e.g., ⁇ about 50kD, preferably ⁇ about 45 kD, ⁇ about 40 kD, ⁇ about 35 kD, ⁇ about 30 kD, ⁇ about 25 kD, ⁇ about 20 kD, ⁇ about 15 kD, ⁇ about 10 kD, ⁇ about 5 kD, or more preferably ⁇ about 2kD) dextran, or a pluronic acid.
  • a negatively charged polysaccharide or heteropolysaccharide for example, heparin, heparan sul
  • the emulsifying agent is selected from the group consisting of PEG 400 Monoleate (polyoxyethylene monooleate), PEG 400 Monostearate (polyoxyethylene monostearate), PEG 400 Monolaurate (polyoxyethylene monolaurate), potassium oleate, sodium lauryl sulfate, sodium oleate, Span® 20 (sorbitan monolaurate), Span® 40 (sorbitan monopalmitate), Span® 60 (sorbitan monostearate), Span® 65 (sorbitan tristearate), Span® 80 (sorbitan monooleate), Span® 85 (sorbitan trioleate), triethanolamine oleate, Tween® 20 (polyoxyethylene sorbitan monolaurate), Tween® 21 (polyoxyethylene sorbitan monolaurate), Tween® 40 (polyoxyethylene sorbitan monopalmitate), Tween® 60 (polyoxyethylene sorbitan monostearate), Tween®
  • a pluronic acid and an organosulfur compound such as DMSO, wherein the pluronic acid is optionally Pluronic® 10R5, Pluronic® 17R2, Pluronic® 17R4, Pluronic® 25R2, Pluronic® 25R4, Pluronic® 31R1, Pluronic® F-108, Pluronic® F-108NF, Pluronic® F-108 Pastille, Pluronic® F-108NF Prill Poloxamer 338, Pluronic® F-127 NF, Pluronic® F-127NF 500 BHT Prill, Pluronic® F-127NF Prill Poloxamer 407, Pluronic® F 38,
  • one or more steps of the method can be automated.
  • a housing according to any of the preceding embodiments, further comprising, for each filter of the array, a third pre-filtration port on the first surface which is connected to the pre-filtration chamber of the filter or optionally a third port on the second surface which passes to the first surface and is connected to the pre-filtration chamber of the filter.
  • the third pre-filtration port is configured to fittingly and/or sealingly engage a dispensing end of a receptacle or an additional port sealing connection on the seating structure.
  • the receptacle is a pipette tip, a syringe, or a fluid delivery pipe.
  • the third pre-filtration port on the first surface can be located between the two pre-filtration ports, optionally wherein the three pre-filtration ports are collinear and the third pre-filtration port is about 4.5 mm or 9 mm or 13.5mm or 18mm from one of the two pre-filtration ports.
  • a housing for a filter array comprising: a first (e.g., upper) surface, a second (e.g., lower) surface, and a periphery, which are configured to house (e.g., enclose) a filter array comprising a plurality of filters; for each filter of the array, at least three pre-filtration ports on the first surface which are connected to a pre-filtration chamber of the filter, and at least two post- filtration ports on the second surface which are connected to a post-filtration chamber of the filter, and optionally a third port on the second surface which passes to the first surface and is connected to the pre- filtration chamber of the filter.
  • the third pre-filtration port is configured to fittingly and/or sealingly engage a dispensing end of a receptacle or an additional port sealing connection on the seating structure.
  • the receptacle is a pipette tip, a syringe, or a fluid delivery pipe.
  • the third pre-filtration port on the first surface can be located between the two pre-filtration ports, optionally wherein the three pre-filtration ports are collinear and the third pre- filtration port is about 4.5mm or 9 mm or 13.5mm or 18mm from one of the two pre-filtration ports.
  • a seat for the housing comprising: an interface configured to engage the second surface and the periphery of the housing; for each filter of the array, at least two interface ports on the interface which are configured to engage the at least two post-filtration ports on the second surface of the housing.
  • an assembly comprising the housing and the housing seat.
  • a kit comprising the housing, the housing seat, the tube holder rack, and/or the tube holder rack set.
  • a base plate comprising the housing seat mounted to the base plate, a recess for the tube holder rack or the tube holder rack set, the tube holder rack or the tube holder rack set, and/or the chute.
  • a device comprising the base plate and one or more pumps (e.g., syringe pumps) configured to control flow in and/or out of the filters.
  • a method of filtering a liquid sample comprising: 1) picking up a liquid sample (e.g., in a pipette tip or a syringe) from a sample tube, optionally wherein the top portion of the pipette tip or syringe is filled with a filtration solution and the bottom portion is filled with the sample; 2) expelling the liquid sample into a pre-filtration port of the filter array housing on the device of any of the preceding embodiments; 3) controlling the liquid flow in the pre-filtration chamber and the post-filtration chamber of each filter, such that the flows are substantially anti-parallel to each other and substantially tangential to the filter membrane surface, and the flow rate entering one post-filtration port is less than the flow rate exiting the other post-filtration port, thereby drawing fluid flow across the filter membrane, optionally drawing the smaller or more easily shape-conforming components in the liquid sample across the filter into the post-filtration chamber to be removed from the filter during filtration, and hence deta
  • the method further comprises a step of priming the device before step 1) for one or more times with the filtration solution, wherein the filtration solution optionally comprises a standard biological buffer or saline such as PBS (phosphate-buffered saline), an anticoagulant such as heparin, a mild chelating agent such as citrate, and/or a protein.
  • the method further comprises providing a pre-filtration solution through the third pre-filtration chamber to contact the sample, for example, a blood sample that comprises rouleaux (stacks or aggregates of red blood cells).
  • the pre-filtration solution comprises an emulsifying agent and/or a cellular membrane charging agent, and/or the pre-filtration solution is a hyperosmotic saline solution between about 320 mOsm and about 1000 mOsm, such as between about 350 mOsm and about 600 mOsm, between about 360 mOsm and about 390 mOsm, or between about 400 mOsm and about 450 mOsm.
  • the method can further comprise applying a flow such that the larger components are lifted off the filter, optionally wherein the flow is applied across the filter from the post-filtration chamber to the pre-filtration chamber or the flow is created by flow within the pre-filtration chamber, drawing solution originating from the reservoir or well on the first surface of the filter housing.
  • the method can further comprise drawing the larger components into the pipette tip or syringe, optionally wherein the larger components are the desired component and are recovered from the pre-filtration chamber and/or wherein the smaller components are the desired component and are flushed from the post-filtration chamber.
  • the method can further comprise delivering the larger components and/or the smaller components into a product tube.
  • the filtration rate across the filter can be between about 1 ⁇ L/s and about 100 ⁇ L/s.
  • FIG.1 is the top view of a region of a microfabricated chip of an exemplary embodiment of the present invention.
  • the dark areas are the precision manufactured slots in the filter that has a filtration area of 1 cm 2 .
  • FIG.2 is a schematic representation of a microfabricated filter of an exemplary embodiment of the present invention.
  • FIG.3 depicts filters of an exemplary embodiment of the present invention having electrodes incorporated into their surfaces.
  • A) a 20-fold magnification of a portion of a microfabricated filter having 2 micron slot widths.
  • FIG.4 depicts a cross section of a pore in a microfabricated filter of an exemplary embodiment of the present invention.
  • the pore depth corresponds to the filter thickness.
  • Y represents the right angle between the surface of the filter and the side of a pore cut perpendicularly through the filter, while X is the tapering angle by which a tapered pore differs in its direction or orientation through the filter from a non- tapered pore.
  • FIG.5 depicts a filtration unit of an exemplary embodiment of the present invention having a microfabricated filter (3) separating the filtration chamber into an upper antechamber (4) and a post-filtration subchamber (5).
  • the unit has valves to control fluid flow into and out of the unit: valve A (6) controls the flow of sample from the loading reservoir (10) into the filtration unit, valve B (7) controls fluid flow through the chamber by connection to a syringe pump, and valve C (8) is used for the introduction of wash solution into the chamber.
  • FIG.6 is a diagram of an automated system of an exemplary embodiment of the present invention that comprises an inlet for the addition of a blood sample (11); a filtration chamber (12) that comprises acoustic mixing chips (13) and microfabricated filters (103); a magnetic capture column (14) having adjacent magnets (15); a mixing/filtration chamber (112); a magnetic separation chamber (16) comprising an electromagnetic chip (17), and a vessel for rare cell collection (18).
  • FIG.7 depicts a three-dimensional perspective view of a filtration chamber of an exemplary embodiment of the present invention that has two filters (203) that comprise slots (202) and a chip having acoustic elements (200) (the acoustic elements may not be visible on the chip surface, but are shown here for illustrative purposes). In this simplified depiction, the width of the slots is not shown.
  • FIG.8 depicts a cross-sectional view of a filtration chamber of an exemplary embodiment of the present invention having two filters (303) after filtering has been completed, and after the addition of magnetic beads (19) to a sample comprising target cells (20).
  • the acoustic elements are turned on during a mixing operation.
  • FIG.9 depicts a cross-sectional view of a feature of an automated system of an exemplary embodiment of the present invention: a magnetic capture column (114). Magnets (115) are positioned adjacent to the separation column.
  • FIG.10 depicts a three-dimensional perspective view of a chamber (416) of an automated system of an exemplary embodiment of the present invention that comprises a multiple force chip that can separate rare cells from a fluid sample.
  • the chamber has an inlet (429) and an outlet (430) for fluid flow through the chamber.
  • a cut-away view shows the chip has an electrode layer (427) that comprises an electrode array for dielectrophoretic separation and an electromagnetic layer (417) that comprises electromagnetic units (421) an electrode array on another layer.
  • Target cells (420) are bound to magnetic beads (419) for electromagnetic capture.
  • FIG.11 shows a graph illustrating the theoretical comparison between the DEP spectra for an nRBC (Xs) and a RBC (circles) when the cells are suspended in a medium of electrical conductivity of 0.2 S/m.
  • FIG.12 shows FISH analysis of nucleated fetal cells isolated using the methods of an exemplary embodiment of the present invention using a Y chromosome marker that has detected a male fetal cell in a maternal blood sample.
  • FIG.13 shows a process flow chart for enriching fetal nucleated RBCs from maternal blood.
  • FIG.14 is a schematic depiction of a filtration unit of an exemplary embodiment of the present invention.
  • FIG.15 shows a model of an automated system of an exemplary embodiment of the present invention.
  • FIG.16 depicts the filtration process of an automated system of an exemplary embodiment of the present invention.
  • A) shows the filtration unit having a loading reservoir (510) connected through a valve (506) to a filtration chamber that comprises an antechamber (504) separated from a post-filtration subchamber (505) by a microfabricated filter (503).
  • a wash pump (526) is connected to the lower chamber through a valve (508) for pumping wash buffer (524) through the lower subchamber.
  • Another valve (507) leads to another negative pressure pump used to promote fluid flow through the filtration chamber and out through an exit conduit (530).
  • a collection vessel (518) can reversibly engage the upper chamber (504).
  • B) shows a blood sample (525) loaded into the loading reservoir (510).
  • valve (507) that leads to a negative pressure pump used to promote fluid flow through the filtration chamber is open
  • D) and E) show the blood sample being filtered through the chamber.
  • wash buffer introduced through the loading reservoir is filtered through the chamber.
  • valve (508) is open, while the loading reservoir valve (506) is closed, and wash buffer is pumped from the wash pump (526) into the lower chamber.
  • the filtration valve (507) and wash pump valve (508) are closed and in I) and J) the chamber is rotated 90 degrees.
  • K) shows the collection vessel (518) engaging the antechamber (504) so that fluid flow generated by the wash pump (526) causes rare target cells (520) retained in the antechamber to flow into the collection tube.
  • FIG.17 depicts a fluorescently labeled breast cancer cell in a background of unlabeled blood cells after enrichment by microfiltration.
  • FIG.18 depicts two configurations of dielectrophoresis chips of an exemplary embodiment of the present invention.
  • FIG.19 depicts a separation chamber of an exemplary embodiment of the present invention comprising a dielectrophoresis chip.
  • FIG.20 is a graph illustrating the theoretical comparison between the DEP spectra for MDA231 cancer cells (solid line) T-lymphocytes (dashed line) and erythrocytes (small dashes) when the cells are suspended in a medium of electrical conductivity of 10 mS/m.
  • FIG.21 A and B depict breast cancer cells from a spiked blood sample retained on electrodes of an exemplary dielectrophoresis chip.
  • FIG.22 depicts white blood cells of a blood sample retained on electrodes of an exemplary dielectrophoresis chip.
  • FIG.23 is a schematic representation of a filtration unit of an automated system of an exemplary embodiment of the present invention.
  • the filtration unit has a loading reservoir (610) connected through valve A (606) to a filtration chamber that comprises an antechamber (604) separated from a post- filtration subchamber (605) by a microfabricated filter (603).
  • a suction-type pump can be attached through tubing that connects to the waste port (634), where filtered sample exits the chamber.
  • a side port (632) can be used for attaching a syringe pump for pumping wash buffer through the lower subchamber (605).
  • the filtration chamber (including the antechamber (604), post-filtration subchamber (605), filter (603), and side port (632), all depicted within the circle in the figure) can rotate within the frame (636) of the filtration unit, so that enriched cells of the antechamber can be collected via the collection port (635).
  • FIG.24 is a diagram showing the overall process of fetal cell enrichment from a blood sample, and the presence of enriched fetal cells in the supernatant of a second wash of the blood sample (box labeled Supernatant (W2)) and in the retained cells after the filtration step (box labeled Enriched cells).
  • the diagram shows, from upper left to lower right, blood cell processing steps” two washes (W1 and W2), Selective sedimentation of red blood cells and removal of white blood cells with a combined reagent (AVIPrep + AVIBeads + Antibodies), Filtration of the supernatant of the sedimentation, and collection of enriched fetal cells.
  • the diagram shows the level of enrichment of nucleated cells of various sample fractions during the procedure, and the sample fractions that were analyzed using FISH.
  • FIG.25 shows a picture of the filter cartridge evaluated (right) and comparison to a regular disc syringe filter (left) with inserted top view image of the microfabricated silicon filter chip where the dark slots are the filter“pores” (a), described in U.S. Patent No.: 6,949,355; and a sketch of the filter cartridge structure (b).
  • FIG.26 shows dot plots of the leucocytes isolated from whole blood with Lyse No Wash, Lyse Wash and filtration procedures (from top row to bottom row).
  • P1 is the Trucount TM counting beads population and
  • P2 is the leucocytes population gated on CD45+ cells.
  • FIG.28 shows dot plots of whole blood stained with reagents in Viability kit, left panel is the result of whole blood lysed with ammonium chloride and right panel is the result of cells recovered from filtration (a); and dot plots of cells recovered from filtration stained with reagent in FITC Annexin V Apoptosis Detection Kit, left panel is the result of blood filtered within an hour after drawn and right panel is the result of blood filtered 8 h later after drawn (b).
  • FIG.29 shows an exemplary embodiment of a cartridge.
  • FIG.30 a-d show cell viability after ammonium chloride lysing.
  • FIG.31 shows cell viability after filtration.
  • FIG.32 illustrates an exemplary filter work process.
  • Suction on the bottom one is simultaneous as output on the right one, but faster so that blood is drawn through the filter in the differential.
  • the suction on the bottom one is turned off, and the nucleated cells are pushed back from the filter, which has been flipped upside down at this time to dispense the cells directly into a cytometry tube (as in step 6 but with the syringe replaced with a receiving cytometry tube).
  • FIG.33 shows an exemplary embodiment of a filtration chamber wherein the antechamber and the post-filtration subchamber both have an inlet and an outlet that allow fluid to flow trough.
  • the fluid in the antechamber flows antiparallel to the fluid in the post- filtration subchamber.
  • FIG.34 shows an exemplary embodiment of a multiplex configuration of eight filtration chambers that each contains an independent filtration chamber with fluidic paths similar to that illustrated in Figure 33.
  • FIG.35 shows an exemplary embodiment of an automated system for separating and analyzing a target component of a fluid sample, wherein the sample may be collected by a syphon that is placed into the sample, and the sample may pass continuously through the antechamber and then be fed directly into an analytical instrument, which in this schematic is shown as the flow-cell of a flow cytometer.
  • FIG.36 shows a schematic representation of an exemplary embodiment of a high-rinse capacity filtration chamber, wherein the same fluidic path present in Figure 33 now has a rinsing reagent (buffer or buffer plus biomarker, or any suitable substance) introduced from above and passed through both filters to maximize the interaction between the sample and the bottom microfabricated filter.
  • a rinsing reagent buffer or buffer plus biomarker, or any suitable substance
  • FIG.37 shows an exemplary embodiment of two filtration chambers in tandem, wherein the sample may be cleared of debris and small components in the first filtration chamber, then the second filtration chamber separates larger cells from smaller cells among those remaining. For example, leukocytes may be preferentially directed to the Recovery 1 port, and the larger tumor cells may continue to the Recovery 2 port.
  • FIG.38 shows an exemplary embodiment of a filtration chamber with multiple recovery ports, wherein the microfabricated filter contains an array of slots with increasing width such that each port will output cells of progressively larger size and the ports may be spaced as to deliver their output directly into a multi-well screening plate.
  • FIG.39 compares the Ficoll method with the lysis method.
  • FIG.40 on the left is a graphical display of process flow using RedSift Cell Processor for tissue preparation.
  • Top right Recovery efficiencies (as a percent of whole blood, ⁇ SE) using a range of starting volumes of whole blood.
  • Bottom right comparison of recovery efficiency between 200 ⁇ L whole blood processed by filter and same volume processed by lysis.
  • FIG.41 shows cell subpopulations were elucidated by flow cytometry in one sample.
  • FIG.42 shows filtered cells are amenable to cell culture.
  • FIG.43 is a graphical display of process flow using RedSift Cell Processor for tissue preparation.
  • FIG.44 shows K562 leukemia cell line was spiked into buffer (top left), or whole peripheral blood buffered in EDTA (top right), Streck (bottom left) or Heparin (bottom right) then filtered prior to measuring calcein fluorescence in the spiked tumor cells.
  • FIG.45 shows filtered cells are amenable to cell culture.
  • FIG.46 shows K562 cells were spiked in graded quantities from 1000 to 12 cells into buffer (top) or into whole blood (bottom).
  • FIG.47 shows counts from recovery experiments in FIG.46 plotted by quantity of Spiked K562 cells.
  • FIG.48 shows other tumor cell types also tested after spiking the cells into buffer (top) then filtering, or into peripheral whole blood then filtering.
  • FIG. 49 shows remo val of RBCs and PLTs by RedSift filtration.
  • Top left panel describes the morphological characteristics in flow cytometry as forward scatter (FS) against side scatter (SS).
  • Top right panel shows the entire cell set stained with CD235, plotted against SS to highlight the CD235 positive RBCs.
  • the CD235 negative set from die top right panel were redisplayed in the bottom-left panel showing the CD45 binding against SS of only the CD235 negati ve ceils.
  • the CD45-negative ceils in the bottom left panel are redisplayed in the bottom right panel showing CD41 binding against SS.
  • FIG. 5 ⁇ shows RedSift Filtered Peripheral Blood and all its subpopulations.
  • Top left panel shows cytometric morphology as FS against SS.
  • Top center panel shows the entire cell set by CD235 binding against SS.
  • Top right panel shows only ceils gated as CD235 negative (i.e., non-RBC) by CD45 binding against SS.
  • Bottom, left panel shows only cells gated as lymphocytes from top right panel by CD 19 binding.
  • Bottom center panel shows same lymphocytes gated set by CD3 against SS.
  • Bottom right panel shows the same Lymphocytes gated set by CD 16 and CD56 against CD3 to separate out T cells and NK cells as labelled within the panel.
  • FIG. 51 shows effect of lysis on Morphology observed by FACS, Flow cytometric
  • morphology shown as FS against SS, is shown for all the lysis samples to facilitate comparisons.
  • FIG. 52 shows effect of ly sis on left-over RBC subpopulation.
  • the entire cell set is shown, for all lysed samples, by CD235-binding against SS to show RBC content within each sample. Note that in most cases it is difficult to elucidate where RBCs start.
  • FIG. 53 shows lysis effect on non RBC subpopulations showing CD45 binding.
  • the cells gated as CD235 negative are shown here by CD45 binding against SS to demonstrate distribution of WBCs. Note that since this is a CD235 negative gate, the CD45 negative cells are not RBC.
  • FIG. 54 shows lysis effect on B cells.
  • the cells set gated as lymphocytes, from figure 5, were displayed by CD 19 binding against SS to demonstrate distribution of B cells.
  • FIG. 55 shows lysis effect on T cells.
  • the cells set gated as lymphocytes, from figure 5, were displayed by CD3 binding against SS to demonstrate distribution of T cells.
  • FIG. 56 shows lysis effect on NK cells. For all lysis samples, the cells set gated as
  • lymphocytes from figure 5, were displayed by CD 16 and CD56 binding against CD3 to demonstrate distribution of NK cells and T cells, as labelled within each of the panels.
  • FIG. 57 shows donut charts comparing the WBC subpopulations from all sample preparation options.
  • the rings represent, from outside to inside, RedSift (RS), VersaLyse (VL), FACS- Lyse (FL), and Pharm-Lyse (PL).
  • the left chart shows relative concentrations of granulocytes, monocytes, lymphocytes, and blasts as a proportion of total WBC.
  • Hie right chart breaks out only lymphocytes and shows B cells, T cells, and NK ceils as a proportion of total lymphocytes within each sample.
  • FIG. 58 shows donut charts comparing the effects of centrifugation wash on WBC
  • the rings represent, from outside to inside, VersaLyse (VL), FACS-Lyse (FL), and Pharm-Lyse (PL).
  • VL VersaLyse
  • FL FACS-Lyse
  • PL Pharm-Lyse
  • the left chart shows relative concentrations of monocytes, blasts, granulocytes, B cells, NK cells and T cells as a proportion of total WBC after lysis (L) but without centrifugation wash.
  • the right chart shows the same populations in in the Lyse-Wash samples (LW).
  • FIG.59 shows an exemplary housing for a filter array (left panel), and the right panel of the figure shows the shape of a filter to be housed in the housing.
  • FIG.60 shows a cross section of an exemplary housing on a seat, forming fluid connections.
  • FIG.61 shows an exemplary seat for the filter array housing.
  • FIG.62 shows the tubing behind the interface of the exemplary seat for the filter array housing.
  • FIG.63 shows an exemplary assembly and the array interconnect subassembly shows interaction between the black valves and the filter arrays.
  • FIG.64 shows the assembly placed on the base plate.
  • FIG.65 shows an exemplary tube holder rack set, comprising one sample tube holder rack and a product tube rack.
  • FIG.66 shows an exemplary base plate (no pipette tip rack shown).
  • FIG.67 shows an exemplary base plate with a gantry for moving pipette tips and a chute for disposing the pipette tips.
  • FIG.68 shows an exemplary chute for disposing the pipette tips.
  • FIG.69 is a bottom view of the base plate, showing an outflow manifold attached to the housing seat, and the baseplate (red) contains the motion methods, and the outflow manifold (grey).
  • FIG.70 shows the inside, bottom view, of an exemplary device.
  • FIG.71 shows the inflow manifold which is a valve arrangement that interconnects fluids to all the pump syringes.
  • FIG.72 shows the front and back views of an exemplary device.
  • FIG.73 is a cross section that shows the fluidic path and components.
  • FIG.74 shows an exemplary array housing forming fluidic connections with the seat.
  • a third pre-filtration port is located between the two pre-filtration ports.
  • A“component” of a sample or“sample component” is any constituent of a sample, and can be an ion, molecule, compound, molecular complex, organelle, virus, cell, aggregate, or particle of any type, including colloids, aggregates, particulates, crystals, minerals, etc.
  • a component of a sample can be soluble or insoluble in the sample media or a provided sample buffer or sample solution.
  • a component of a sample can be in gaseous, liquid, or solid form.
  • a component of a sample may be a moiety or may not be a moiety.
  • A“moiety” or“moiety of interest” is any entity whose isolation, purification and/or manipulation is desirable.
  • a moiety can be a solid, including a suspended solid, or can be in soluble form.
  • a moiety can be a molecule.
  • Molecules that can be manipulated include, but are not limited to, inorganic molecules, including ions and inorganic compounds, or can be organic molecules, including amino acids, peptides, proteins, glycoproteins, lipoproteins, glycolipoproteins, lipids, fats, sterols, sugars, carbohydrates, nucleic acid molecules, small organic molecules, or complex organic molecules.
  • a moiety can also be a molecular complex, can be an organelle, can be one or more cells, including prokaryotic and eukaryotic cells, or can be one or more etiological agents, including viruses, parasites, or prions, or portions thereof.
  • a moiety can also be a crystal, mineral, colloid, fragment, micelle, droplet, bubble, or the like, and can comprise one or more inorganic materials such as polymeric materials, metals, minerals, glass, ceramics, and the like.
  • Moieties can also be aggregates of molecules, complexes, cells, organelles, viruses, etiological agents, crystals, colloids, or fragments.
  • Cells can be any cells, including prokaryotic and eukaryotic cells.
  • Eukaryotic cells can be of any type. Of particular interest are cells such as, but not limited to, white blood cells, malignant cells, stem cells, progenitor cells, fetal cells, and cells infected with an etiological agent, and bacterial cells. Moieties can also be artificial particles such polystyrene microbeads, microbeads of other polymer compositions, magnetic microbeads, and carbon microbeads.
  • “manipulation” refers to moving or processing of the moieties, which results in one-, two- or three-dimensional movement of the moiety, whether within a single chamber or on a single chip, or between or among multiple chips and/or chambers.
  • Moieties that are manipulated by the methods of the present invention can optionally be coupled to binding partners, such as microparticles.
  • Non-limiting examples of the manipulations include transportation, capture, focusing, enrichment, concentration, aggregation, trapping, repulsion, levitation, separation, isolation or linear or other directed motion of the moieties.
  • the binding partner and the physical force used in the method must be compatible.
  • binding partners with magnetic properties must be used with magnetic force.
  • binding partners with certain dielectric properties e.g., plastic particles, polystyrene microbeads
  • Binding partner refers to any substances that both bind to the moieties with desired affinity or specificity and are manipulatable with the desired physical force(s).
  • Non-limiting examples of the binding partners include cells, cellular organelles, viruses, microparticles or an aggregate or complex thereof, or an aggregate or complex of molecules.
  • “Coupled” means bound.
  • a moiety can be coupled to a microparticle by specific or nonspecific binding.
  • the binding can be covalent or noncovalent, reversible or irreversible.
  • A“specific binding member” is one of two different molecules having an area on the surface or in a cavity that specifically binds to and is thereby defined as complementary with a particular spatial and chemical organization of the other molecule.
  • a specific binding member can be a member of an
  • immunological pair such as antigen-antibody or antibody-antibody
  • an“antibody” is an immunoglobulin molecule, and can be, as a non-limiting example, an IgG, an IgM, or other type of immunoglobulin molecule. As used herein,“antibody” also refers to a portion of an antibody molecule that retains the binding specificity of the antibody from which it is derived (for example, single chain antibodies or Fab fragments).
  • A“nucleic acid molecule” is a polynucleotide.
  • a nucleic acid molecule can be DNA, RNA, or a combination of both.
  • a nucleic acid molecule can also include sugars other than ribose and deoxyribose incorporated into the backbone, and thus can be other than DNA or RNA.
  • a nucleic acid can comprise nucleobases that are naturally occurring or that do not occur in nature, such as xanthine, derivatives of nucleobases, such as 2-aminoadenine, and the like.
  • a nucleic acid molecule of the present invention can have linkages other than phosphodiester linkages.
  • a nucleic acid molecule of the present invention can be a peptide nucleic acid molecule, in which nucleobases are linked to a peptide backbone.
  • a nucleic acid molecule can be of any length, and can be single-stranded, double-stranded, or triple-stranded, or any combination thereof.
  • “Homogeneous manipulation” refers to the manipulation of particles in a mixture using physical forces, wherein all particles of the mixture have the same response to the applied force.
  • “Selective manipulation” refers to the manipulation of particles using physical forces, in which different particles in a mixture have different responses to the applied force.
  • A“fluid sample” is any fluid from which components are to be separated or analyzed.
  • a sample can be from any source, such as an organism, group of organisms from the same or different species, from the environment, such as from a body of water or from the soil, or from a food source or an industrial source.
  • a sample can be an unprocessed or a processed sample.
  • a sample can be a gas, a liquid, or a semi-solid, and can be a solution or a suspension.
  • a sample can be an extract, for example a liquid extract of a soil or food sample, an extract of a throat or genital swab, or an extract of a fecal sample, or a wash of an internal area of the body.
  • A“blood sample” as used herein can refer to a processed or unprocessed blood sample, i.e., it can be a centrifuged, filtered, extracted, or otherwise treated blood sample, including a blood sample to which one or more reagents such as, but not limited to, anticoagulants or stabilizers have been added.
  • An example of blood sample is a buffy coat that is obtained by processing human blood for enriching white blood cells.
  • Another example of a blood sample is a blood sample that has been“washed” to remove serum components by centrifuging the sample to pellet cells, removing the serum supernatant, and resuspending the cells in a solution or buffer.
  • Other blood samples include cord blood samples, bone marrow aspirates, internal blood or peripheral blood.
  • a blood sample can be of any volume, and can be from any subject such as an animal or human. A preferred subject is a human.
  • A“rare cell” is a cell that is either 1) of a cell type that is less than 1% of the total nucleated cell population in a fluid sample, or 2) of a cell type that is present at less than one million cells per milliliter of fluid sample.
  • A“rare cell of interest” is a cell whose enrichment is desirable.
  • A“white blood cell” or“WBC” is a leukocyte, or a cell of the hematopoietic lineage that is not a reticulocyte or platelet and that can be found in the blood of an animal or human.
  • Leukocytes can include nature killer cells (“NK cells”) and lymphocytes, such as B lymphocytes (“B cells”) or T lymphocytes (“T cells”).
  • NK cells nature killer cells
  • B cells B lymphocytes
  • T lymphocytes T cells
  • Leukocytes can also include phagocytic cells, such as monocytes, macrophages, and granulocytes, including basophils, eosinophils and neutrophils.
  • Leukocytes can also comprise mast cells.
  • A“red blood cell” or“RBC” is an erythrocyte. Unless designated a“nucleated red blood cell” (“nRBC”) or“fetal nucleated red blood cell” or nucleated fetal red blood cell, as used herein,“red blood cell” is used to mean a non-nucleated red blood cell.
  • “Neoplastic cells” or“tumor cells” refers to abnormal cells that have uncontrolled cellular proliferation and can continue to grow after the stimuli that induced the new growth has been withdrawn. Neoplastic cells tend to show partial or complete lack of structural organization and functional coordination with the normal tissue, and may be benign or malignant.
  • A“malignant cell” is a cell having the property of locally invasive and destructive growth and metastasis.
  • “malignant cells” include, but are not limited to, leukemia cells, lymphoma cells, cancer cells of solid tumors, metastatic solid tumor cells (e.g., breast cancer cells, prostate cancer cells, lung cancer cells, colon cancer cells) in various body fluids including blood, bone marrow, ascitic fluids, stool, urine, bronchial washes etc.
  • A“cancerous cell” is a cell that exhibits deregulated growth and, in most cases, has lost at least one of its differentiated properties, such as, but not limited to, characteristic morphology, non-migratory behavior, cell-cell interaction and cell-signaling behavior, protein expression and secretion pattern, etc.
  • Cancer refers to a neoplastic disease that the natural course of which is fatal. Cancer cells, unlike benign tumor cells, exhibit the properties of invasion and metastasis and are highly anaplastic. Cancer cells include the two broad categories of carcinoma and sarcoma.
  • A“stem cell” is an undifferentiated cell that can give rise, through one or more cell division cycles, to at least one differentiated cell type.
  • A“progenitor cell” is a committed but undifferentiated cell that can give rise, through one or more cell division cycles, to at least one differentiated cell type.
  • a stem cell gives rise to a progenitor cell through one or more cell divisions in response to a particular stimulus or set of stimuli, and a progenitor gives rise to one or more differentiated cell types in response to a particular stimulus or set of stimuli.
  • An“etiological agent” refers to any causal factor, such as bacteria, fungus, protozoan, virus, parasite or prion, that can infect a subject.
  • An etiological agent can cause symptoms or a disease state in the subject it infects.
  • a human etiological agent is an etiological agent that can infect a human subject.
  • Such human etiological agents may be specific for humans, such as a specific human etiological agent, or may infect a variety of species, such as a promiscuous human etiological agent.
  • “Subject” refers to any organism, such as an animal or a human.
  • An animal can include any animal, such as a feral animal, a companion animal such as a dog or cat, an agricultural animal such as a pig or a cow, or a pleasure animal such as a horse.
  • A“chamber” is a structure that is capable of containing a fluid sample, in which at least one processing step can be performed.
  • a chamber may have various dimensions and its volume may vary between 0.01 microliters and 0.5 liter.
  • A“filtration chamber” is a chamber through which or in which a fluid sample can be filtered.
  • A“filter” is a structure that comprises one or more pores or slots of particular dimensions (that can be within a particular range), that allow the passage of some sample components but not others from one side of the filter to the other, based on the size, shape, deformability, binding affinity and/or binding specificity of the components.
  • a filter can be made of any suitable material that prevents passage of insoluble components, such as metal, ceramics, glass, silicon, plastics, polymers, fibers (such as paper or fabric), etc.
  • A“filtration unit” is a filtration chamber and the associated inlets, valves, and conduits that allow sample and solutions to be introduced into the filtration chamber and sample components to be removed from the filtration chamber.
  • a filtration unit optionally also comprises a loading reservoir.
  • A“cartridge” is a structure that comprises at least one chamber that is part of a manual or automated system and one or more conduits for the transport of fluid into or out of at least one chamber.
  • a cartridge may or may not comprise one or more chips.
  • An“automated system for separating a target component from a fluid sample” or an“automated system” is a device that comprises at least one filtration chamber, automated means for directing fluid flow through the filtration chamber, and at least one power source for providing fluid flow and, optionally, providing a signal source for the generation of forces on active chips.
  • An automated system of the present invention can also optionally include one or more active chips, separation chambers, separation columns, or permanent magnets.
  • A“port” is an opening in the housing of a chamber through which a fluid sample can enter or exit the chamber.
  • a port can be of any dimensions, but preferably is of a shape and size that allows a sample to be dispensed into a chamber by pumping a fluid through a conduit, or by means of a pipette, syringe, or other means of dispensing or transporting a sample.
  • An“inlet” is a point of entrance for sample, solutions, buffers, or reagents into a fluidic chamber.
  • An inlet can be a port of a chamber, or can be an opening in a conduit that leads, directly or indirectly, to a chamber of an automated system.
  • An“outlet” is the opening at which sample, sample components, or reagents exit a fluidic chamber.
  • the sample components and reagents that leave a chamber can be waste, i.e., sample components that are not to be used further, or can be sample components or reagents to be recovered, such as, for example, reusable reagents or target cells to be further analyzed or manipulated.
  • An outlet can be a port of a chamber, but preferably is an opening in a conduit that, directly or indirectly, leads from a chamber of an automated system.
  • A“conduit” is a means for fluid to be transported from a container to a chamber of the present invention.
  • a conduit directly or indirectly engages a port in the housing of a chamber.
  • a conduit can comprise any material that permits the passage of a fluid through it.
  • Conduits can comprise tubing, such as, for example, rubber, Teflon, or tygon tubing.
  • Conduits can also be molded out of a polymer or plastic, or drilled, etched, or machined into a metal, glass or ceramic substrate. Conduits can thus be integral to structures such as, for example, a cartridge of the present invention.
  • a conduit can be of any dimensions, but preferably ranges from 10 microns to 5 millimeters in internal diameter.
  • a conduit is preferably enclosed (other than fluid entry and exit points), or can be open at its upper surface, as a canal-type conduit.
  • A“chip” is a solid substrate on which one or more processes such as physical, chemical, biochemical, biological or biophysical processes can be carried out, or a solid substrate that comprises or supports one or more applied force-generating elements for carrying out one or more physical, chemical, biochemical, biological, or biophysical processes.
  • processes can be assays, including biochemical, cellular, and chemical assays; separations, including separations mediated by electrical, magnetic, physical, and chemical (including biochemical) forces or interactions; chemical reactions, enzymatic reactions, and binding interactions, including captures.
  • the micro structures or micro-scale structures such as, channels and wells, bricks, dams, filters, electrode elements, electromagnetic elements, or acoustic elements, may be incorporated into or fabricated on the substrate for facilitating physical, biophysical, biological, biochemical, chemical reactions or processes on the chip.
  • the chip may be thin in one dimension and may have various shapes in other dimensions, for example, a rectangle, a circle, an ellipse, or other irregular shapes.
  • the size of the major surface of chips of the present invention can vary considerably, e.g., from about 1 mm 2 to about 0.25 m 2 . Preferably, the size of the chips is from about 4 mm 2 to about 25 cm 2 with a characteristic dimension from about 1 mm to about 5 cm.
  • the chip surfaces may be flat, or not flat.
  • the chips with non- flat surfaces may include channels or wells fabricated on the surfaces.
  • a chip can have one or more openings, such as pores or slots.
  • An“active chip” is a chip that comprises micro-scale structures that are built into or onto a chip that when energized by an external power source can generate at least one physical force that can perform a processing step or task or an analysis step or task, such as, but not limited to, mixing, translocation, focusing, separation, concentration, capture, isolation, or enrichment.
  • An active chip uses applied physical forces to promote, enhance, or facilitate desired biochemical reactions or processing steps or tasks or analysis steps or tasks.
  • “applied physical forces” are physical forces that, when energy is provided by a power source that is external to an active chip, are generated by micro-scale structures built into or onto a chip.
  • Micro-scale structures are structures integral to or attached on a chip, wafer, or chamber that have characteristic dimensions of scale for use in microfluidic applications ranging from about 0.1 micron to about 20 mm.
  • Example of micro-scale structures that can be on chips of the present invention are wells, channels, dams, bricks, filters, scaffolds, electrodes, electromagnetic units, acoustic elements, or microfabricated pumps or valves.
  • a variety of micro-scale structures are disclosed in United States Patent Application Number 09/679,024, having attorney docket number 471842000400, entitled“Apparatuses Containing Multiple Active Force Generating Elements and Uses Thereof” filed October 4, 2000, herein incorporated by reference in its entirety.
  • Micro-scale structures that can, when energy, such as an electrical signal, is applied, generate physical forces useful in the present invention can be referred to as“physical force-generating elements”“physical force elements”,“active force elements”, or“active elements”.
  • micro-scale structures are disclosed in United States Patent Application Number 09/679,024, having attorney docket number 471842000400, entitled“Apparatuses Containing Multiple Active Force Generating Elements and Uses Thereof” filed October 4, 2000, herein incorporated by reference in its entirety.
  • Micro-scale structures that can, when energy, such as an electrical signal, is applied, generate physical forces useful in the present invention can be referred to as“physical force-generating elements”,“physical force elements”,“active force elements”, or“active elements”.
  • A“multiple force chip” or“multiforce chip” is a chip that generates physical force fields and that has at least two different types of built-in structures each of which is, in combination with an external power source, capable of generating one type of physical field.
  • a full description of the multiple force chip is provided in United States Application Number 09/679,024 having attorney docket number 471842000400, entitled“Apparatuses Containing Multiple Active Force Generating Elements and Uses Thereof” filed October 4, 2000, herein incorporated by reference in its entirety.
  • “Acoustic forces” are the forces exerted, directly or indirectly on moieties (e.g., particles and/or molecules) by an acoustic wave field.
  • Acoustic forces can be used for manipulating (e.g., trapping, moving, directing, handling) particles in fluid.
  • Acoustic waves both standing acoustic wave and traveling acoustic wave, can exert forces directly on moieties and such forces are called“acoustic radiation forces”.
  • Acoustic wave may also exert forces on the fluid medium in which the moieties are placed, or suspended, or dissolved and result in so-called acoustic streaming.
  • the acoustic streaming will exert forces on the moieties placed, suspended or dissolved in such a fluid medium.
  • the acoustic wave fields can exert forces on moieties in directly.
  • “Acoustic elements” are structures that can generate an acoustic wave field in response to a power signal.
  • Preferred acoustic elements are piezoelectric transducers that can generate vibrational (mechanical) energy in response to applied AC voltages. The vibrational energy can be transferred to a fluid that is in proximity to the transducers, causing an acoustic force to be exerted on particles (such as, for example, cells) in the fluid.
  • particles such as, for example, cells
  • “Piezoelectic transducers” are structures capable of generating an acoustic field in response to an electrical signal.
  • Non-limiting examples of the piezoelectric transducers are ceramic disks (e.g. PZT, Lead Zirconium Titinate) covered on both surfaces with metal film electrodes, piezoelectric thin films (e.g. zinc-oxide).
  • “Mixing”, as used herein, means the use of physical forces to cause movement in a sample, solution, or mixture, such that components of the sample, solution, or mixture become interspersed. Preferred methods of mixing for use in the present invention include use of acoustic forces.
  • Processing refers to the preparation of a sample for analysis, and can comprise one or multiple steps or tasks. Generally a processing task serves to separate components of a sample, concentrate components of a sample, at least partially purify components of a sample, or structurally alter components of a sample (for example, by lysis or denaturation).
  • “isolating” means separating a desirable sample component from other non- desirable components of a sample, such that preferably, at least 15%, more preferably at least 30%, even more preferably at least 50%, and further preferably, at least 80% of the desirable sample components present in the original sample are retained, and preferably at least 50%, more preferably at least 80%, even more preferably, at least 95%, and yet more preferably, at least 99%, of at least one nondesirable component of the original component is removed, from the final preparation.
  • “Enrich” means increase the concentration of a sample component of a sample relative to other sample components (which can be the result of reducing the concentration of other sample components), or increase the concentration of a sample component.
  • “enriching” nucleated fetal cells from a blood sample means increasing the proportion of nucleated fetal cells to all cells in the blood sample
  • enriching cancer cells of a blood sample can mean increasing the concentration of cancer cells in the sample (for example, by reducing the sample volume) or reducing the concentration of other cellular components of the blood sample
  • “enriching” cancer cells in a urine sample can mean increasing their concentration in the sample.
  • “Separation” is a process in which one or more components of a sample are spatially separated from one or more other components of a sample.
  • a separation can be performed such that one or more sample components of interest is translocated to or retained in one or more areas of a separation apparatus and at least some of the remaining components are translocated away from the area or areas where the one or more sample components of interest are translocated to and/or retained in, or in which one or more sample components is retained in one or more areas and at least some or the remaining components are removed from the area or areas.
  • one or more components of a sample can be translocated to and/or retained in one or more areas and one or more sample components can be removed from the area or areas.
  • sample components can be translocated to one or more areas and one or more sample components of interest or one or more components of a sample to be translocated to one or more other areas.
  • Separations can be achieved through, for example, filtration, or the use of physical, chemical, electrical, or magnetic forces.
  • forces that can be used in separations are gravity, mass flow, dielectrophoretic forces, traveling-wave dielectrophoretic forces, and electromagnetic forces.
  • “Separating a sample component from a (fluid) sample” means separating a sample component from other components of the original sample, or from components of the sample that are remaining after one or more processing steps.“Removing a sample component from a (fluid) sample” means removing a sample component from other components of the original sample, or from components of the sample that are remaining after one or more processing steps.
  • “Capture” is a type of separation in which one or more moieties or sample components is retained in or on one or more areas of a surface, chamber, chip, tube, or any vessel that contains a sample, where the remainder of the sample can be removed from that area.
  • An“assay” is a test performed on a sample or a component of a sample.
  • An assay can test for the presence of a component, the amount or concentration of a component, the composition of a component, the activity of a component, etc.
  • Assays that can be performed in conjunction with the compositions and methods of the present invention include, but are not limited to, immunocytochemical assays, interphase FISH (fluorescence in situ hybridization), karyotyping, immunological assays, biochemical assays, binding assays, cellular assays, genetic assays, gene expression assays and protein expression assays.
  • A“binding assay” is an assay that tests for the presence or concentration of an entity by detecting binding of the entity to a specific binding member, or that tests the ability of an entity to bind another entity, or tests the binding affinity of one entity for another entity.
  • An entity can be an organic or inorganic molecule, a molecular complex that comprises, organic, inorganic, or a combination of organic and inorganic compounds, an organelle, a virus, or a cell.
  • Binding assays can use detectable labels or signal generating systems that give rise to detectable signals in the presence of the bound entity.
  • Standard binding assays include those that rely on nucleic acid hybridization to detect specific nucleic acid sequences, those that rely on antibody binding to entities, and those that rely on ligands binding to receptors.
  • A“biochemical assay” is an assay that tests for the presence, concentration, or activity of one or more components of a sample.
  • A“cellular assay” is an assay that tests for a cellular process, such as, but not limited to, a metabolic activity, a catabolic activity, an ion channel activity, an intracellular signaling activity, a receptor- linked signaling activity, a transcriptional activity, a translational activity, or a secretory activity.
  • A“genetic assay” is an assay that tests for the presence or sequence of a genetic element, where a genetic element can be any segment of a DNA or RNA molecule, including, but not limited to, a gene, a repetitive element, a transposable element, a regulatory element, a telomere, a centromere, or DNA or RNA of unknown function.
  • genetic assays can be gene expression assays, PCR assays, karyotyping, or FISH.
  • Genetic assays can use nucleic acid hybridization techniques, can comprise nucleic acid sequencing reactions, or can use one or more enzymes such as polymerases, as, for example a genetic assay based on PCR.
  • a genetic assay can use one or more detectable labels, such as, but not limited to, fluorochromes, radioisotopes, or signal generating systems.
  • detectable labels such as, but not limited to, fluorochromes, radioisotopes, or signal generating systems.
  • “Polymerase chain reaction” or“PCR” refers to method for amplifying specific sequences of nucleotides (amplicon). PCR depends on the ability of a nucleic acid polymerase, preferably a thermostable one, to extend a primer on a template containing the amplicon.
  • RT-PCR is a PCR based on a template (cDNA) generated from reverse transcription from mRNA prepared from a sample.
  • Quantitative Reverse Transcription PCR (qRT-PCR) or the Real-Time RT-PCR is a RT-PCR in which the RT-PCR products for each sample in every cycle are quantified.
  • “FISH” or“fluorescence in situ hybridization” is an assay wherein a genetic marker can be localized to a chromosome by hybridization.
  • a nucleic acid probe that is fluorescently labeled is hybridized to interphase chromosomes that are prepared on a slide. The presence and location of a hybridizing probe can be visualized by fluorescence microscopy.
  • the probe can also include an enzyme and be used in conjunction with a fluorescent enzyme substrate.
  • “Karyotyping” refers to the analysis of chromosomes that includes the presence and number of chromosomes of each type (for example, each of the 24 chromosomes of the human haplotype
  • chromosomes 1-22, X, and Y chromosomes 1-22, X, and Y
  • Karyotyping typically involves performing a chromosome spread of a cell in metaphase. The chromosomes can then be visualized using, for example, but not limited to, stains or genetic probes to distinguish the specific chromosomes.
  • A“gene expression assay” is an assay that tests for the presence or quantity of one or more gene expression products, i.e. messenger RNAs.
  • the one or more types of mRNAs can be assayed simultaneously on cells of the interest from a sample.
  • the number and/or the types of mRNA molecules to be assayed in the gene expression assays may be different.
  • A“protein expression assay” is an assay that tests for the presence or quantity of one or more proteins. One or more types of protein can be assayed
  • the number and/or the types of protein molecules to be assayed in the protein expression assays may be different.
  • “Histological examination” refers to the examination of cells using histochemical or stains or specific binding members (generally coupled to detectable labels) that can determine the type of cell, the expression of particular markers by the cell, or can reveal structural features of the cell (such as the nucleus, cytoskeleton, etc.) or the state or function of a cell.
  • cells can be prepared on slides and“stained” using dyes or specific binding members directly or indirectly bound to detectable labels, for histological examination.
  • dyes that can be used in histological examination are nuclear stains, such as Hoechst stains, or cell viability stains, such as Trypan blue, or cellular structure stains such as Wright or Giemsa, enzyme activity benzidine for HRP to form visible precipitate.
  • specific binding members that can be used in histological examination of fetal red blood cells are antibodies that specifically recognize fetal or embryonic hemoglobin.
  • An“electrode” is a structure of highly electrically conductive material.
  • a highly conductive material is a material with a conductivity greater than that of surrounding structures or materials. Suitable highly electrically conductive materials include metals, such as gold, chromium, platinum, aluminum, and the like, and can also include nonmetals, such as carbon and conductive polymers.
  • An electrode can be any shape, such as rectangular, circular, castellated, etc. Electrodes can also comprise doped semi-conductors, where a semi-conducting material is mixed with small amounts of other“impurity” materials. For example, phosphorous-doped silicon may be used as conductive materials for forming electrodes.
  • A“well” is a structure in a chip, with a lower surface surrounded on at least two sides by one or more walls that extend from the lower surface of the well or channel.
  • the walls can extend upward from the lower surface of a well or channel at any angle or in any way.
  • the walls can be of an irregular conformation, that is, they may extend upward in a sigmoidal or otherwise curved or multi-angled fashion.
  • the lower surface of the well or channel can be at the same level as the upper surface of a chip or higher than the upper surface of a chip, or lower than the upper surface of a chip, such that the well is a depression in the surface of a chip.
  • the sides or walls of a well or channel can comprise materials other than those that make up the lower surface of a chip.
  • A“channel” is a structure in a chip with a lower surface and at least two walls that extend upward from the lower surface of the channel, and in which the length of two opposite walls is greater than the distance between the two opposite walls. A channel therefore allows for flow of a fluid along its internal length.
  • a channel can be covered (a“tunnel”) or open.
  • A“pore” is an opening in a surface, such as a filter of the present invention, that provides fluid communication between one side of the surface and the other.
  • a pore can be of any size and of any shape, but preferably a pore is of a size and shape that restricts passage of at least one insoluble sample component from one side of a filter to the other side of a filter based on the size, shape, deformability, binding affinity and/or binding specificity (or lack thereof), of the sample component.
  • A“slot” is an opening in a surface, such as a filter of the present invention.
  • the slot length is longer than its width (slot length and slot width refer to the slots dimensions in the plane or the surface of the filter into which the sample components will go through, and slot depth refers to the thickness of the filter).
  • the term“slot” therefore describes the shape of a pore, which will in some cases be approximately rectangular, ellipsoid, or that of a quadrilateral or parallelogram.
  • “Bricks” are structures that can be built into or onto a surface that can restrict the passage of sample components between bricks.
  • the design and use of one type of bricks (called“obstacles”) on a chip is described in U.S. Patent No.5,837,115 issued Nov.17, 1998 to Austin et al., herein incorporated by reference in its entirety.
  • A“dam” is a structure that can be built onto the lower surface of a chamber that extends upward toward the upper surface of a chamber leaving a space of defined width between the top of the dam and the top of the chamber.
  • the width of the space between the top of the dam and the upper wall of the chamber is such that fluid sample can pass through the space, but at least one sample component is unable to pass through the space based on its size, shape, or deformability (or lack thereof).
  • Continuous flow means that fluid is pumped or injected into a chamber of the present invention continuously during the separation process. This allows for components of a sample that are not selectively retained in a chamber to be flushed out of the chamber during the separation process.
  • Binding partner refers to any substances that both bind to the moieties with desired affinity or specificity and are manipulatable with the desired physical force(s).
  • Non-limiting examples of the binding partners include microparticles.
  • A“microparticle” is a structure of any shape and of any composition that is manipulatable by desired physical force(s).
  • the microparticles used in the methods could have a dimension from about 0.01 micron to about ten centimeters.
  • the microparticles used in the methods have a dimension from about 0.1 micron to about several hundred microns.
  • Such particles or microparticles can be comprised of any suitable material, such as glass or ceramics, and/or one or more polymers, such as, for example, nylon, polytetrafluoroethylene (TEFLON TM ), polystyrene, polyacrylamide, sepaharose, agarose, cellulose, cellulose derivatives, or dextran, and/or can comprise metals.
  • microparticles include, but are not limited to, magnetic beads, magnetic particles, plastic particles, ceramic particles, carbon particles, polystyrene microbeads, glass beads, hollow glass spheres, metal particles, particles of complex compositions, microfabricated free-standing microstructures, etc.
  • the examples of microfabricated free-standing microstructures may include those described in“Design of asynchronous dielectric micromotors” by Hagedorn et al., in Journal of Electrostatics, Volume: 33, Pages 159-185 (1994).
  • Particles of complex compositions refer to the particles that comprise or consists of multiple compositional elements, for example, a metallic sphere covered with a thin layer of non-conducting polymer film.
  • a preparation of microparticles is a composition that comprises microparticles of one or more types and can optionally include at least one other compound, molecule, structure, solution, reagent, particle, or chemical entity.
  • a preparation of microparticles can be a suspension of microparticles in a buffer, and can optionally include specific binding members, enzymes, inert particles, surfactants, ligands, detergents, etc.
  • the term“substantially anti-parallel” and“substantially opposite” are understood to mean“approximately anti-parallel” and“approximately opposite”, respectively, such as within about 30°, preferably within about 20°, more preferably within about 10°, and most preferably within about 5° or less of being perfectly anti-parallel or opposite.
  • the term“engaged” refers to any mode of mechanical or physical attachment, interlocking, mating, binding, or coupling, such that members that are said to be“engaged” do not come apart or detach from one another without some positive effort, application of energy, or the like.
  • the present invention includes several general and useful aspects, including:
  • a filtration chamber comprising a microfabricated filter enclosed in a housing, wherein the filtration chamber comprises an antechamber and a post-filtration subchamber, and the fluid flow path in the antechamber is substantially opposite to the fluid flow path in the post-filtration subchamber;
  • a filtration chamber comprising a microfabricated filter enclosed in a housing, wherein the surface of said filter and/or the inner surface of said housing are modified by vapor deposition, sublimation, vapor-phase surface reaction, or particle sputtering to produce a uniform coating;
  • a filtration chamber comprising a microfabricated filter enclosed in a housing, wherein the surface of said filter and/or the inner surface of said housing are modified by a metal nitride, a metal halide, a Parylene or derivative thereof, a polytetrafluoroethylene (PTFE), a Teflon-AF or a perfluorocarbon;
  • a metal nitride a metal halide, a Parylene or derivative thereof, a polytetrafluoroethylene (PTFE), a Teflon-AF or a perfluorocarbon
  • an automated filtration unit for separating a target component in a fluid sample comprising a filtration chamber disclosed herein;
  • an automated system for separating and analyzing a target component in a fluid sample comprising an automated filtration unit disclosed herein and an analysis apparatus connected to the filtration unit;
  • a method for separating a target component in a fluid sample comprising: a) dispensing a fluid sample into the filtration chamber disclosed herein; and b) providing a fluid flow of the fluid sample through the filtration chamber, wherein the target component of the fluid sample is retained by or passes through the filter;
  • a method of separating a target component in a fluid sample using the automated filtration unit disclosed herein comprising: a) dispensing the fluid sample into the filtration chamber; and b) providing a fluid flow of the fluid sample through the filtration chamber, wherein the target component of the fluid sample is retained by or flows through the filter; and
  • a method of enriching and analyzing a component in a fluid sample using the automated system disclosed herein comprising: a) dispensing the fluid sample into the filtration chamber; b) providing a fluid flow of the fluid sample through the antechamber of the filtration chamber and a fluid flow of a solution through the post-filtration subchamber of the filtration chamber, wherein the target component of the fluid sample is retained in the antechamber and non-target components flow through the filter into the post-filtration subchamber; c) labeling the target component; and d) analyzing the labeled target component using the analysis apparatus.
  • the present invention provides a filtration chamber comprising a microfabricated filter enclosed in a housing.
  • a filtration chamber of the present invention comprises one or more microfabricated filters that are internal to the chamber, the filter or filters can divide the chamber into subchambers.
  • a filtration chamber comprises a single internal microfabricated filter
  • the filtration chamber can comprise a prefiltration“antechamber”, or where appropriate,“upper subchamber” and a“post-filtration subchamber”, or, where appropriate,“lower subchamber”.
  • a microfabricated filter can form a wall of a filtration chamber, and during filtration, filterable sample components exit the chamber via the filter.
  • a filtration chamber of the present invention has at least one port that allows for the introduction of a sample into the chamber, and conduits can transport sample to and from a filtration chamber of the present invention.
  • sample components that flow through one or more filters can flow into one or more areas of the chamber and then out of the chamber through conduits, and, preferably but optionally, from the conduits into a vessel, such as a waste vessel.
  • the filtration chamber can also optionally have one or more additional ports for the additions of one or more reagents, solutions, or buffers. Throughout this description, it is understood that the inflow ports or outflow ports may be used with flow in the direction opposite to their named function.
  • the filtration chamber may comprise an additional filter, or where appropriate, a“suprafilter”.
  • the suprafilter between the antechamber and the suprachamber, may be any filter sufficiently rigid to maintain its flatness in slow flow conditions and be produced by any method that results in holes or slots with openings smaller than 5 microns.
  • the suprafilter may further divide the antechamber or post-filtration subchamber.
  • the filtration antechamber may comprise an inflow port, an outflow port, and an additional inflow port, further where the additional inflow port is separated from the antechamber by another microfabricated filter thereby creating a suprachamber.
  • a filtration chamber of the present invention can comprise one or more fluid-impermeable materials, such as but not limited to, metals, polymers, plastics, ceramics, glass, silicon, or silicon dioxide.
  • a filtration chamber of the present invention has a volumetric capacity of from about 0.01 milliliters to about ten liters, more preferably from about 0.2 milliliters to about two liters.
  • a filtration chamber can have a volume of from about 1 milliliter to about 80 milliliters.
  • a filtration chamber of the present invention can comprise or engage any number of filters.
  • a filtration chamber comprises one filter (see, for example Figure 5 and Figure 14).
  • a filtration chamber comprises more than one filter, such as the chamber exemplified in Figure 6 and Figure 7.
  • filter chamber configurations are possible.
  • a filtration chamber in which one or more walls of the filter chamber comprises a microfabricated filter.
  • a filter chamber in which a filter chamber engages one or more filters.
  • the filters can be permanently engaged with the chamber, or can be removable (for example, they can be inserted into slots or tracks provided on the chamber).
  • a filter can be provided as a wall of a chamber, or internal to a chamber, and filters can optionally be provided in tandem for sequential filtering. Where filters are inserted into a chamber, they are inserted to form a tight seal with the walls of a chamber, such that during the filtration operation, fluid flow through the chamber (from one side of a filter to the other) must be through the pores of the filter.
  • a filtration chamber of, for example, approximately one centimeter by one centimeter by 0.2 to ten centimeters in dimensions can have one or more filters comprising from four to 1,000,000 slots, preferably from 100 to 250,000 slots.
  • the slots are preferably of rectangular shape, with a slot length of from about 0.1 to about 1,000 microns, and slot width is preferably from about 0.1 to about 100 microns, depending on the application.
  • slots can allow for the passage of mature red blood cells (lacking nuclei) through the channels and thus out of the chamber, while not or minimally allowing cells having a greater diameter or shape (for example but not limited to, nucleated cells such as white blood cells and nucleated red blood cells) to exit the chamber.
  • a filtration chamber that can allow the removal of red blood cells by fluid flow through the chamber, while retaining other cells of a blood sample, is illustrated in Figure 7, Figure 14, and Figure 16.
  • slot widths between 2.5 and 6.0 microns, more preferably between 2.2 and 4.0 microns, could be used. Slot length could vary between, for example, 20 and 200 microns.
  • a filtration chamber of the present invention may be configured to allow parallel or anti-parallel fluid flow in the antechamber and the post-filtration subchamber.
  • the antechamber may have two ports, an inflow port and an out flow port.
  • the post-filtration subchamber may have two ports, an inflow port and an outflow port.
  • the ports may be arranged in such a way that fluid flows in the antechamber and in the post-filtration subchamber are substantially opposite, or anti-parallel, of each other.
  • the inflow port of the antechamber may be used to dispense a fluid sample, such as a blood sample, a cell suspension, or the like, into the filtration chamber.
  • the device has a single antechamber with two ports for inflow and outflow, one on either side of the one or more filters, such that blood samples can flow through the antechamber.
  • blood samples can be pumped through the antechamber to fill the chamber.
  • one opening comprises a reservoir at its end
  • particles such as cells and compounds can optionally be added via the reservoir.
  • either particles, compounds, or both can be added to the antechamber at an opening that is not connected to a reservoir.
  • the antechamber may comprise more than one inflow and/or outflow ports.
  • an additional inflow port may be used for provide inflow of a solution for rinsing, or provide a fluidic force to push components of a fluid sample across the filter.
  • the additional inflow port may provide fluid flow to the suprafilter.
  • the post-filtration subchamber is also a single flow-through channel, with an opening at one end for the introduction of solutions, and an opening at the other end for outflow of solutions.
  • the post-filtration subchamber may comprise more than one inflow and/or outflow ports. For example, multiple outflow ports in the post-filtration subchamber may be used to collect different filtration components based on the size, shape, deformability, binding affinity and/or binding specificity of the components.
  • the fluid flow in the antechamber and the post-filtration subchamber may be such that a negative pressure may be created to draw components or cells through the filter.
  • the outflow from the bottom chamber is greater than the inflow into the bottom chamber such that a portion of the fluid sample traversing the antechamber may be drawn into the post-filtration subchamber such that the red blood cells and platelets will be separated from the white blood cells and other nucleated cells that will be retained in the antechamber by the filter.
  • the outflow fluid may contain fewer cells than the inflow fluid.
  • the fluid flow of the antechamber and post-filtration subchamber may be configured so that they have different flow rates. It is contemplated that the difference in the fluid flow in the antechamber and post-filtration subchamber may create a fluid force across the filter between the antechamber and post-filtration subchamber.
  • the flow rate of the fluid in the antechamber and post-filtration subchamber may be controlled by a pressure control unit, such as a pump, at the inflow and/or outflow ports.
  • the pressure control unit may be adjusted by an automatic control system, such as a computer running an algorithm.
  • the filtration chamber may include one or more surface contours to affect the flow of a sample, a solution such as wash or elution solution or both.
  • contours may deflect, disperse or direct a sample to assist in the spreading of the sample along the filter.
  • contours may deflect, disperse or direct a wash solution such that the wash solution washes the chamber or filter with greater efficiency.
  • Such surface contours may be in any appropriate configuration.
  • the contours may include surfaces that project generally toward the chip or may project generally away from the chip. They may generally encircle the filter. Contours may include but are not limited to projections, recessed portions, slots, deflection structures such as ball-like portions, bubbles (formed from e.g.
  • the outflow port of the antechamber may be connected to a collection chamber, wherein the target components of the fluid sample, such as nucleated cells from a blood sample, or cancerous cells from a cell suspension, may be collected after unwanted components have been separated by filtration.
  • the filtration chamber of the present invention may be formed by two housing parts, for example, a top housing part and a bottom housing part, which may reversibly engage to form the filtration chamber that encloses the filter.
  • the housing parts may be bound together using any suitable methods, such as but not limited to, laser bonding, adhesive material, or the like.
  • the bottom housing part can be in the form of a tray or tank, and preferably has at least one inlet and at least one outlet for allowing buffer to flow through the chamber.
  • E. Surface Treatment or Modification [00302]
  • the present invention provides treatment or modifications to the surface of a microfabricated filter and/or the inner surface of a housing that encloses the microfabricated filter to improve its filtering efficiency.
  • the surface treatment produces a uniform coating of the filter and the housing.
  • one or both surfaces of the filter is treated or coated or modified to increase its filtering efficiency.
  • the surface modifications may facilitate the filtration of components of the fluid sample across the filter, or reduce blocking of the slots on the filter by components of the fluid sample, such as cells, cell debris, protein aggregates, lipids, or the like.
  • one or both surfaces of the filter is treated or modified to reduce the possibility of sample components (such as but not limited to cells) interacting with or adhering to the filter.
  • the surface of the filter and/or the inner surface of the housing may be modified by a metal nitride, a metal halide, a Parylene, a polytetrafluoroethylene (PTFE), a Teflon-AF or a perfluorocarbon.
  • the perfluorocarbon may be in liquid form.
  • the perfluorocarbon may be 1H,1H,2H,2H-perfluorooctyltriethoxysilane, 1H,1H,2H,2H-perfluorodecyltriethoxysilane, trichloro(1H,1H,2H,2H-perfluorooctyl)silane or trichloro(octadecyl)silane, which may be in liquid form.
  • the perfluorocarbon may be covalently bound to the surface.
  • the surface modification of the filter and/or inner surface of the housing may be via vapor deposition, sublimation, vapor-phase surface reaction, or particle sputtering to produce a uniform coating.
  • a filter and/or housing can be physically or chemically treated, for example, to alter its surface properties (e.g., hydrophobic, hydrophilic).
  • surface properties e.g., hydrophobic, hydrophilic
  • vapor deposition, sublimation, vapor-phase surface reaction, or particle sputtering are some of the methods that can be used to treat or modify the surface of a filter and/or housing. Any suitable vapor deposition methods can be used, e.g., physical vapor deposition, plasma-enhanced chemical vapor deposition, chemical vapor deposition, etc.
  • Suitable materials for physical vapor deposition, chemical vapor deposition, plasma-enhanced chemical vapor deposition or particle sputtering may include, but are not limited to, a metal nitride or a metal halide, such as titanium nitride, silicon nitride, zinc nitride, indium nitride, boron nitride, Parylene or a derivative thereof, such as Parylene, Parylene-N, Parylene-D, Parylene AF-4, Parylene SF, and Parylene HT.
  • Polytetrafluoroethylene (PTFE) or Teflon-AF can also be used for chemical vapor deposition.
  • a filter and/or housing can be heated or treated with plasma in chamber with a low nitrogen or ammonia or nitrous gas or other gases or any combination or sequence of these, modified to silicon nitride or can be treated with at least one acid or at least one base, to apply the desired surface charge and species.
  • a glass or silica filter and/or housing can be heated in a nitrogen or argon environment to remove oxide from the surface of the filter and/or housing. Heating times and temperatures can vary depending on the filter and/or housing material and the degree of reaction desired.
  • a glass filter and/or housing can be heated to a temperature of from about 200 to 1200 degrees Celsius for from about thirty minutes to twenty-four hours.
  • a filter and/or housing can be treated with one or more acids or one or more bases to increase the electropositivity of the filter surface.
  • a filter and/or housing that comprises glass or silica is treated with at least one acid.
  • An acid used in treating a filter and/or housing of the present invention can be any acid.
  • the acid can be formic acid, oxalic acid, ascorbic acid.
  • the acid can be of a concentration about 0.1 N or greater, and preferably is about 0.5 N or higher in concentration, and more preferably is greater than about 1 N in concentration.
  • the concentration of acid preferably is from about 1 N to about 10 N.
  • the incubation time can be from one minute to days, but preferably is from about 5 minutes to about 2 hours.
  • Optimal concentrations and incubation times for treating a microfabricated filter and/or housing to increase its hydrophilicity can be determined empirically.
  • the microfabricated filter and/or housing can be placed in a solution of acid for any length of time, preferably for more than one minute, and more preferably for more than about five minutes.
  • Acid treatment can be done under any non-freezing and non-boiling temperature, preferably at a temperature greater than or equal to room temperature.
  • a reducing agent may be used in place of an acid or in addition to an acid or in any sequence with an acid, such as, but not limited to, hydrazine, lithium aluminum hydride, borohydrides, sulfites, phosphites, dithiothreitol, iron-containing compounds such as iron(II) sulfate.
  • the reducing solution can be of a concentration of about 0.01 M or greater, and preferably is greater than about 0.05 M, and more preferably greater than about 0.1 M in concentration.
  • the microfabricated filter and/or housing can be placed in a reducing solution for any length of time, preferably for more than one minute, and more preferably for more than about five minutes.
  • Treatment can be done under any non-frozen and non-boiling temperature, preferably at a temperature greater than or equal to room temperature.
  • the effectiveness of a physical or chemical treatment in increasing the hydrophilicity of a filter and/or housing surface can be tested by measuring the spread of a drop of water placed on the surface of a treated and non-treated filter and/or housing, where increased spreading of a drop of uniform volume indicates increased hydrophilicity of a surface ( Figure 5).
  • the effectiveness of a filter and/or housing treatment can also be tested by incubating a treated filter and/or housing with cells or biological samples to determine the degree of sample component adhesion to the treated filter and/or housing.
  • the surface of a filter and/or housing can chemically treated to alter the surface properties of the filter and/or housing.
  • a glass, silica, or polymeric filter and/or housing can be derivatized by any of various chemical treatments to add chemical groups that can decrease the interaction of sample components with the filter and/or housing surface.
  • One or more compounds can also be adsorbed onto or conjugated to the surface of a microfabricated filter and/or housing made of any suitable material, such as, for example, one or more metals, one or more ceramics, one or more polymers, glass, silica, silicon nitride, or combinations thereof.
  • a microfabricated filter and/or housing of the present invention is coated with a compound to increase the efficiency of filtration by reducing the interaction of sample components with the filter and/or housing surface.
  • the surface of a filter and/or housing can be coated with a molecule, such as, but not limited to, a protein, peptide, or polymer, including naturally occurring or synthetic polymers.
  • a molecule such as, but not limited to, a protein, peptide, or polymer, including naturally occurring or synthetic polymers.
  • the material used to coat the filter and/or housing is preferably biocompatible, meaning it does not have deleterious effects on cells or other components of biological samples, such as proteins, nucleic acids, etc.
  • Albumin proteins such as bovine serum albumin (BSA) are examples of proteins that can be used to coat a microfabricated filter and/or housing of the present invention.
  • BSA bovine serum albumin
  • Polymers used to coat a filter and/or housing can be any polymer that does not promote cell sticking to the filter and/or housing, for example, non- hydrophobic polymers such as, but not limited to, polyethylene glycol (PEG), polyvinylacetate (PVA), and polyvinylpyrrolidone (PVP), and a cellulose or cellulose-like derivative.
  • non- hydrophobic polymers such as, but not limited to, polyethylene glycol (PEG), polyvinylacetate (PVA), and polyvinylpyrrolidone (PVP), and a cellulose or cellulose-like derivative.
  • a filter and/or housing made of, for example, metal, ceramics, a polymer, glass, or silica can be coated with a compound by any feasible means, such as, for example, adsorption or chemical conjugation.
  • a filter and/or housing can be treated with at least one acid or at least one base, or with at least one acid and at least one base, prior to coating the filter and/or housing with a compound or polymer.
  • a filter and/or housing made of a polymer, glass, or silica is treated with at least one acid and then incubated in a solution of the coating compound for a period of time ranging from minutes to days.
  • a glass filter and/or housing can be incubated in acid, rinsed with water, and then incubated in a solution of BSA, PEG, or PVP.
  • the filter and/or housing can be rinsed in water (for example, deionized water) or a buffered solution before acid or base treatment or treatment with an oxidizing agent, and, preferably again before coating the filter and/or housing with a compound or polymer.
  • rinses can also be performed between treatments, for example, between treatment with an oxidizing agent and an acid, or between treatment with an acid and a base.
  • a filter and/or housing can be rinsed in water or an aqueous solution that has a pH of between about 3.5 and about 10.5, and more preferably between about 5 and about 9.
  • Non-limiting examples of suitable aqueous solutions for rinsing microfabricated filter and/or housing can include salt solutions (where salt solutions can range in concentration from the micromolar range to 5M or more), biological buffer solutions, cell media, or dilutions or combinations thereof. Rinsing can be performed for any length of time, for example from minutes to hours.
  • the concentration of a compound or polymer solution used to coat a filter and/or housing can vary from about 0.02% to 20% or more, and will depend in part on the compound used.
  • the incubation in coating solution can be from minutes to days, and preferably is from about 10 minutes to two hours.
  • the filter and/or housing can be rinsed in water or a buffer.
  • the treatment methods of the present invention can also be applied to chips other than those that comprise pores for filtration.
  • chips that comprise metals, ceramics, one or more polymers, silicon, silicon dioxide, or glass can be physically or chemically treated using the methods of the present invention.
  • Such chips can be used, for example, in separation, analysis, and detection devices in which biological species such as cells, organelles, complexes, or biomolecules (for example, nucleic acids, proteins, small molecules) are separated, detected, or analyzed.
  • the treatment of the chip can enhance or reduce the interaction of the biological species with the chip surface, depending of the treatment used, the properties of the biological species being manipulated, and the nature of the manipulation.
  • a chip can be coated with a hydrophilic or hydrophobic polymer, depending on the biological species being manipulated and the nature of the manipulation.
  • coating the surface of the chip with a hydrophilic polymer may reduce or minimize the interaction between the surface of the chip and the cells.
  • F. Multiplexing In some embodiments of the present invention, more than one filtration chambers may be combined in a multiplex configuration. For example, at least 2, 3, 4, 5, 6, 7, 8, 9, 10 or more filtration chambers may be combined.
  • Figure 34 shows an exemplary embodiment wherein eight filtration chambers are combined.
  • each filtration chamber of the multiplex configuration is independent of each other, i.e., is not in fluidic connection with other filtration chambers in the multiplex configuration.
  • some or all of the filtration chambers of the multiplex configuration may be in fluidic connection with each other.
  • some or all of the filtration chambers may have a common housing, or may be connected with each other by a fluidic channel or conduit.
  • the filtration chambers in a multiplex configuration may be arranged side by side, as shown in Figure 34, or arranged in linear fashion, or both.
  • the filtration chambers in a multiplex configuration may be arranged in the same orientation, or opposite orientation, or a combination thereof.
  • at least two filtration chambers operate in tandem further wherein the slots of the filters within each filtration chamber are of different widths where the filtration chambers are arranged in order of increasing slot widths.
  • At least two filtration chambers are arranged in tandem and where subsequent filtration chambers comprise filters of increasing slot widths.
  • the filter contains slot widths of increasing size along the fluidic path and further where a suprafiltration chamber exists and the post-filtration chamber contains multiple partitions that direct the fluidic flow out through one outflow port per partition.
  • the outflow ports from each partition segment of the post- filtration chamber may be aligned with and deposit its outflow directly into individual wells of a multiwell drug screening plate with wells spaced every 2.25mm or every 4.5mm or every 9mm or every 18mm.
  • Figure 37 illustrates another embodiment of a multiplex configuration.
  • the two filtration chambers are in fluidic connection through the antechamber between a suprafilter and a microfabricated filter.
  • the filters of the filtration chambers may have different slot sizes, so that different components may be recovered in recovery areas 1 and 2.
  • G. Automated Filtration Unit [00324]
  • a filtration chamber of the present invention is part of a filtration unit which comprise a means to control fluid flow through the filtration chamber. Any suitable mechanisms may be used to control the fluid flow in the filtration chamber, such as fluidic pumps, valves, conduits, channels, or the like.
  • a control algorithm for example, a computer program, may be used to control the fluid flow. Fluid flow in both the antechamber and post-filtration subchamber may be controlled by the control algorithm.
  • multiple fluidic pumps may be used to separately control the flow rate in the antechamber and post-filtration subchamber.
  • a feed pump (3) may be used to control the fluid flow rate in the antechamber, and a buffer pump (1) and a waste pump (2) may be used to control the fluid flow rate in the post-filtration subchamber.
  • the fluid flow of the antechamber and post-filtration subchamber may be configured so that they have different flow rates. It is contemplated that the difference in the fluid flow in the antechamber and post-filtration subchamber may create a fluid force across the filter between the antechamber and post-filtration subchamber.
  • the fluid flow in the antechamber and the post-filtration subchamber may be such that a negative pressure (5) may be created to draw components or cells through the filter.
  • the outflow from the bottom chamber is greater than the inflow into the bottom chamber such that a portion of the fluid sample traversing the antechamber may be drawn into the post-filtration subchamber such that the red blood cells and platelets will be separated from the white blood cells and other nucleated cells that will be retained in the antechamber by the filter.
  • the outflow fluid may contain fewer cells than the inflow fluid.
  • one preferred filtration unit of the present invention comprises a valve-controlled inlet for the addition of sample (valve A (6)), a valve connected to a conduit through which negative pressure is applied for the filtration of the sample (valve B (7)), and a valve controlling the flow of wash buffer into the filtration chamber for washing the chamber (valve C (8)).
  • a filtration unit can comprise valves that can optionally be under automatic control that allow sample to enter the chamber, waste to exit the chamber, and negative pressure to provide fluid flow for filtration.
  • a needle (but not limited to stated object) can be used.
  • a needle may be connected to the container (e.g. tubing or chamber) that can hold a volume.
  • the needle may collect cells from a tube containing a solution and dispense the solution into another chamber using a device to push or pull a solution (e.g. pump or syringe).
  • the inflow port of the antechamber may be connected to a column, so that a specific binding member for an unwanted component of the sample fluid may be immobilized on a solid surface in the column.
  • a specific binding member for an unwanted component of the sample fluid may be immobilized on a solid surface in the column.
  • a lectin, a receptor ligand or an antibody may be immobilized in the column to remove red blood cells, white blood cells, or platelets from a blood sample.
  • H. Automated System for Separating and Analyzing Components of a Fluid Sample [00331] Further provided herein is an automated system for separating and analyzing a target components of a fluid sample, which comprise a filtration chamber in fluid connection with an apparatus for analyzing the target component separated by the filtration chamber.
  • the antechamber of the filtration chamber may be directly connected to the apparatus, so that the target component, such as nucleated cells or rare cells retained by the filter, may directly enter the apparatus for analysis.
  • the outflow port of the antechamber, or the collection chamber may also be connected to the apparatus, for example, a flow cytometer, so that the separated component may be directly analyzed without further manipulation.
  • the target component by be labeled before the analysis.
  • traveling-wave dielectrophoretic forces can be generated by electrodes built onto a chip that is part of a filtration chamber, and can be used to move sample components such as cells away from a filter.
  • the microelectrodes are fabricated onto the filter surfaces and the electrodes are arranged so that the traveling wave dielectrophoresis can cause the sample components such as cells to move on the electrode plane or the filter surface through which the filtration process occur.
  • a full description of the traveling wave dielectrophoresis is provided in United States Application Number 09/679,024 having attorney docket number 471842000400, entitled“Apparatuses Containing Multiple Active Force Generating Elements and Uses Thereof” filed October 4, 2000, herein incorporated by reference in its entirety.
  • interdigitated microelectrodes are fabricated onto the filter surfaces such as those shown in Figure 2 or described in“Novel dielectrophoresis-based device of the selective retention of viable cells in cell culture media” by Docoslis et al, in Biotechnology and
  • the negative dielectrophoretic forces generated by the electrodes can repel the sample components such as the cells from the filter surface or from the filter slots so that the collected cells on the filters are not clogging the filters during the filtration process.
  • electrode elements can be energized periodically throughout the filtration process, during periods when fluid flow is halted or greatly reduced.
  • Filters having slots in the micron range that incorporate electrodes that can generate dielectrophoretic forces are illustrated in Figure 3 (A and B).
  • filters have been made in which the interdigitated electrodes of 18 micron width and 18 micron gaps were fabricated on the filters, which were made on silicon substrates.
  • Individual filter slots were of rectangular shape with dimensions of 100 micron (length) by 2– 3.8 micron (width).
  • Each filter had a unique slot size (e.g. length by width: 100 micron by 2.4 micron, 100 micron by 3 micron, 100 micron by 3.8 micron).
  • the gap between the adjacent filter slots was 20 micron.
  • the adjacent slots were not aligned; instead, they were offset.
  • the offset distance between neighboring columns of the filter slots were 50 micron or 30 micron, alternatively.
  • the filter slots were positioned with respect to the electrodes so that the slot center lines along the length direction were aligned with the center line of the electrodes, or the electrode edges, or the center line of the gaps between the electrodes.
  • Electrodes may also be positioned on the housing of the filtration chamber that encloses the filter.
  • electrodes may be positioned in an antechamber and/or a post-filtration subchamber.
  • the electrodes may be positioned in relation to the filter in such a way that dielectrophoretic forces are generated around the filter slots.
  • the dielectrophoretic forces may keep the cells or other sample components away from the filter slots or filter surface.
  • Dielectrophoresis refers to the movement of polarized particles in a non-uniform AC electrical field.
  • a particle When a particle is placed in an electrical field, if the dielectric properties of the particle and its surrounding medium are different, the particle will experience dielectric polarization. Thus, electrical charges are induced at the particle/medium interface. If the applied field is non-uniform, then the interaction between the non-uniform field and the induced polarization charges will produce net force acting on the particle to cause particle motion towards the region of strong or weak field intensity. The net force acting on the particle is called dielectrophoretic force and the particle motion is dielectrophoresis. Dielectrophoretic force depends on the dielectric properties of the particles, particle surrounding medium, the frequency of the applied electrical field and the field distribution.
  • Traveling-wave dielectrophoresis is similar to dielectrophoresis in which the traveling-electric field interacts with the field-induced polarization and generates electrical forces acting on the particles. Particles are caused to move either with or against the direction of the traveling field. Traveling-wave dielectrophoretic forces depend on the dielectric properties of the particles and their suspending medium, the frequency and the magnitude of the traveling-field.
  • dielectrophoresis and traveling-wave dielectrophoresis and the use of dielectrophoresis for manipulation and processing of microparticles may be found in various publications (e.g.,“Non-uniform Spatial Distributions of Both the Magnitude and Phase of AC Electric Fields determine Dielectrophoretic Forces by Wang et al., in Biochim Biophys Acta Vol.1243, 1995, pages 185-194”,“Dielectrophoretic Manipulation of Particles” by Wang et al, in IEEE Transaction on Industry Applications, Vol.33, No.3, May/June, 1997, pages 660-669,“Electrokinetic behavior of colloidal particles in traveling electric fields: studies using yeast cells” by Huang et al, in J.
  • microparticles with dielectrophoresis and traveling wave dielectrophoresis include concentration/aggregation, trapping, repulsion, linear or other directed motion, levitation, or separation of particles.
  • Particles may be focused, enriched and trapped in specific regions of the electrode reaction chamber. Particles may be separated into different subpopulations over a microscopic scale. Relevant to the filtration methods of the present invention, particles may be transported over certain distances.
  • the electrical field distribution necessary for specific particle manipulation depends on the dimension and geometry of microelectrode structures and may be designed using dielectrophoresis theory and electrical field simulation methods.
  • the dielectrophoretic force F DEP z acting on a particle of radius r subjected to a non-uniform electrical field can be given by
  • E rms is the RMS value of the field strength
  • H m is the dielectric permitivity of the medium.
  • F DEP is the particle dielectric polarization factor or dielectrophoresis polarization factor, given by
  • H p and V p are the effective permitivity and conductivity of the particle, respectively. These parameters may be frequency dependent. For example, a typical biological cell will have frequency dependent, effective conductivity and permitivity, at least, because of cytoplasm membrane polarization.
  • V 1 V
  • dielectrophoresis there are generally two types of dielectrophoresis, positive dielectrophoresis and negative dielectrophoresis.
  • positive dielectrophoresis particles are moved by dielectrophoresis forces towards the strong field regions.
  • negative dielectrophoresis particles are moved by dielectrophoresis forces towards weak field regions. Whether particles exhibit positive and negative dielectrophoresis depends on whether particles are more or less polarizable than the surrounding medium.
  • electrode patterns on one or more filters of a filtration chamber can be designed to cause sample components such as cells to exhibit negative dielectrophoresis, resulting in sample components such as cells being repelled away from the electrodes on the filter surfaces.
  • Traveling-wave DEP force refers to the force that is generated on particles or molecules due to a traveling-wave electric field.
  • a traveling-wave electric field is characterized by the non-uniform distribution of the phase values of AC electric field components.
  • TWD is the particle polarization factor, given by
  • the parameters ⁇ p and ⁇ p are the effective permittivity and conductivity of the particle, respectively. These parameters may be frequency dependent.
  • Particles such as biological cells having different dielectric property will experience different dielectrophoretic forces.
  • traveling-wave DEP forces acting on a particle of 10 micron in diameter can vary somewhere between 0.01 and 10000 pN.
  • a traveling wave electric field can be established by applying appropriate AC signals to the microelectrodes appropriately arranged on a chip.
  • For generating a traveling-wave-electric field it is necessary to apply at least three types of electrical signals each having a different phase value.
  • An example to produce a traveling wave electric field is to use four phase-quardrature signals (0, 90, 180 and 270 degrees) to energize four linear, parallel electrodes patterned on the chip surfaces. Such four electrodes form a basic, repeating unit. Depending on the applications, there may be more than two such units that are located next to each other. This will produce a traveling-electric field in the spaces above or near the electrodes.
  • dielectrophoretic and traveling-wave dielectrophoretic forces acting on particles depend on not only the field distributions (e.g., the magnitude, frequency and phase distribution of electrical field components; the modulation of the field for magnitude and/or frequency) but also the dielectric properties of the particles and the medium in which particles are suspended or placed.
  • field distributions e.g., the magnitude, frequency and phase distribution of electrical field components; the modulation of the field for magnitude and/or frequency
  • the particles which are less polarizable than the surrounding medium will experience negative dielectrophoretic forces and are directed towards the weak field regions.
  • particles may experience dielectrophoretic forces that drive them in the same direction as the field traveling direction or against it, dependent on the polarization factor ] TWD .
  • the following papers provide basic theories and practices for dielectrophoresis and traveling-wave- dielectrophoresis: Huang, et al., J. Phys. D: Appl. Phys.26:1528-1535 (1993);Wang, et al., Biochim.
  • a filtration chamber can also preferably comprise or engage at least a portion of at least one active chip, where an active chip is a chip that uses applied physical forces to promote, enhance, or facilitate processing or desired biochemical reactions of a sample, or and to decrease or reduce any undesired effects that might otherwise occur to or in a sample.
  • An active chip of a filtration chamber of the present invention preferably comprises acoustic elements, electrodes, or even electromagnetic elements.
  • An active chip can be used to transmit a physical force that can prevent clogging of the slots or around the structures used to create a filter (for example, blocks, dams, or channels, slots etched into and through the filter substrate) by components of the sample that are too large to go through the pores or slots or openings, or become aggregated at the pores or slots or openings.
  • acoustic elements can cause mixing of the components within the chamber, thereby dislodging nonfilterable components from the slots or pores.
  • a pattern of electrodes on a chip can provide negative dielectrophoresis of sample components to move the nonfilterable components from the vicinity of the slots, channels, or openings around structures and allow access of filterable sample components to the slots or openings.
  • Example of such electrode arrays fabricated onto a filter under a different operating mechanism of “dielectrophoretic-base selective retention” have been described in“Novel dielectrophoresis-based device of the selective retention of viable cells in cell culture media” by Docoslis et al, in Biotechnology and
  • Electrodes can also be incorporated onto active chips that are used in filtration chambers of the present invention to improve filtration efficiency.
  • a filtration chamber can also comprise a chip that comprises electromagnetic elements.
  • electromagnetic elements can be used for the capture of sample components before or, preferably, after, filtering of the sample.
  • Sample components can be captured after being bound to magnetic beads.
  • the captured sample components can be either undesirable components to be retained in the chamber after the sample containing desirable components has already been removed from the chamber, or the captured sample components can be desirable components captured in the chamber after filtration.
  • An acoustic force chip can engage or be part of a filtration chamber, or one or more acoustic elements can be provided on one or more walls of a filtration chamber. Mixing of a sample by the activation of the acoustic force chip can occur during the filtration procedure.
  • a power supply is used to transmit an electric signal to the acoustic elements of one or more acoustic chips or one or more acoustic elements on one or more walls or a chamber.
  • One or more acoustic elements can be active continuously throughout the filtration procedure, or can be activated for intervals (pulses) during the filtration procedure.
  • Sample components and, optionally, solutions or reagents added to the sample can be mixed by acoustic forces that act on both the fluid and the moieties, including, but not limited to, molecules, complexes, cells, and microparticles, in the chamber.
  • Acoustic forces can cause mixing by acoustic streaming of fluid that occurs when acoustic elements, when energized by electrical signals generate mechanical vibrations that are transmitted into and through the fluid.
  • acoustic energy can cause movement of sample components and/or reagents by generating acoustic waves that generate acoustic radiation forces on the sample components (moieties) or reagents themselves.
  • Acoustic force refers to the force that is generated on moieties, e.g., particles and/or molecules, by an acoustic wave field. (It may also be termed acoustic radiation forces.)
  • the acoustic forces can be used for manipulating, e.g., trapping, moving, directing, handling, mixing, particles in fluid.
  • the use of the acoustic force in a standing ultrasound wave for particle manipulation has been demonstrated for concentrating erythrocytes (Yasuda et al, J. Acoust. Soc.
  • An acoustic wave can be established by an acoustic transducer, e.g., piezoelectric ceramics such as PZT material.
  • the piezoelectric transducers are made from“piezoelectric materials” that produce an electric field when exposed to a change in dimension caused by an imposed mechanical force (piezoelectric or generator effect). Conversely, an applied electric field will produce a mechanical stress (electrostrictive or motor effect) in the materials. They transform energy from mechanical to electrical and vice-versa.
  • AC voltages are applied to the piezoelectric transducers, the vibration occurs to the transducers and such vibration can be coupled into a fluid that is placed in the chamber comprising the piezoelectric transducers.
  • An acoustic chip can comprise acoustic transducers so that when AC signals at appropriate frequencies are applied to the electrodes on the acoustic transducers, the alternating mechanical stress is produced within the piezoelectric materials and is transmitted into the liquid solutions in the chamber.
  • the chamber is set up so that a standing acoustic wave is established along the direction (e.g.: z-axis) of wave propagation and reflection, the standing wave spatially varying along the z axis in a fluid can be expressed as:
  • the standing-wave acoustic field may be generated by the
  • U m and U p are the density of the particle and the medium
  • J m and J p are the compressibility of the particle and medium, respectively.
  • the compressibility of a material is the product of the density of the material and the velocity of acoustic-wave in the material.
  • the compressibility is sometimes termed acoustic impedance.
  • A is termed as the acoustic-polarization-factor.
  • the acoustic radiation forces acting on particles depend on acoustic energy density distribution and on particle density and compressibility. Particles having different density and compressibility will experience different acoustic-radiation-forces when they are placed into the same standing acoustic wave field.
  • the acoustic radiation force acting on a particle of 10 micron in diameter can vary somewhere between ⁇ 0.01 and > 1000 pN, depending on the established acoustic energy density distribution.
  • acoustic forces on particles may also be generated by various special cases of acoustic waves.
  • acoustic forces may be produced by a focused beam (“Acoustic radiation force on a small compressible sphere in a focused beam” by Wu and Du, J. Acoust. Soc. Am., 87:997-1003 (1990)), or by acoustic tweezers (“Acoustic tweezers” by Wu J. Acoust. Soc. Am., 89:2140-2143 (1991)).
  • Acoustic wave field established in a fluid can also induce a time-independent fluid flow, as termed acoustic streaming.
  • acoustic streaming may also be utilized in biochip applications or microfluidic applications for transporting or pumping fluids.
  • acoustic-wave fluid flow may be exploited for manipulating molecules or particles in fluids.
  • the acoustic streaming depends on acoustic field distributions and on fluid properties (“Nonlinear phenomena” by Rooney J.A. in“Methods of Experimental Physics: Ultrasonics, Editor: P.D. Edmonds”, Chapter 6.4, pages 319-327, Academic Press, 1981;“Acoustic Streaming” by Nyborg W.L.M. in“Physical Acoustics, Vol. II-Part B, Properties of Polymers and Nonlinear Acoustics”, Chapter 11, pages 265-330, 1965).
  • one or more active chips can also be used to promote mixing of reagents, solutions, or buffers, that can be added to a filtration chamber, before, during, or after the addition of a sample and the filtration process.
  • reagents such as, but not limited to specific binding members that can aid in the removal of undesirable sample components, or in the capture of desirable sample components, can be added to a filtration chamber after the filtration process has been completed and the conduits have been closed off.
  • the acoustic elements of the active chip can be used to promote mixing of one or more specific binding members with the sample whose volume has been reduced by filtration.
  • the present invention includes a microfabricated filter that comprises at least one tapered pore, where a pore is an opening in the filter.
  • a pore can be of any shape and any dimensions.
  • a pore can be quadrilateral, rectangular, ellipsoid, or circular in shape, or of any other shape.
  • a pore can have a diameter (or widest dimension) from about 0.1 micron to about 1000 microns, preferably from about 20 to about 200 microns, depending on the filtering application.
  • a pore is made during the machining of a filter, and is micro-etched or bored into the filter material that comprises a hard, fluid- impermeable material such as glass, silicon, ceramic, metal or hard plastic such as acrylic, polycarbonate, or polyimide. It is also possible to use a relatively non-hard surface for the filter that is supported on a hard solid support.
  • the filter comprises a hard material that is not deformable by the pressure (such as suction pressure) used in generating fluid flow through the filter.
  • a slot is a pore with a length that is greater than its width, where“length” and“width” are dimensions of the opening in the plane of the filter. (The“depth” of the slot corresponds to the thickness of the filter.) That is,“slot” describes the shape of the opening, which will in most cases be approximately rectangular or ellipsoid, but can also approximate a quadrilateral or parallelogram.
  • the shape of the slot can vary at the ends (for example, be regular or irregular in shape, curved or angular), but preferably the long sides of the slot are a consistent distance from one another for most of the length of the slot, that distance being the slot width.
  • the long sides of a slot will be parallel or very nearly parallel, for most of the length of the slot.
  • the filters used for filtration in the present invention are microfabricated or micro- machined filters so that the pores or the slots within a filter can achieve precise and uniform dimensions.
  • Such precise and uniform pore or slot dimensions are a distinct advantage of the microfabricated or micro- machined filters of the present invention, in comparison with the conventional membrane filters made of materials such as nylon, polycarbonate, polyester, mixed cellulose ester, polytetrafluoroethylene, polyethersulfone, etc.
  • individual pores are isolated, have similar or almost identical feature sizes, and are patterned on a filter. Such filters allow precise separation of particles based on their sizes and other properties.
  • the filtration area of a filter is determined by the area of the substrate comprising the pores.
  • the filtration area for microfabricated filters of the present invention can be between about 0.01 mm 2 and about 0.1 m 2 .
  • the filtration area is between about 0.25 mm 2 and about 25 cm 2 , and more preferably is between about 0.5 mm 2 and about 10 cm 2 .
  • the large filtration areas allow the filters of the invention to process sample volumes from about 10 microliters to about 10 liters.
  • the percent of the filtration area encompassed by pores can be from about 1% to about 70%, preferably is from about 10% to about 50%, and more preferably is from about 15 to about 40%.
  • the filtration area of a microfabricated filter of the present invention can comprise any number of pores, and preferably comprises at least two pores, but more preferably the number of pores in the filtration area of a filter of the present invention ranges from about 4 to about 1,000,000, and even more preferably ranges from about 100 to about 250,000.
  • the thickness of the filter in the filtration area can range from about 10 to about 500 microns, but is preferably in the range of between about 40 and about 100 microns.
  • the microfabricated filters of the present invention have slots or pores that are etched through the filter substrate itself.
  • the pores or openings of the filters can be made by using microfabrication or micromachining techniques on substrate materials, including, but not limited to, silicon, silicon dioxide, ceramics, glass, polymers such as polyimide, polyamide, etc.
  • substrate materials including, but not limited to, silicon, silicon dioxide, ceramics, glass, polymers such as polyimide, polyamide, etc.
  • Various fabrication methods as known to those skilled in the art of microlithography and microfabrication (See, for example, Rai-Choudhury P. (Editor), Handbook of Microlithography, Micromachining and Microfabrication, Volume 2: Micromachining and microfabrication. SPIE Optical Engineering Press, Bellingham, Washington, USA (1997)), may be used. In many cases, standard microfabrication and micromachining methods and protocols may be involved.
  • the protocols in the microfabrication may include many basic steps, for example, photolithographic mask generation, deposition of photoresist, deposition of“sacrificial” material layers, photoresist patterning with masks and developers, or“sacrificial” material layer patterning.
  • Pores can be made by etching into the substrate under certain masking process so that the regions that have been masked are not etched off and the regions that have not been mask-protected are etched off.
  • the etching method can be dry-etching such as deep RIE (reactive ion etching), laser ablation, or can be wet etching involving the use of wet chemicals.
  • the material may be grown by a positive method whereby the slots or pores appear as the substrate material is depositioned or grown around them or the material may be grown around a masking resist that when removed will produce the holes or slots.
  • the aspect ratio refers to the ratio of the slot depth (corresponding to the thickness of the filter in the region of the pores) to the slot width or slot length.
  • the fabrication of filter slots with higher aspect ratios may involve deep etching methods. Many fabrication methods, such as deep RIE, useful for the fabrication of MEMS (microelectronic mechanical systems) devices can be used or employed in making the microfabricated filters.
  • the resulting pores can, as a result of the high aspect ratio and the etching method, have a slight tapering, such that their openings are narrower on one side of the filter than the other.
  • the angle Y, of a hypothetical pore bored straight through the filter substrate is 90 degrees
  • the tapering angle X by which a tapered pore of a microfabricated filter of the present invention differs from the perpendicular is between about 0 degree and about 90 degrees, and preferably between 0.1 degrees and 45 degrees and most preferably between about 0.5 degrees and 10 degrees, depending on the thickness of the filter (pore depth).
  • the present invention includes microfabricated filters comprising two or more tapered pores.
  • the substrate on which the filter pores, slots or openings are fabricated or machined may be silicon, silicon dioxide, plastic, glass, ceramics or other solid materials.
  • the solid materials may be porous or non-porous. Those who are skilled in microfabrication and micromachining fabrication may readily choose and determine the fabrication protocols and materials to be used for fabrication of particular filter geometries.
  • the filter slots, pores or openings can be made with precise geometries.
  • the accuracy of a single dimension of the filter slots e.g. slot length, slot width
  • the accuracy of the critical, single dimension of the filter pores e.g. slot width for oblong or quadrilateral shaped slots
  • the filters of the present invention are made within, preferably, less than 2 microns, more preferably, less than 1 micron, or even more preferably less than 0.5 micron.
  • filters of the present invention can be made using the track-etch technique, in which filters made of glass, silicon, silicon dioxides, or polymers such as polycarbonate or polyester with discrete pores having relatively-uniform pore sizes are made.
  • the filter can be made by adapting and applying the track-etch technique described for Nucleopore Track-etch membranes to filter substrates.
  • a thin polymer film is tracked with energetic heavy ions to produce latent tracks on the film. The film is then put in an etchant to produce pores.
  • Preferred filters for the cell separation methods and systems of the present invention include microfabricated or micromachined filters that can be made with precise geometries for the openings on the filters. Individual openings are isolated with similar or almost identical feature sizes and are patterned on a filter. The openings can be of different shapes such as, for example, circular, quadrilateral, or elliptical. Such filters allow precise separation of particles based on their sizes and other properties.
  • the present invention provides methods of separating a target component of a fluid sample using filtration through a filtration chamber of the present invention that comprises a microfabricated filter enclosed in a housing.
  • the filtration chamber may be configured to allow substantially anti-parallel flow in the antechamber and post-filtration subchamber.
  • the surface of the filter and/or the inner surface of the housing may be modified by vapor deposition, sublimation, vapor-phase surface reaction, or particle sputtering to produce a uniform coating.
  • the surface of the filter and/or the inner surface of said housing are modified by vapor deposition, sublimation, vapor-phase surface reaction, or particle sputtering to produce a uniform coating.
  • the method includes: dispensing a sample into a filtration chamber that comprises or engages a microfabricated filter enclosed in a housing; providing fluid flow of the sample through the filtration chamber, such that the target component of the fluid sample flows through or is retained by the one or more microfabricated filters. Separation of the components may be based on the size, shape, deformability, binding affinity and/or binding specificity of the components.
  • the method may further comprise manipulating the fluid sample with a physical force, wherein said manipulation is effected through a structure that is external to the filter and/or a structure that is built-in on the filter.
  • the method may further comprise collecting the target component, such as nucleated cells or rare cells from said filtration chamber.
  • filtration can separate soluble and small components of a sample from at least a portion of the nucleated cells or rare cells that are in the sample, in order to concentrate the cells to facilitate further separation and analysis.
  • filtration can remove undesirable components from a sample, such as, but not limited to, undesirable cell types.
  • filtration reduces the volume of a sample by at least 50% or removes greater than 50% of the cellular components of a sample
  • filtration can be considered a debulking step.
  • the present invention contemplates the use of filtration for debulking as well as other functions in the processing of a fluid sample, such as, for example, concentration of sample components or separation of sample components (including, for example, removal of undesirable sample components and retention of desirable sample components).
  • a sample can be any fluid sample, such as an environmental sample, including air samples, water samples, food samples, and biological samples, including suspensions, extracts, or leachates of environmental or biological samples.
  • Biological samples can be blood, a bone marrow sample, an effusion of any type, ascitic fluid, pelvic wash fluid, or pleural fluid, spinal fluid, lymph, serum, mucus, sputum, saliva, urine, semen, ocular fluid, extracts of nasal, throat or genital swabs, cell suspension from digested tissue, or extracts of fecal material.
  • Biological samples can also be samples of organs or tissues, including tumors, such as fine needle aspirates and core-needle biopsy, or samples from perfusions of organs or tissues.
  • Biological samples can also be samples of cell cultures, including both primary cultures and cell lines.
  • the volume of a sample can be very small, such as in the microliter range, and may even require dilution, or a sample can be very large, such as up to about two liters for ascites fluid.
  • a preferred sample is a blood sample.
  • a blood sample can be any blood sample, recently taken from a subject, taken from storage, or removed from a source external to a subject, such as clothing, upholstery, tools, etc.
  • a blood sample can therefore be an extract obtained, for example, by soaking an article containing blood in a buffer or solution.
  • a blood sample can be unprocessed or partially processed, for example, a blood sample that has been dialyzed, had reagents added to it, etc.
  • a blood sample can be of any volume. For example, a blood sample can be less than five microliters, or more than 5 liters, depending on the application.
  • a blood sample that is processed using the methods of the present invention will be from about 10 microliters to about 2 liters in volume, more preferably from about one milliliter to about 250 milliliters in volume, and most preferably between about 5 and 50 milliliters in volume.
  • the rare cells to be enriched from a sample can be of any cell type present at less than one million cells per milliliter of fluid sample or that constitute less than 1% of the total nucleated cell population in a fluid sample.
  • Rare cells can be, for example, bacterial cells, fungal cells, parasite cells, cells infected by parasites, bacteria, or viruses, or eukaryotic cells such as but not limited to fibroblasts or blood cells.
  • Rare blood cells can be RBCs (for example, if the sample is an extract or leachate containing less than one million red blood cells per milliliter), subpopulations of blood cells and blood cell types, such as WBCs, or subtypes of WBCs (for example, T cells or macrophages), nucleated red blood cells, or can be fetal cells (including but not limited to nucleated red blood cells, trophoblasts, granulocytes, or monocytes).
  • Rare cells can be stem or progenitor cells of any type. Rare cells can also be cancer cells, including but not limited to neoplastic cells, malignant cells, and metastatic cells. Rare cells of a blood sample can also be non-hematopoietic cells, such as but not limited to epithelial cells.
  • the present invention includes methods for rare cell isolation from blood samples that include the selection of a blood sample of a particular gestational age for isolation of particular fetal cell types.
  • a maternal blood sample for the isolation of fetal nucleated cells is selected to be from the gestational age of between about 4 weeks and about 37 weeks, preferably about 7 weeks and about 24 weeks, and more preferably between about 10 weeks and about 20 weeks.
  • a maternal blood sample for the isolation of fetal nucleated cells is drawn from a pregnant subject at the gestational age of between about 4 weeks and about 37 weeks, preferably about 7 weeks and about 24 weeks, and more preferably between about 10 weeks and about 20 weeks.
  • a pregnant subject can also include a woman of the given gestational age that has aborted within twenty-four hours of the blood sample draw.
  • the present invention also includes methods for isolating fetal cells from a maternal blood sample in which the supernatant of a second centrifugation performed on the blood sample to wash the cells prior to a debulking or separation step is used as at least a part of the sample from which fetal cells are isolated.
  • a sample can be dispensed into a filtration chamber of the present invention by any convenient means.
  • sample can be introduced using a conduit (such as tubing) through which a sample is pumped or injected into the chamber, or can be directly poured, injected, or dispensed or pipetted manually, by gravity feed, or by a machine.
  • Dispensing of a sample into a filtration chamber of the present invention can be directly into the filtration chamber, via a loading reservoir that feeds directly or indirectly into a filtration chamber, or can be into a conduit that leads to a filtration chamber, or into a vessel that leads, via one or more conduits, to a filtration chamber.
  • a needle in fluid communication with tubing or a chamber can also be used to enter a tube.
  • the needle may collect cells from a tube containing a solution and dispense the solution into another chamber using a device to push or pull a solution (e.g. pump or syringe).
  • filtering is effected by providing fluid flow through the chamber.
  • Fluid flow can be provided by any means, including positive or negative pressure (for example, by a manual or machine operated syringe-type system), pumping, or even gravity.
  • the filtration chamber can have ports that are connected to conduits through which a buffer or solution and the fluid sample or components thereof can flow.
  • a filtration unit can also have valves that can control fluid flow through the chamber.
  • filter slots can allow the passage of fluid, soluble components of the samples, and filterable non-soluble components of a fluid sample through a filter, but, because of the slot dimensions, can prevent the passage of other components of the fluid sample through the filter.
  • fluid flow in the antechamber and post-filtration subchamber are substantially anti-parallel.
  • the flow can be effected by automated means through the inflow and/or outflow ports of the filtration chamber.
  • a fluid flow of a solution substantially perpendicular to the anti-parallel flow may be introduced.
  • the antechamber may be used for a fluid flow across the filter(s) to push the components of the fluid sample across the filter(s).
  • fluid flow through a filtration chamber of the present invention is automated, and performed by a pump or positive or negative pressure system, but this is not a requirement of the present invention.
  • the optimal flow rate will depend on the sample being filtered, including the concentration of filterable and non-filterable components in the sample and their ability to aggregate and clog the filter.
  • the flow rate through the filtration chamber can be from less than 1 milliliter per hour to more than 1000 milliliters per hour, and flow rate is in no way limiting for the practice of the present invention.
  • filtration of a blood sample occurs at a rate of from 5 to 500 milliliters per hour, and more preferably at a rate of between about 5 and about 40 milliliters per hour.
  • Blood (either whole blood or diluted whole blood) may be introduced into the antechamber by engaging the delivery mechanism, namely a pipette sealed to the inflow port and driven by a pump or gravity, or by any flow generating method, and delivering a known quantity of the blood continuously through the antechamber of the filter and collecting the debulked blood from the outflow port of the antechamber.
  • a fixed volume of blood or blood mixture may be delivered into a reservoir that is part of the inflow port, and a flow mechanism will engage with the outflow port of the antechamber and draw said sample continuously through the antechamber until the desired volume is collected.
  • the bottom chamber will have an inflow and an outflow port, both of which will be connected to pumps where the outflow rate will be greater than the inflow rate such that some contents from the top chamber are slowly drawn across the filter and into the post-filtration subchamber.
  • the flow through the post-filtration subchamber will preferably be in the opposite direction to flow in the top chamber, or antiparallel flow, such that particles traversing the filter will not have an opportunity to diffuse back through the filter into a region of the blood which may not contain as many of those particles, as depicted in Figure 33. In so doing, the blood will be cleared of the smaller particles, namely platelets and/or red blood cells, and preferably both.
  • the traversing of the filter material may optionally be aided by electrostatic, electromagnetic, electrophoretic, or electroosmotic flow by introducing two or more electrodes into any of the ports, or by connecting to electrodes integrated into the unit, potentially forming the ceiling and floor of the opposing chambers.
  • the separation of the particles by size may be aided by oscillatory flow produced by oscillating the pumps or by introducing an acoustic force to the flow across the filters.
  • This acoustic force may be a pressure wave from impact anywhere along the fluidics, or created by a speaker or piezoelectric device embedded in the waste chamber (post-filtration subchamber) or anywhere along the post-filtration subchamber fluidics.
  • the device may be operated oriented upside-down, or on its side such that the function of the bottom chamber of removing unwanted particles may actually be on a side chamber or top chamber.
  • preferably desirable components such as rare cells whose enrichment is desired, are retained by the filter.
  • desirable components such as rare cells whose enrichment is desired
  • as rare cells of interest of the sample are retained by the filter and one or more undesirable components of the sample flow through the filter, thereby enriching the rare cells of interest of the sample by increasing the proportion of the rare cells to total cells in the filter-retained portion of the sample, although that is not a requirement of the present invention.
  • filtration can enrich rare cells of a fluid sample by reducing the volume of the sample and thereby concentrating rare cells.
  • a combined solution of the present invention can comprise at least one specific binding member that can selectively bind undesirable components of a blood sample (such as but not limited to white blood cells, platelets, serum proteins) and have less binding to desirable components.
  • a specific binding member that can selectively bind non-RBC undesirable components of a blood sample can be used to remove the undesirable components of the sample, increasing the relative proportion of rare cells in the sample, and thus contribute to the enrichment of rare cells of the sample.
  • selectively binds is meant that a specific binding member used in the methods of the present invention to remove one or more undesirable sample components does not appreciably bind to rare cells of interest of the fluid sample.
  • bind is meant that not more than 30%, preferably not more than 20%, more preferably not more than 10%, and yet more preferably not more than 1.0% of one or more rare cells of interest are bound by the specific binding member used to remove non-RBC undesirable components from the fluid sample.
  • the undesirable components of a blood sample will be white blood cells.
  • a combined solution of the present invention can be used for sedimenting red blood cells and selectively removing white blood cells from a blood sample.
  • a specific binding member that can specifically bind white blood cells can be as non-limiting examples, an antibody, a ligand for a receptor, transporter, channel or other moiety of the surface of a white blood cell, or a lectin or other protein that can specifically bind particular carbohydrate moieties on the surface of a white blood cell (for example, a selectin).
  • a specific binding member that selectively binds white blood cells is an antibody that binds white blood cells but does not appreciably bind fetal nucleated cells, such as, for example, an antibody to CD3, CD11b, CD14, CD17, CD31, CD45, CD50, CD53, CD63, CD69, CD81, CD84, CD102, CD166, CD138, CD27, CD49 (for plasma cells), CD235a (for RBCs), CD71 (for nucleated RBCs and fetal RBCs), CD19, CD20 (for B-cells), CD56/CD16 (for NK cells), CD34 (for stem cells), CD8/CD4 (for T cells), and/or CD62p (for activated platelets).
  • an antibody that binds white blood cells but does not appreciably bind fetal nucleated cells such as, for example, an antibody to CD3, CD11b, CD14, CD17, CD31, CD45, CD50, CD53, CD63, CD69, CD81, CD84
  • Antibodies can be purchased commercially from suppliers such as, for example Dako, BD Pharmingen, Antigenix America, Neomarkers, Leinco Technologies, Research & Diagnostic Systems, Serotec, United States Biological, Bender Medsystems Diagnostics, Ancell, Leinco Technologies, Cortex Biochem, CalTag, Biodesign, Biomeda, Accurate Chemicals & Scientific and Chemicon International. Antibodies can be tested for their ability to bind an efficiently remove white blood cells and allow for the enrichment of rare cells of interest from a sample using capture assays well known in the art.
  • Specific binding members that selectively bind to one or more undesirable components of the present invention can be used to capture one or more non-RBC undesirable components, such that one or more desirable components of the fluid sample can be removed from the area or vessel where the undesirable components are bound. In this way, the undesirable components can be separated from other components of the sample that include the rare cells to be separated.
  • the capture can be affected by attaching the specific binding members that recognize the undesirable component or components to a solid support, or by binding secondary specific binding members that recognize the specific binding members that bind the undesirable component or components, to a solid support, such that the undesirable components become attached to the solid support.
  • specific binding members that selectively bind undesirable sample components provided in a combined solution of the present invention are coupled to a solid support, such as microparticles, but this is not a requirement of the present invention.
  • Magnetic beads are preferred solid supports for use in the methods of the present invention to which specific binding members that selectively bind undesirable sample components can be coupled.
  • Magnetic beads are known in the art, and are available commercially.
  • Methods of coupling molecules, including proteins such as antibodies and lectins, to microparticles such as magnetic beads are known in the art.
  • Preferred magnetic beads of the present invention are from 0.02 to 20 microns in diameter, preferably from 0.05 to 10 microns in diameter, and more preferably from 0.05 to 5 microns in diameter, and even more preferably from 0.05 to 3 microns in diameter and are preferably provided in a combined solution of the present invention coated with a primary specific binding member, such as an antibody that can bind a cell that is to be removed from the sample, or a secondary specific binding member, such as streptavidin, that can bind primary specific binding members that bind undesirable sample components (such as biotinylated primary specific binding members).
  • a primary specific binding member such as an antibody that can bind a cell that is to be removed from the sample
  • a secondary specific binding member such as streptavidin
  • the fluid sample is a maternal blood sample
  • the rare cells whose separation is desirable are fetal cells
  • the undesirable components of the sample to be removed from the sample are white blood cells.
  • a specific binding member that selectively binds white blood cells is used to remove the white blood cells from the sample by magnetic capture.
  • the specific binding member provided is attached to magnetic beads for direct capture, or, is provided in biotinylated form for indirect capture of white blood cells by streptavidin-coated magnetic beads.
  • a combined solution for enriching rare cells of a blood sample of the present invention can also include other components, such as, but not limited to, salts, buffering agents, agents for maintaining a particular osmolality, chelators, proteins, lipids, small molecules, anticoagulants, etc.
  • a combined solution comprises physiological salt solutions, such as PBS, PBS lacking calcium and magnesium or Hank’s balanced salt solution.
  • physiological salt solutions such as PBS, PBS lacking calcium and magnesium or Hank’s balanced salt solution.
  • EDTA or heparin are present to prevent red blood cell clotting.
  • the present invention also includes the use of an antibody or molecule capable of specifically binding a platelet or a molecule associated with a platelet.
  • antibodies or molecules or the present invention may specifically bind CD31, CD36, CD41, CD42(a,b,c), CD51, CD51/61, CD138, CD27, CD49 (for plasma cells), CD235a (for RBCs), CD71 (for nucleated RBCs and fetal RBCs), CD19, CD20 (for B-cells), CD56/CD16 (for NK cells), CD34 (for stem cells), CD8/CD4 (for T cells), and/or CD62p (for activated platelets).
  • CD31 is an endothelial and platelet cell marker that has minimal binding to fetal cells. Its use in separating platelets from a blood sample is described in the examples. Improved Magnet Configurations for Capture of Sample Components
  • a debulked sample such as a debulked blood sample
  • one or more specific binding members such as, but not limited to, antibodies, that specifically recognize one or more undesirable components of a fluid sample.
  • mixing and incubation of one or more specific binding members with the sample can optionally be performed in a filtration chamber.
  • the one or more undesirable components can be captured, either directly or indirectly, via their binding to the specific binding member.
  • a specific binding member can be bound to a solid support, such as a bead, membrane, or column matrix, and following incubation of the fluid sample with the specific binding member, the fluid sample, containing unbound components, can be removed from the solid support.
  • one or more primary specific binding members can be incubated with the fluid sample, and, preferably following washing to remove unbound specific binding members, the fluid sample can be contacted with a secondary specific binding member that can bind or is bound to a solid support. In this way the one or more undesirable components of the sample can become bound to a solid support, enabling separation of the undesirable components from the fluid sample.
  • a debulked blood sample from a pregnant individual is incubated with magnetic beads that are coated with antibody that specifically binds white blood cells and does not appreciably bind fetal nucleated cells.
  • the magnetic beads are collected using capture by activated electromagnetic units (such as on an electromagnetic chip), or capture by at least one permanent magnet that is in physical proximity to a vessel, such as a tube or column, that contains the fluid sample. After capture of the magnetic beads by the magnet, the remaining fluid sample is removed from the vessel.
  • the sample can be removed manually, such as by pipetting, or by physical forces such as gravity, or by fluid flow through a separation column. In this way, undesirable white blood cells can be selectively removed from a maternal blood sample.
  • the sample can optionally be further filtered using a microfabricated filter of the present invention. Filtration preferably removes residual red blood cells from the sample and can also further concentrate the sample.
  • the sample is transported through a separation column that comprises or engages at least one magnet. As the sample flows through the column, undesirable components that are bound to the magnetic beads adhere to one or more walls of the tube adjacent to the magnet or magnets.
  • a magnetic separator such as the magnetic separator manufactured by Immunicon (Huntingdon Valley, PA). Magnetic capture can also employ electromagnetic chips that comprise electromagnetic physical force-generating elements, such as those described in U.S.
  • a tube that contains the sample and magnetic beads is positioned next to one or more magnets for the capture of non-desirable components bound to magnetic beads. The supernatant, depleted of the one or more non-desirable components, can be removed from the tube after the beads have collected at the tube wall.
  • removal of white blood cells from a sample is performed simultaneously with debulking the blood sample by selective sedimentation of red blood cells.
  • a solution that selectively sediments red blood cells is added to a blood sample, and a specific binding member that specifically binds white blood cells that is bound to a solid support, such as magnetic beads, is added to the blood sample.
  • a specific binding member that specifically binds white blood cells that is bound to a solid support, such as magnetic beads is added to the blood sample.
  • red blood cells are allowed to settle, and white blood cells are captured, such as by magnetic capture. This can be conveniently performed in a tube to which a sedimenting solution and the specific binding member, preferably bound to magnetic beads, can be added.
  • the tube can be rocked for a period of time for mixing the sample, and then positioned next to one or more magnets for the capture of the magnetic beads.
  • approximately 99% of RBCs and 99% of WBCs can be removed from a sample.
  • the supernatant can be removed from the tube and subjected to filtration using a microfabricated filter of the present invention. Filtration removes remaining RBCs, resulting in a sample in which rare cells, such as, for example, fetal cells, cancer cells, or stem cells, have been enriched.
  • Undesirable components of a sample can be removed by methods other than those using specific binding members.
  • the dielectrical properties of particular cell types can be exploited to separate undesirable components dielectrophoretically.
  • Figure 22 depicts white blood cells of a diluted blood sample retained on electrodes of a dielectrophoresis chip after red blood cells have been washed through the chamber.
  • a solution that sediments red blood cells can also include one or more additional specific binding members that can be used to selectively remove undesirable sample components other than red blood cells from the blood sample.
  • the present invention includes a combined sedimenting solution for enriching rare cells of a blood sample that sediments red blood cells and provides reagents for the removal of other undesirable components of the sample.
  • a combined solution for processing a blood sample comprises: dextran; at least one specific binding member that can induce agglutination of red blood cells; and at least one additional specific binding member that can specifically bind undesirable components of the sample other than RBCs. Additional Enrichment Steps
  • the present invention also contemplates using filtration in combination with other steps that can be used in enriching rare cells of a fluid sample.
  • debulking steps or separation steps can be used prior to or following filtration, such as but not limited to as disclosed in United States Patent Application number 10/701,684, entitled“Methods, Compositions, and Automated Systems for Separating Rare Cells from Fluid Samples” filed November 4, 2003, United States Patent Application number 10/268,312, entitled “Methods, Compositions, and Automated Systems for Separating Rare Cells from Fluid Samples” filed October 10, 2002, both of which are incorporated herein by reference for all disclosure relating to debulking and separation procedures that can be used in enriching rare cells of a fluid sample. M.
  • the present invention also includes method of separating a target component in a fluid sample using the automated filtration unit disclosed herein, comprising: a) dispensing the fluid sample into the filtration chamber; and b) providing a fluid flow of the fluid sample through the antechamber of the filtration chamber and a fluid flow of a solution through the post-filtration subchamber of the filtration chamber, wherein the target component of the fluid sample is retained by or flows through the filter.
  • a sample can be any fluid sample, such as an environmental sample, including air samples, water samples, food samples, and biological samples, including extracts of biological samples.
  • Biological samples can be blood, a bone marrow sample, an effusion of any type, ascitic fluid, pelvic wash fluid, pleural fluid, spinal fluid, lymph, serum, mucus, sputum, saliva, urine, vaginal or uterine washes, semen, ocular fluid, extracts of nasal, throat or genital swabs, cell suspension from digested tissue, or extracts of fecal material.
  • Biological samples can also be samples of organs or tissues, including tumors, such as fine needle aspirates, core-needle biopsy, or samples from perfusions of organs or tissues.
  • Biological samples can also be samples of cell cultures, including both primary cultures and cell lines.
  • the volume of a sample can be very small, such as in the microliter range, and may even require dilution, or a sample can be very large, such as up to 10 liters for ascites fluid.
  • One preferred sample is a urine sample.
  • Another preferred sample is a blood sample.
  • the fluid sample is a prepared cell sample with labeling reagent meant to bind or absorb or be taken up by the cells and the component being removed is the unbound or interstitial components of the labeling reagent.
  • a biological sample can be any sample, recently taken from a subject, taken from storage, or removed from a source external to a subject, such as clothing, upholstery, tools, etc.
  • a blood sample can therefore be an extract obtained, for example, by soaking an article containing blood in a buffer or solution.
  • a biological sample can be unprocessed or partially processed, for example, a blood sample that has been dialyzed, had reagents added to it, etc.
  • a biological sample can be of any volume.
  • a blood sample can be less than five microliters, or more than 5 liters, depending on the application.
  • a biological sample that is processed using the methods of the present invention will be from about 10 microliters to about 2 liters in volume, more preferably from about one milliliter to about 250 milliliters in volume, and most preferably between about 5 and 50 milliliters in volume.
  • one or more samples can be provided in one or more tubes that can be placed in a rack of the automated system.
  • the rack can be automatically or manually engaged with the automated system for sample manipulations.
  • a sample can be dispensed into an automated system of the present invention by pipetting or injecting the sample through an inlet of an automated system, or can be poured, pipetted, or pumped into a conduit or reservoir of the automated system.
  • the sample will be in a tube that provides for optimal separation of sedimented cells, but it can be in any type of vessel for holding a liquid sample, such as a plate, dish, well, or chamber.
  • solutions or reagents Prior to the dispensing of a sample into a vessel or chamber of the automated system, solutions or reagents can optionally be added to the sample. Solutions or reagents can optionally be added to a sample before the sample is introduced into an automated system of the present invention, or after the sample is introduced into an automated system of the present invention. If a solution or reagent is added to a sample after the sample is introduced into an automated system of the present invention, it can optionally be added to the sample while the sample is contained within a tube, vessel, or reservoir prior to its mixing or incubation step, the settling step, or its introduction into a filtration chamber.
  • a solution or reagent can be added to a sample through one or more conduits, such as tubing, where the mixing of sample with a solution or reagent takes place in conduits. It is also possible to add one or more solutions or reagents after the sample is introduced into a chamber of the present invention (such as, but not limited to, a filtration chamber), by adding one or more of these directly to the chamber, or through conduits that lead to the chamber.
  • a chamber of the present invention such as, but not limited to, a filtration chamber
  • the sample (and, optionally, any solutions, or reagents) can be introduced into the automated system by positive or negative pressure, such as by a syringe-type pump.
  • the sample can be added to the automated system all at once, or can be added gradually, so that as a portion of the sample is being filtered, additional sample is added.
  • a sample can also be added in batches, such that a first portion of a sample is added and filtered through a chamber, and then further batches of a sample are added and filtered in succession. Filtering the Sample Through a Filtration Chamber of the Automated Filtration Unit
  • a sample can be filtered in an automated filtration unit of the present invention before or after undergoing one or more debulking steps or one or more separation steps. These debulking or separation steps can include but are not limited to a RBC sedimentation step or removal by specific binding members.
  • the sample can be directly transferred to a filtration chamber (such as by manual or automated dispensing) or can enter a filtration chamber through a conduit. After a sample is added to a filtration chamber, it is filtered to reduce the volume of the sample, and, optionally, to remove undesirable components of a sample.
  • fluid flow is directed through the chamber. Fluid flow through the chamber is preferably directed by automatic rather than manual means, such as by an automatic syringe-type pump. The pump can operate by exerting positive or negative pressure through conduits leading to the filtration chamber.
  • fluid flow in the antechamber and post-filtration subchamber are substantially anti-parallel.
  • the flow can be effected by automated means through the inflow and/or outflow ports of the filtration chamber.
  • a fluid flow of a solution substantially perpendicular to the anti-parallel flow may be introduced.
  • the antechamber may be used for a fluid flow across the filter(s) to push the components of the fluid sample across the filter(s).
  • the flow rate in the antechamber and the flow rate in the post-filtration subchamber may be different, such that a fluidic force is generated on components of the fluid sample to flow from the antechamber to the post-filtration subchamber.
  • “filter rate” refers to the fluidic flow rate across the filter
  • “feed rate” refers to the fluidic flow rate in the antechamber
  • “buffer rate” and“waste rate” refers to the fluidic flow rate in inflow port and outflow port of the post-filtration subchamber, respectively.
  • the inflow rate and outflow rate of the post-filtration subchamber may be different to generate the desired fluidic force to direct the fluid flow across the filter.
  • the rate of fluid flow through a filtration chamber can be any rate that allows for effective filtering, and for a whole blood sample is preferably up to about 10 mL/min, more preferably between about 10 and about 500 ⁇ L/min, and most preferably between about 80 and about 140 ⁇ L/min.
  • the rate of fluid flow in the antechamber may be about 1-10 times the filter rate.
  • a pump or fluid dispensing system can optionally direct fluid flow of a buffer or solution into the chamber to wash additional filterable sample components through the chamber.
  • pores or slots in the filter or filters can allow the passage of fluid, soluble components of the samples, and some non-soluble components of a fluid sample through one or more filters, but, because of their dimensions, can prevent the passage of other components of the fluid sample through the one or more filters.
  • a fluid sample can be dispensed into a filtration chamber that comprises at least one filter that comprises a plurality of slots.
  • the chamber can have ports that are optionally connected to conduits through which a buffer or solution and the fluid sample or components thereof can flow.
  • the slots can allow the passage of fluid and, optionally, some components of a fluid sample through the filter, but prevent the passage of other components of the fluid sample through the filter.
  • an active chip that is part of the filtration chamber can be used to mix the sample during the filtration procedure.
  • an active chip can be an acoustic chip that comprises one or more acoustic elements. When an electric signal from a power supply activates the acoustic elements, they provide vibrational energy that causes mixing of the components of a sample.
  • An active chip that is part of a filtration chamber of the present invention can also be a
  • dielectrophoresis chip that comprises microelectrodes on the surface of a filter.
  • the electrodes on the surface of the filter/chip are preferably activated intermittently, when fluid flow is halted or greatly reduced.
  • Mixing of a sample during filtration is performed to avoid reductions in the efficiency of filtration based on aggregation of sample components, and in particular their tendency to collect, in response to fluid flow through the chamber, at positions in the chamber where filtering based on size or shape occurs, such as dams, slots, etc.
  • Mixing can be done continuously through the filtration procedure, such as through a continuous activation of acoustic elements, or can be done in intervals, such as through brief activation of acoustic elements or electrodes during the filtration procedure.
  • the dielectrophoretic force is generated in short intervals (for example, from about two seconds to about 15 minutes, preferably from about two to about 30 seconds in length) during the filtration procedure; for example, pulses can be given every five seconds to about every fifteen minutes during the filtration procedure, or more preferably between about every ten seconds to about every one minute during the filtration procedure.
  • the dielectrophoretic forces generated serve to move sample components away from features that provide the filtering function, such as, but not limited to, slots.
  • filtered sample fluid can be removed from the filtration chamber by automated fluid flow through conduits that lead to one or more vessels for containing the filtered sample.
  • these vessels are waste receptacles.
  • fluid flow can optionally be directed in the reverse direction through the filter to suspend retained components that may have settled or lodged against the filter.
  • sample components that remain in the filtration chamber after the filtration procedure can be directed out of the chamber through additional ports and conduits that can lead to collection tubes or vessels or to other elements of the automated system for further processing steps, or can be removed from the filtration chamber or a collection vessel by pipetting or a fluid uptake means.
  • Ports can have valves or other mechanisms for controlling fluid flow. The opening and closing of ports can be automatically controlled.
  • ports that can allow the flow of debulked (retained) sample out of a filtration chamber can be closed during the filtration procedure, and conduits that allow the flow of filtered sample out of a filtration chamber can optionally be closed after the filtration procedure to allow efficient removal of remaining sample components.
  • buffer can be washed through the filtration chamber to wash through any residual components, such as undesirable cells.
  • the buffer can be conveniently directed through the filtration chamber in the same manner as the sample, that is, preferably by automated fluid flow such as by a pump or pressure system, or by gravity, or the buffer can use a different fluid flow means than the sample.
  • One or more washes can be performed, using the same or different wash buffers.
  • air can be forced through the filtration chamber, for example by positive pressure or pumping, to push residual cells through the filtration chamber.
  • the feed rate may be less than or equal to the filter rate, such as the rinsing reagent, such as EDTA, may cross the filter into the antechamber, removing any residual component blocking the slots on the filter.
  • the separated target component may be labeled using the automated filtration unit of the present invention.
  • separated nucleated cells or rare cells may be labeled with an antibody or assay reagent for further analysis.
  • the antibody or assay reagent may be conjugated with a detectable molecule, such as a radioactive or fluorescent dye.
  • the labeling reagent may be added to the collection chamber, where the target component is collected after filtration.
  • the labeling reagent may be added to the antechamber or the post- filtration subchamber, depending on where the target component is located. Adding the reagent may be carried out by the fluidic pumps and conduits of the automated filtration unit, and controlled by the control algorithm.
  • the fluid flow may be paused in the filtration chamber to allow effective binding between the target component and the labeling reagent.
  • a labeling time of suitable length may be used, for example, about 1-10 min.
  • the unbound labeling reagent may be rinsed away by adding a rinsing buffer to the filtration chamber. Recovering
  • the target component on the filter is lifted from filter slots and pushed into the collection chamber.
  • a fluidic force may be generated that lift any components blocking the filter slots, for example, by pausing the outflow in the post-filtration subchamber, or by reducing the outflow rate of the post-filtration subchamber so that it is less than the inflow rate of the post-filtration subchamber.
  • the lifting step may be via increasing the buffer rate and the feed rate to about 1-10 mL/min and about 0.5-5 mL/min, respectively.
  • the duration of the lifting step may vary, for example, from 10 ms to 1 s or longer.
  • the lifting step may be performed intermittently throughout the filtration, so that optimal filtration effect is achieved.
  • the speed at which the wash buffer flows through the chamber may be greater than that of a sample. Selective removal of undesirable components of a sample
  • sample components that remain in the filtration chamber either before, during, or after the filtration procedure can be directed by fluid flow to an element of the automated system in which undesirable components of a sample can be separated from the sample.
  • one or more specific binding members prior to either adding the sample to the filtration chamber or removing the debulked sample retained in the filtration chamber, can be added to the debulked sample and either mixed before the and afterwards in the filtration chamber, using, for example, one or more active chips that engage or are a part of the filtration chamber to provide physical forces for mixing.
  • one or more specific binding member is added to the debulked sample in the filtration chamber, ports of the chamber are closed, and acoustic elements are activated either continuously or in pulsed, during the incubation of debulked sample and specific binding members.
  • one or more specific binding members are antibodies that are bound to magnetic beads.
  • the specific binding members can be antibodies that bind desirable sample components, such as fetal nucleated cells, but preferably the specific binding members are antibodies that bind undesirable sample components, such as white blood cells while having minimal binding to desirable sample components.
  • sample components that remain in the filtration chamber after the filtration procedure are incubated with magnetic beads, and following incubation, are directed by fluid flow to a separation column.
  • a separation column used in the methods of the present invention is a cylindrical glass, plastic, or polymeric column with a volumetric capacity of between about one milliliter and ten milliliters, having entry and exit ports at opposite ends of the column.
  • a separation column used in the methods of the present invention comprises or can be positioned alongside at least one magnet that runs along the length of the column.
  • the magnet can be a permanent magnet, or can be one or more electromagnetic units on one or more chips that is activated by a power source.
  • Sample components that remain in the filtration chamber after the filtration procedure can be directed by fluid flow to a separation column.
  • Reagents preferably including a preparation of magnetic beads
  • reagents are added prior to transfer of sample components to a separation chamber.
  • a preparation of magnetic beads added to the sample comprises at least one specific binding member, preferably a specific binding member that can directly bind at least one undesirable component of the sample.
  • a primary specific binding partner is preferably added to the sample before the preparation of magnetic beads comprising a secondary specific binding partner is added to the sample, but this is not a requirement of the present invention.
  • Bead preparations and primary specific binding partners can be added to a sample before or after the addition of the sample to a separation column, separately or together.
  • the sample and magnetic bead preparation are preferably incubated together for between about five and about sixty minutes before magnetic separation.
  • the incubation can occur prior to the addition of the sample to the separation column, in conduits, chambers, or vessels of the automated system.
  • the incubation can occur in a separation column, prior to activating the one or more electromagnetic elements.
  • incubation of a sample with magnetic beads comprising specific binding members occurs in a filtration chamber following filtration of the sample, and after conduits leading into and out of the filtration chamber has been closed.
  • magnetic beads comprising secondary specific binding members are employed, optionally more than one incubation can be performed (for example, a first incubation of sample with a primary specific binding member, and a second incubation of sample with beads comprising a secondary specific binding member).
  • Separation of undesirable components of a sample can be accomplished by magnetic forces that cause the electromagnetic beads that directly or indirectly bind the undesirable components. This can occur when the sample and magnetic beads are added to the column, or, in embodiments where one or more electromagnetic units are employed, by activating the electromagnetic units with a power supply.
  • Non-captured sample components can be removed from the separation column by fluid flow. Preferably, non-captured sample components exit the column through a portal that engages a conduit.
  • a sample can optionally be directed by fluid flow to a separation chamber for the separation of rare cells.
  • the debulked sample is preferably but optionally transferred to a second filtration chamber prior to being transferred to a separation chamber for separation rare cells of the sample.
  • a second filtration chamber allows for further reduction of the volume of a sample, and also optionally allows for the addition of specific binding members that can be used in the separation of rare cells and mixing of one or more specific binding members with a sample. Transfer of a sample from a separation column to a separation chamber is by fluid flow through conduits that lead from a separation column to a second filtration chamber.
  • a second filtration chamber preferably comprises at least one filter that comprises slots, and fluid flow through the chamber at a rate of between about one and about 500 milliliters per hour, more preferably between about two and about 100 milliliters per hour, and most preferably between about five and about fifty milliliters per hour drives the filtration of sample. In this way, the volume of a debulked sample from which undesirable components have been selectively removed can be further reduced.
  • a second filtration chamber can comprise or engage one or more active chips. Active chips, such as acoustic chips or dielectrophoresis chips, can be used for mixing of the sample prior to, during, or after the filtration procedure.
  • a second filtration chamber can also optionally be used for the addition of one or more reagents that can be used for the separation of rare cells to a sample.
  • conduits that carry sample or sample components out of the chamber can be closed, and one or more conduits leading into the chamber can be used for the addition of one or more reagents, buffers, or solutions, such as, but not limited to, specific binding members that can bind rare cells.
  • the one or more reagents, buffers, or solutions can be mixed in the closed-off separation chamber, for example, by activation of one or more acoustic elements or a plurality of electrodes on one or more active chips that can produce physical forces that can move components of the sample and thus provide a mixing function.
  • magnetic beads that are coated with at least one antibody that recognizes a rare cell are added to the sample in the filtration chamber.
  • the magnetic beads are added via a conduit, and are mixed with the sample by activation of one or more active chips that are integral to or engage a second filtration chamber.
  • the incubation of specific binding members with a sample can be from about five minutes to about two hours, preferably from about eight to about thirty minutes, in duration, and mixing can occur periodically or continuously throughout the incubation.
  • a second filtration chamber that is not used for the addition and mixing of one or more reagents, solutions, or buffers with a sample. It is also within the scope of the present invention to have a chamber that precedes a separation chamber for the separation of rare cells that can be used for the addition and mixing of one or more reagents, solutions, or buffers with a sample, but that does not perform a filtering function. It is also within the scope of the present invention to have a sample transferred from a separation column to a separation chamber, without an intervening filtration or mixing chamber. In aspects where the methods are directed toward the separation of rare cells from a blood sample, however, the use of a second filtration chamber that is also used for the addition and mixing of one or more reagents with a sample is preferred.
  • a separation chamber for the separation of rare cells comprises or engages at least one active chip that can perform a separation.
  • Such chips comprise functional elements that can, at least in part, generate physical forces that can be used to move or manipulate sample components from one area of a chamber to another area of a chamber.
  • Preferred functional elements of a chip for manipulating sample components are electrodes and electromagnetic units.
  • the forces used to translocate sample components on an active chip of the present invention can be dielectrophoretic forces, electromagnetic forces, traveling wave dielectrophoretic forces, or traveling wave electromagnetic forces.
  • An active chip used for separating rare cells is preferably part of a chamber.
  • the chamber can be of any suitable material and of any size and dimensions, but preferably a chamber that comprises an active chip used for separating rare cells from a sample (a“separation chamber”) has a volumetric capacity of from about one microliter to ten milliliters, more preferably from about ten microliters to about one milliliter.
  • the active chip is a dielectrophoresis or traveling wave dielectrophoresis chip that comprises electrodes.
  • Such chips and their uses are described in U.S. Application Serial Number 09/973,629, entitled“An Integrated Biochip System for Sample Preparation and Analysis”, filed October 9, 2001; U.S. application 09/686,737, filed Oct.10, 2000 entitled
  • the active chip is an electromagnetic chip that comprises electromagnetic units, such as, for example, the electromagnetic chips described in U.S. Patent No.6,355,491 entitled“Individually Addressable Micro-Electromagnetic Unit Array Chips” issued March 12, 2002 to Zhou et al., United States Application Serial Number 09/955,343 having attorney docket number ART-00104.P.2, filed September 18, 2001, entitled“Individually Addressable Micro- Electromagnetic Unit Array Chips”, and United States Application Serial Number 09/685,410 having attorney docket number ART-00104.P.1.1, filed October 10, 2000, entitled“Individually Addressable Micro- Electromagnetic Unit Array Chips in Horizontal Configurations”.
  • electromagnetic units such as, for example, the electromagnetic chips described in U.S. Patent No.6,355,491 entitled“Individually Addressable Micro-Electromagnetic Unit Array Chips” issued March 12, 2002 to Zhou et al., United States Application Serial Number 09/955,343 having attorney docket
  • Electromagnetic chips can be used for separation by magnetophoresis or traveling wave electromagnetophoresis.
  • rare cells can be incubated, before or after addition to a chamber that comprises an electromagnetic chip, with magnetic beads comprising specific binding members that can directly or indirectly bind the rare cells.
  • the sample is mixed with the magnetic beads comprising a specific binding member in a mixing chamber.
  • a mixing chamber comprises an acoustic chip for the mixing of the sample and beads.
  • the cells can be directed through conduits from the mixing chamber to the separating chamber.
  • the rare cells can be separated from the fluid sample by magnetic capture on the surface of the active chip of the separation chamber, and other sample components can be washed away by fluid flow.
  • the methods of the present invention also include embodiments in which an active chip used for separation of rare cells is a multiple-force chip.
  • a multiple-force chip used for the separation of rare cells can comprise both electrodes and electromagnetic units. This can provide for the separation of more than one type of sample component.
  • magnetic capture can be used to isolated rare cells, while negative dielectrophoresis is used to remove undesirable cells from the chamber that comprises the multiple-force chip.
  • the captured rare cells can be recovered by removing the physical force that causes them to adhere to the chip surface, and collecting the cells in a vessel using fluid flow.
  • a solution that sediments red blood cells can also include one or more additional specific binding members that can be used to selectively remove undesirable sample components other than red blood cells from the blood sample.
  • the present invention includes a combined sedimenting solution for enriching rare cells of a blood sample that sediments red blood cells and provides reagents for the removal of other undesirable components of the sample.
  • a combined solution for processing a blood sample comprises: dextran; at least one specific binding member that can induce agglutination of red blood cells; and at least one additional specific binding member that can specifically bind undesirable components of the sample other than RBCs. Addition of Sedimenting Solution to Sample
  • a red blood cell sedimenting solution can be added to a blood sample by any convenient means, such as pipeting, automatic liquid uptake/dispensing devices or systems, pumping through conduits, etc.
  • the amount of sedimenting solution that is added to a blood sample can vary, and will largely be determined by the concentration of dextran and specific binding members in the sedimenting solution (as well as other components), so that their concentrations will be optimal when mixed with the blood sample.
  • the volume of a blood sample is assessed, and an appropriate proportional volume of sedimenting solution, ranging from 0.01 to 100 times the sample volume, preferably ranging from 0.1 times to 10 times the sample volume, and more preferably from 0.25 to 5 times the sample volume, and even more preferably from 0.5 times to 2 times the sample volume, is added to the blood sample.
  • an appropriate proportional volume of sedimenting solution ranging from 0.01 to 100 times the sample volume, preferably ranging from 0.1 times to 10 times the sample volume, and more preferably from 0.25 to 5 times the sample volume, and even more preferably from 0.5 times to 2 times the sample volume, is added to the blood sample.
  • a blood sample, or a portion thereof to a red blood cell sedimenting solution.
  • a known volume of sedimenting solution can be provided in a tube or other vessel, and a measured volume of a blood sample can be added to the sedimenting solution.
  • a combined solution of the present invention can comprise at least one specific binding member that can selectively bind undesirable components of a blood sample (including but not limited to red blood cells, white blood cells, platelets, serum proteins) and have less binding to desirable components.
  • a specific binding member that can selectively bind undesirable components of a sample can be used to remove the undesirable components of the sample, increasing the relative proportion of rare cells in the sample, and thus contribute to the enrichment of rare cells of the sample.
  • selectively binds is meant that a specific binding member used in the methods of the present invention to remove one or more undesirable sample components does not appreciably bind to desirable cells of the sample.
  • bind is meant that not more than 30%, preferably not more than 10%, and more preferably not more than 1.0% of one or more desirable cells are bound by the specific binding member used to remove undesirable components from the sample.
  • the undesirable components of a blood sample will be white blood cells.
  • a combined solution of the present invention can be used for sedimenting red blood cells and selectively removing white blood cells from a blood sample.
  • a specific binding member that can specifically bind white blood cells can be as nonlimiting examples, an antibody, a ligand for a receptor, transporter, channel or other moiety of the surface of a white blood cell, or a lectin or other protein that can specifically bind particular carbohydrate moieties on the surface of a white blood cell (for example, sulfated Lewis-type carbohydrates, glycolipids, proteoglycans or selectin).
  • a specific binding member that selectively binds white blood cells is an antibody that binds white blood cells but does not appreciably bind fetal nucleated cells, such as, for example, an antibody to CD3, CD11b, CD14, CD17, CD31, CD45, CD50, CD53, CD63, CD69, CD81, CD84, CD102, CD166, CD138, CD27, CD49 (for plasma cells), CD235a (for RBCs), CD71 (for nucleated RBCs and fetal RBCs), CD19, CD20 (for B-cells), CD56/CD16 (for NK cells), CD34 (for stem cells), CD8/CD4 (for T cells), and/or CD62p (for activated platelets).
  • Antibodies can be purchased commercially from suppliers such as, for example Dako, BD Pharmingen, Antigenix America, Neomarkers, Leinco Technologies, Research & Diagnostic Systems, Serotec, United States Biological, Bender Medsystems Diagnostics, Ancell, Leinco Technologies, Cortex Biochem, CalTag, Biodesign, Biomeda, Accurate Chemicals & Scientific and Chemicon International. Antibodies can be tested for their ability to bind an efficiently remove white blood cells and allow for the enrichment of desirable cells from a sample using capture assays well known in the art.
  • Specific binding members that selectively bind to one or more undesirable components of the present invention can be used to capture one or more undesirable components, such that one or more desirable components of the fluid sample can be removed from the area or vessel where the undesirable components are bound. In this way, the undesirable components can be separated from other components of the sample that include the rare cells to be separated.
  • the capture can be affected by attaching the specific binding members that recognize the undesirable component or components to a solid support, or by binding secondary specific binding members that recognize the specific binding members that bind the undesirable component or components, to a solid support, such that the undesirable components become attached to the solid support.
  • specific binding members that selectively bind undesirable sample components provided in a combined solution of the present invention are coupled to a solid support, such as microparticles, but this is not a requirement of the present invention.
  • Magnetic beads are preferred solid supports for use in the methods of the present invention to which specific binding members that selectively bind undesirable sample components can be coupled.
  • Magnetic beads are known in the art, and are available commercially. Methods of coupling molecules, including proteins such as antibodies, lectins and avidin and its derivatives, to microparticles such as magnetic beads are known in the art.
  • Preferred magnetic beads of the present invention are from 0.02 to 20 microns in diameter, preferably from 0.05 to 10 microns in diameter, and more preferably from 0.05 to 5 microns in diameter, and even more preferably from 0.05 to 3 microns in diameter and are preferably provided in a combined solution of the present invention coated with a primary specific binding member, such as an antibody that can bind a cell that is to be removed from the sample, or a secondary specific binding member, such as streptavidin or neutravidin, that can bind primary specific binding members that bind undesirable sample components (such as biotinylated primary specific binding members).
  • a primary specific binding member such as an antibody that can bind a cell that is to be removed from the sample
  • a secondary specific binding member such as streptavidin or neutravidin
  • the fluid sample is a maternal blood sample
  • the rare cells whose separation are desirable are fetal cells
  • the undesirable components of the sample to be removed from the sample are white blood cells and other serum components.
  • a specific binding member that selectively binds white blood cells is used to remove the white blood cells from the sample by magnetic capture.
  • the specific binding member provided is attached to magnetic beads for direct capture, or, is provided in biotinylated form for indirect capture of white blood cells by streptavidin-coated magnetic beads.
  • a combined solution for enriching rare cells of a blood sample of the present invention can also include other components, such as, but not limited to, salts, buffering agents, agents for maintaining a particular osmolality, chelators, proteins, lipids, small molecules, anticoagulants, etc.
  • a combined solution comprises physiological salt solutions, such as PBS, PBS lacking calcium and magnesium or Hank’s balanced salt solution.
  • physiological salt solutions such as PBS, PBS lacking calcium and magnesium or Hank’s balanced salt solution.
  • EDTA or heparin or ACD are present to prevent red blood cell clotting.
  • the blood sample and red blood cell sedimenting solution are mixed so that the chemical RBC aggregating agent (such as a polymer, such as, for example, dextran) and one or more specific binding members of the sedimenting solution, as well as the components of the blood sample are distributed throughout the sample vessel.
  • the chemical RBC aggregating agent such as a polymer, such as, for example, dextran
  • Mixing can be achieved means such as electrically powered acoustic mixing, stirring, rocking, inversion, agitation, etc., with methods such as rocking and inversion, that are least likely to disrupt cells, being favored.
  • the sample mixed with sedimenting solution is allowed to incubate to allow red blood cells to sediment.
  • the vessel comprising the sample is stationary during the sedimentation period so that the cells can settle efficiently.
  • Sedimentation can be performed at any temperature from about 5o C to about 37o C. In most cases, it is convenient to perform the steps of the method from about 15o C to about 27o C.
  • the optimal time for the sedimentation incubation can be determined empirically for a given sedimenting solution, while varying such parameters as the concentration of dextran and specific binding members in the solution, the dilution factor of the blood sample after adding the sedimenting solution, and the temperature of incubation.
  • the sedimentation incubation is from five minutes to twenty four hours in length, more preferably from ten minutes to four hours in length, and most preferably from about fifteen minutes to about one hour in length. In some preferred aspects of the present invention, the incubation period is about thirty minutes. N.
  • the present invention also includes methods of enriching and analyzing a component in a fluid sample using the automated system disclosed herein, comprising: a) dispensing the fluid sample into the filtration chamber; b) providing a fluid flow of the fluid sample through the antechamber of the filtration chamber and a fluid flow of a solution through the post-filtration subchamber of the filtration chamber, wherein the target component of the fluid sample is retained or flows through the filter; and c) analyzing the labeled target component using the analysis apparatus.
  • a method for separating a target component in a fluid sample comprises: a) passing a fluid sample that comprises or is suspected of comprising a target component and cell aggregates through a microfabricated filter so that said target component, if present in said fluid sample, is retained by or passes through said microfabricated filter, and b) prior to and/or concurrently with passing said fluid sample through said microfabricated filter, contacting said fluid sample with an emulsifying agent and/or a cellular membrane charging agent to reduce or disaggregate said cell aggregates, if present in said fluid sample; and/or, prior to and/or concurrently with passing said fluid sample through said microfabricated filter, contacting said fluid sample with a hyperosmotic saline solution between about 300 mOsm and about 1000 mOsm, optionally between about 350 mOsm and about 1000 mOsm, between about 350 mOsm and about 600 mO
  • the method comprises, prior to passing the fluid sample through the
  • the method comprises, concurrently with passing the fluid sample through the microfabricated filter, contacting the fluid sample with a hyperosmotic solution.
  • the hyperosmotic solution is a hyperosmotic saline solution, e.g., a hyperosmotic NaCl solution.
  • the hyperosmotic solution has an osmolarity between about 300 mOsm and about 1000 mOsm.
  • the hyperosmotic solution has an osmolarity between about 350 mOsm and about 1000 mOsm, between about 350 mOsm and about 600 mOsm, between about 400 mOsm and about 600 mOsm, between about 450 mOsm and about 600 mOsm, or between about 550 mOsm and about 600 mOsm.
  • the hyperosmotic solution is free of calcium and/or protein such that it reduces cell membrane cohesion.
  • the hyperosmotic solution is substantially free of calcium and/or protein - for example, the hyperosmotic solution contains less than about 10 -6 % (w/w), less than about 10 -5 % (w/w), less than about 10 -4 % (w/w), less than about 0.001% (w/w), less than about 0.01% (w/w), less than about 0.1% (w/w), or less than about 1% (w/w) of calcium and/or protein.
  • the method comprises, prior to passing the fluid sample through the
  • the fluid sample is contacted with a hyperosmotic solution as a pre-filtration solution to reduce or disaggregate cell aggregates present in the fluid sample.
  • the fluid sample is contacted with the pre-filtration solution, such as a hyperosmotic saline solution, for about 1 second, or about 2, 3, 4, or 5 seconds.
  • the fluid sample is contacted with the pre-filtration solution for between about 5 and 10 seconds, between about 10 and 15 seconds, between about 15 and 20 second, or more than about 20 seconds.
  • the fluid sample is contacted with the pre-filtration solution for about 30 seconds, about 1 minute, about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 minutes, or longer than about 15 minutes.
  • the sample in contact with the pre-filtration hyperosmotic solution is fed into the sample feed channel of the microfabricated filter, and the wash buffer across the microfabricated filter (e.g., an isosmotic buffer) brings the sample to iso-osmosis, effectively removing the hyperosmotic solution from the sample.
  • the wash buffer across the microfabricated filter e.g., an isosmotic buffer
  • the method comprises, prior to passing the fluid sample through the
  • microfabricated filter contacting the fluid sample with an emulsifying agent and/or a cellular membrane charging agent.
  • the method comprises, concurrently with passing the fluid sample through the microfabricated filter, contacting the fluid sample with an emulsifying agent and/or a cellular membrane charging agent.
  • the method comprises, prior to and concurrently with passing the fluid sample through the microfabricated filter, contacting the fluid sample with an emulsifying agent and/or a cellular membrane charging agent.
  • the emulsifying agent and/or the cellular membrane charging agent is used at a first level
  • the emulsifying agent and/or a cellular membrane charging agent is used at a second level, and the first level is higher than the second level.
  • the emulsifying agent is a synthetic emulsifier, a natural emulsifier, a finely divided or finely dispersed solid particle emulsifier, an auxiliary emulsifier, a monomolecular emulsifier, a multimolecular emulsifier, or a solid particle film emulsifier.
  • the emulsifying agent is selected from the group consisting of PEG 400 Monoleate (polyoxyethylene monooleate), PEG 400 Monostearate (polyoxyethylene monostearate), PEG 400 Monolaurate (polyoxyethylene monolaurate), potassium oleate, sodium lauryl sulfate, sodium oleate, Span® 20 (sorbitan monolaurate), Span® 40 (sorbitan monopalmitate), Span® 60 (sorbitan monostearate), Span® 65 (sorbitan tristearate), Span® 80 (sorbitan monooleate), Span® 85 (sorbitan trioleate), triethanolamine oleate, Tween® 20 (polyoxyethylene sorbitan monolaurate), Tween® 21 (polyoxyethylene sorbitan monolaurate), Tween® 40 (polyoxyethylene sorbitan monopalmitate), Tween® 60
  • Tween® 61 polyoxyethylene sorbitan monostearate
  • Tween® 65 polyoxyethylene sorbitan tristearate
  • Tween® 80 polyoxyethylene sorbitan monooleate
  • Tween® 81 polyoxyethylene sorbitan monooleate
  • Tween® 85 polyoxyethylene sorbitan trioleate
  • the emulsifying agent is a pluronic acid or an organosulfur compound.
  • a cellular membrane charging agent disclosed herein confers the same charges on the cellular membrane (e.g., a membrane on the cell surface) so that the cells repel each other, thereby preventing, reducing, or removing cell aggregates.
  • the cellular membrane charging agent may be an agent that confers charges to the cell membrane, the plasma membrane, or membrane of a cellular organelle.
  • the cellular membrane charging agent confers negative charges on the cell surfaces.
  • the cellular membrane charging agent confers positive charges on the cell surfaces.
  • the cellular membrane charging agent is a negatively charged polysaccharide or
  • the cellular membrane charging agent is a pluronic acid, such as the Pluronic® F-68 non-ionic surfactant.
  • the pluronic acid can serve as both an emulsifying agent and a cellular membrane charging agent.
  • Pluronics are copolymers from ethylene- and propylene oxide.
  • the pluronic acid that can be used in the present disclosure is Pluronic® 10R5, Pluronic® 17R2, Pluronic® 17R4, Pluronic® 25R2, Pluronic® 25R4, Pluronic® 31R1, Pluronic® F-108, Pluronic® F-108NF,
  • Pluronic F-68 has a molecular weight of 8400 and consists mainly of ethylene oxid (approx.80 %). It is applied in the culturing of mammalian cells in large batches. It prevents the sticking of air bubbles to cells, which develope during mixing within the fermentor, stabilizes the foam on the surface or improves the resistance of the cell membrane against hydrodynamic shearing.
  • the pluronic acid is used at a level ranging from about 1 mg/mL to about 300 mg/mL, from about 1 mg/mL to about 200 mg/mL, from about 5 mg/mL to about 50 mg/mL, from about 5 mg/mL to about 15 mg/mL, from about 15 mg/mL to about 50 mg/mL, or more than about 300 mg/mL.
  • the pluronic acid is used at about 15 mg/mL, from about 1 mg/mL to about 5 mg/mL, from about 5 mg/mL to about 10 mg/mL, from about 10 mg/mL to about 15 mg/mL, from about 15 mg/mL to about 20 mg/mL, from about 20 mg/mL to about 25 mg/mL, from about 25 mg/mL to about 30 mg/mL, from about 30 mg/mL to about 35 mg/mL, from about 35 mg/mL to about 40 mg/mL, from about 40 mg/mL to about 45 mg/mL, from about 45 mg/mL to about 50 mg/mL, from about 50 mg/mL to about 75 mg/mL, from about 75 mg/mL to about 100 mg/mL, from about 100 mg/mL to about 125 mg/mL, from about 125 mg/mL to about 150 mg/mL, from about 150 mg/mL to about 175 mg/mL, from about 175 mg/m/mL,
  • the organosulfur compound used herein is dimethyl sulfoxide (DMSO).
  • DMSO dimethyl sulfoxide
  • the DMSO is used at a level ranging from about 0.01% (v/v) to about 15% (v/v), from about 0.02% (v/v) to about 0.4% (v/v), or from about 0.01% (v/v) to about 0.5% (v/v).
  • the DMSO is used at about 0.1% (v/v), about 0.2% (v/v), about 0.3% (v/v), about 0.4% (v/v), about 0.5% (v/v), about 0.6% (v/v), about 0.7% (v/v), about 0.8% (v/v), about 0.9% (v/v), about 1.0% (v/v), about 2.0% (v/v), about 3.0% (v/v), about 4.0% (v/v), about 5.0% (v/v), about 6.0% (v/v), about 7.0% (v/v), about 8.0% (v/v), about 9.0% (v/v), about 10.0% (v/v), about 11.0% (v/v), about 12.0% (v/v), about 13.0% (v/v), about 14.0% (v/v), or about 15.0% (v/v).
  • Heparin is a glycosaminoglycan, an acidic mucopolysaccharide composed of D-glucuronic acid and D-glucosamine with a high degree of N-sulphation. It is present in the form of proteoglycan in many mammalian tissues, such as the intestine, liver, lung, being localized in the connective tissue-type mast cells, which line for example the vascular and serosal system of mammals.
  • the main pharmaceutical characteristic of heparin is its ability to enhance the activity of the natural anticoagulant, antithrombin III.
  • Hirudin which is also an anticoagulating agent, is similar to heparin in that they are both negatively charged molecules when contained within an aqueous system such as blood or a blood fluid.
  • Heparins exist naturally bound to proteins, forming so called heparin proteoglycans.
  • the endogenous or native, naturally existing heparin proteoglycans contain 10-15 heparin glycosaminoglycan chains, each chain having a molecular weight in the range of 75 ⁇ 25 kDa, and being bound to one core protein or polypeptide.
  • Each native heparin glycosaminoglycan chain contains several separate heparin units consecutively placed end-to-end, which are cleaved by endoglycosidases in their natural environment.
  • Heparin glycosaminoglycans belong to a larger group of negatively charged heteropolysaccharides, which generally are associated with proteins forming so called proteoglycans.
  • Examples of other naturally existing glycosaminoglycans are for example chondroitin-4- and 6-sulphates, keratan sulfates, dermatan sulfates, hyaluronic acid, heparan sulfates and heparins.
  • Additional synthetic heparin-like compounds are disclosed in U.S.7,504,113, the disclosure of which is incorporated herein in its entirety by reference for all purposes.
  • a heparin or a derivative thereof is used as a cellular membrane charging agent in the methods disclosed herein.
  • the concentration of the heparin or derivative thereof is less than about 0.5 IU/ml, between about 0.5 IU/ml and about 1 IU/ml, between about 1 IU/ml and about 5 IU/ml, between about 5 IU/ml and about 6 IU/ml, between about 6 IU/ml and about 7 IU/ml, between about 7 IU/ml and about 8 IU/ml, between about 8 IU/ml and about 9 IU/ml, between about 9 IU/ml and about 10 IU/ml, between about 10 IU/ml and about 11 IU/ml, between about 11 IU/ml and about 12 IU/ml, between about 12 IU/ml and about 13 IU/ml, between about 13 IU/ml and about 14 IU/ml, between
  • both an emulsifying agent and a cell cellular membrane charging agent are used in the methods disclosed herein.
  • a compound that has the functions of both an emulsifying agent and a cell cellular membrane charging agent for example, a pluronic acid, is used in the methods disclosed herein.
  • the methods disclosed herein use an emulsifying agent but not a cell cellular membrane charging agent.
  • the methods disclosed herein use a cell cellular membrane charging agent but not an emulsifying agent.
  • a cellular membrane charging agent used herein is a low molecular weight ( ⁇ about 50kD, preferably ⁇ about 45 kD, ⁇ about 40 kD, ⁇ about 35 kD, ⁇ about 30 kD, ⁇ about 25 kD, ⁇ about 20 kD, ⁇ about 15 kD, ⁇ about 10 kD, ⁇ about 5 kD, or more preferably ⁇ about 2kD) dextran.
  • the concentration of the low molecular weight dextran used is between about 5 mg/mL and about 10 mg/mL, about 10 mg/mL and about 15 mg/mL, about 15 mg/mL and about 20 mg/mL, about 20 mg/mL and about 25 mg/mL, about 25 mg/mL and about 30 mg/mL, about 30 mg/mL and about 35 mg/mL, about 35 mg/mL and about 40 mg/mL, about 40 mg/mL and about 45 mg/mL, about 45 mg/mL and about 50 mg/mL, about 50 mg/mL and about 55 mg/mL, about 55 mg/mL and about 60 mg/mL, about 60 mg/mL and about 65 mg/mL, or more than about 65 mg/mL.
  • Dextran may be digested or hydrolyzed to make it lower molecular weight.
  • a niacin and salicylic acid combination is used in the solution to reduce or disaggregate the cell aggregates.
  • there is a salicylic acid binding site on the cell surface which coincides with the proteins that mediate cell-to-cell binding (e.g., for platelets).
  • Salicylate binds to a salicylate binding site on the cell membranes (SIGLEC receptors), which for the most part are involved in cell to cell binding.
  • the niacin and salicylic acid combination functions as a cellular membrane charging agent.
  • the solution additionally comprises a niacin and salicylic acid combination.
  • the method can further comprise before the steps a) and/or b), passing the fluid sample through a prefilter that retains aggregated cells and microclots, and allows single cells and smaller particles with a diameter smaller than about 20 ⁇ m to pass through to generate a pre- treated fluid sample that is subject to the steps a) and/or b) subsequently.
  • the method further comprises before passing the fluid sample through the prefilter, treating the fluid sample with a cell aggregation agent to aggregate red blood cells, and removing the aggregated red blood cells.
  • the cell aggregation agent is a dextran, dextran sulfate, dextran or dextran sulfate with a molecular weight less than about 15kD, hetastarch, gelatin, pentastarch, poly ethylene glycol (PEG), fibrinogen, gamma globulin, hespan, pentaspan, hepastarch, ficoll, gum arabic, poyvinylpyrrolidone, or any combination thereof.
  • PEG poly ethylene glycol
  • RBC red blood cell
  • dextran, hespan, pentaspan, hepastarch, ficoll, gum arabic, poyvinylpyrrolidone, other natural or synthetic polymers, nucleic acids, and even some proteins can be used as the cell aggregation agent (see, for example, U.S. Pat. No.5,482,829 and U.S. Patent Application Publication 2009/0081689, herein incorporated by reference in their entireties).
  • the optimal molecular weight and concentration of a cell aggregation agent can be determined empirically.
  • One reagent is based on using reagents to induce cell aggregation.
  • a chemical or protein such as dextran or hepastarch
  • An agent to link cells for example but not limited to an antibody or lectin
  • the combination of the two reagents can induce cell aggregation which may result in cell clumps that will settle with time.
  • One cell aggregation inducing agent for use in a sedimenting solution of the present disclosure or for removal of the aggregate by laminar flow is a polymer such as dextran.
  • the molecular weight of dextran in a cell sedimenting solution is between about 2 and about 2000 kilodaltons, between about 50 and about 500 kilodaltons, or between about 1 and about 15 kilodaltons.
  • Some preferred embodiments are solutions comprising dextran having a molecular weight of between 70 and 200 kilodaltons.
  • the concentration of dextran in a cell sedimenting solution is between about 0.1% and about 20%, more preferably between about 0.2% and about 10%, and more preferably yet between about 1% and about 6%.
  • the solution comprising an emulsifying agent and/or a cellular membrane charging agent may contain Pluronic acid F68 (30mg/ml), DMSO 0.2% (v/v), BSA 0.5%, Heparin
  • the solution is diluted immediately before the filtering process.
  • the Pluronic acid F68 concentration in the solution comprising an emulsifying agent and/or a cellular membrane charging agent ranges from about 5 mg/ml to about 10 mg/ml, about 10 mg/ml to about 15 mg/ml, about 15 mg/ml to about 20 mg/ml, about 20 mg/ml to about 25 mg/ml, about 25 mg/ml to about 30 mg/ml, about 30 mg/ml to about 35 mg/ml, about 35 mg/ml to about 40 mg/ml, about 40 mg/ml to about 45 mg/ml, about 45 mg/ml to about 50 mg/ml, about 50 mg/ml to about 55 mg/ml, about 55 mg/ml to about 60 mg/ml, or more than about 60 mg/ml.
  • the DMSO concentration in the solution comprising an emulsifying agent and/or a cellular membrane charging agent ranges from about 0.01% (v/v) to about 1% (v/v), for example, at about 0.01% (v/v), about 0.02% (v/v), about 0.04% (v/v), about 0.05% (v/v), about 0.08% (v/v), about 0.10% (v/v), about 0.11% (v/v), about 0.12% (v/v), about 0.13% (v/v), about 0.14% (v/v), about 0.15% (v/v), about 0.16% (v/v), about 0.17% (v/v), about 0.18% (v/v), about 0.19% (v/v), about 0.20% (v/v), about 0.21% (v/v), about 0.22% (v/v), about 0.23% (v/v), about 0.24% (v/v), about 0.25% (v/v), about 0.26% (v/v), about 0.26% (
  • the BSA concentration in the solution comprising an emulsifying agent and/or a cellular membrane charging agent ranges from about 0.1% to about 0.2%, about 0.2% to about 0.3%, about 0.3% to about 0.4%, about 0.4% to about 0.5%, about 0.5% to about 0.6%, about 0.6% to about 0.7%, about 0.7% to about 0.8%, about 0.8% to about 0.9%, or about 0.9% to about 1.0%.
  • the heparin concentration in the solution comprising an emulsifying agent and/or a cellular membrane charging agent ranges from about 1 U/mL to about 2 U/mL, about 2 U/mL to about 3 U/mL, about 3 U/mL to about 4 U/mL, about 4 U/mL to about 5 U/mL, about 5 U/mL to about 6 U/mL, about 6 U/mL to about 7 U/mL, about 7 U/mL to about 8 U/mL, about 8 U/mL to about 9 U/mL, about 9 U/mL to about 10 U/mL, about 10 U/mL to about 11 U/mL, about 11 U/mL to about 12 U/mL, about 12 U/mL to about 13 U/mL, about 13 U/mL to about 14 U/mL, about 14 U/mL to about 15 U/mL, about 15 U/mL to about 16 U/mL, about 16 U/mL to about 17
  • the EDTA concentration in the solution comprising an emulsifying agent and/or a cellular membrane charging agent ranges from about 0.5 mM to about 1.0 mM, about 1.0 mM to about 1.5 mM, about 1.5 mM to about 2.0 mM, about 2.0 mM to about 2.5 mM, about 2.5 mM to about 3.0 mM, about 3.0 mM to about 3.5 mM, about 3.5 mM to about 4.0 mM, about 4.0 mM to about 4.5 mM, about 4.5 mM to about 5.0 mM, about 5.0 mM to about 5.5 mM, about 5.5 mM to about 6.0 mM, about 6.0 mM to about 6.5 mM, about 6.5 mM to about 7.0 mM, about 7.0 mM to about 7.5 mM, about 7.5 mM to about 8.0 mM, about 8.0 mM to about 8.5 mM, about
  • a solution for diluting the blood sample before the filtration may, but does not have to, have the disaggregating components.
  • the contents of an exemplary solution used during the filtering for cell separation are: BSA 0.5%, Heparin Sodium (15U/ml), and EDTA 5mM.
  • BSA concentration ranges from about 0.1% to about 0.2%, about 0.2% to about 0.3%, about 0.3% to about 0.4%, about 0.4% to about 0.5%, about 0.5% to about 0.6%, about 0.6% to about 0.7%, about 0.7% to about 0.8%, about 0.8% to about 0.9%, or about 0.9% to about 1.0%.
  • the heparin concentration ranges from about 1 U/mL to about 2 U/mL, about 2 U/mL to about 3 U/mL, about 3 U/mL to about 4 U/mL, about 4 U/mL to about 5 U/mL, about 5 U/mL to about 6 U/mL, about 6 U/mL to about 7 U/mL, about 7 U/mL to about 8 U/mL, about 8 U/mL to about 9 U/mL, about 9 U/mL to about 10 U/mL, about 10 U/mL to about 11 U/mL, about 11 U/mL to about 12 U/mL, about 12 U/mL to about 13 U/mL, about 13 U/mL to about 14 U/mL, about 14 U/mL to about 15 U/mL, about 15 U/mL to about 16 U/mL, about 16 U/mL to about 17 U/mL, about 17 U/mL to about 18 U/mL, about 18 U/mL,
  • the EDTA concentration ranges from about 0.5 mM to about 1.0 mM, about 1.0 mM to about 1.5 mM, about 1.5 mM to about 2.0 mM, about 2.0 mM to about 2.5 mM, about 2.5 mM to about 3.0 mM, about 3.0 mM to about 3.5 mM, about 3.5 mM to about 4.0 mM, about 4.0 mM to about 4.5 mM, about 4.5 mM to about 5.0 mM, about 5.0 mM to about 5.5 mM, about 5.5 mM to about 6.0 mM, about 6.0 mM to about 6.5 mM, about 6.5 mM to about 7.0 mM, about 7.0 mM to about 7.5 mM, about 7.5 mM to about 8.0 mM, about 8.0 mM to about 8.5 mM, about 8.5 mM to about 9.0 mM, about 9.0 mM to about 9.5
  • using a method disclosed herein results in the disaggregation of rouleaux.
  • at least about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 99%, or 100% of the rouleaux formed in the sample are disaggregated.
  • a sample comprising viable cells are subjected to a method disclosed herein.
  • the cells maintain their viability and sustainability after filtration, in which the sample is contacted with an emulsifying agent and/or a cellular membrane charging agent prior to and/or concurrently with passing the sample through a microfabricated filter.
  • an emulsifying agent and/or a cellular membrane charging agent prior to and/or concurrently with passing the sample through a microfabricated filter.
  • the viability of leukocytes recovered from the filter can be tested and compared to that of leukocytes with whole blood lysed with ammonium chloride.
  • an emulsifying agent and/or a cellular membrane charging agent prior to and/or concurrently with the filtration.
  • cells can be stained with FITC Annexin V in conjunction with propidium iodide (PI).
  • a housing for a filter array comprising: a first (e.g., upper) surface, a second (e.g., lower) surface, and a periphery, which are configured to house (e.g., enclose) a filter array comprising a plurality of filters; for each filter of the array, at least two pre-filtration ports on the first surface which are connected to a pre-filtration chamber of the filter, and at least two post-filtration ports on the second surface which are connected to a post-filtration chamber of the filter, optionally the center-to- center distance between any two adjacent pre-filtration ports, one of each for two adjacent filters, and/or the center-to-center distance between any two adjacent post-filtration ports, one of each for two adjacent filters, is between about 1.00 mm and about 1.25 mm (e.g., about 1.125 mm) or a multiple thereof, and/or optionally one or both of the two post-filtration ports are each configured to
  • the center-to-center distance between any two adjacent pre-filtration ports, one of each for two adjacent filters, and/or the center-to-center distance between any two adjacent post-filtration ports, one of each for two adjacent filters is about 2.25 mm, about 4.5 mm, about 9 mm, about 13.5 mm, about 18 mm, about 24 mm, or about 36 mm.
  • the center-to- center distance between the two post-filtration ports and/or between the two pre-filtration ports for the same filter can be between about 18.9 mm and about 36 mm, such as between about 18.9 mm and about 29.5 mm, between about 19 mm and about 35 mm, between about 29.0 mm and about 29.2 mm, for example, about 29.1 mm.
  • FIG.59 An exemplary housing for a filter array is shown in FIG.59 (left panel), and the right panel of the figure shows the shape of a filter to be housed in the housing.
  • the housing can house (e.g., enclose) a filter array comprising 4 filters arranged in parallel.
  • the chip itself is about 31.8 mm by 7.2 mm in outer dimensions. It contains a perimeter without pores for handling, and the filter with the pores is on the inside, and on one end of the filter chip there is a shelf of solid chip material that is over the ports when assembled. In some embodiments, the chip can have a shelf at both ends.
  • FIG.60 shows a cross section of an exemplary housing on a seat, forming fluid connections.
  • a pipette tip engages the pre-filtration port on the left, and can be used to add blood sample and/or retrieve a filtered cell population from which most or all of the red blood cells have been removed.
  • the pre-filtration port on the right is connected to a reservoir on the housing.
  • the two post-filtration ports is each configured to fittingly and/or sealingly engage an o-ring structure, and the figure shows the cross sections of the o-ring structures.
  • a housing for a filter array comprising: a first (e.g., upper) surface, a second (e.g., lower) surface, and a periphery, which are configured to house (e.g., enclose) a filter array comprising a plurality of filters; for each filter of the array, at least three pre-filtration ports on the first surface which are connected to a pre-filtration chamber of the filter, and at least two post-filtration ports on the second surface which are connected to a post-filtration chamber of the filter.
  • FIG.74 shows an exemplary array housing forming fluidic connections with the seat.
  • the third pre-filtration port is located between the two pre-filtration ports, and the three pre-filtration ports can be collinear and the third pre-filtration port can be about 9 mm from one of the two pre-filtration ports.
  • a seat for the housing of the preceding embodiments comprising: an interface configured to engage the second surface and the periphery of the housing; for each filter of the array, at least two interface ports on the interface which are configured to engage the at least two post-filtration ports on the second surface of the housing, optionally the center-to-center distance between any two adjacent interface ports, one of each for two adjacent filters, is between about 1.00 mm and about 1.25 mm (e.g., about 1.125 mm) or a multiple thereof, and/or optionally one or both of the two interface ports each comprises an o-ring structure, or one or both of the two interface ports each comprises a needle configured to insert into and form a sealed fluidic path with the post-
  • the center-to-center distance between any two adjacent interface ports, one of each for two adjacent filters is about 2.25 mm, about 4.5 mm, about 9 mm, about 13.5 mm, about 18 mm, about 24 mm, or about 36 mm.
  • the center-to-center distance between the two interface ports for the same filter can be between about 18.9 mm and about 36 mm, such as between about 18.9 mm and about 29.5 mm, between about 19 mm and about 35 mm, between about 29.0 mm and about 29.2 mm, for example, about 29.1 mm.
  • the seat can be configured to engage a housing enclosing a filter array comprising 2, 3, 4, 6, 8, 12, 16, 24, 32, or 48 filters arranged in parallel.
  • FIG.61 An exemplary seat is shown in FIG.61.
  • the interface on the seat for the filter array have ports spaced about 29.1mm apart, and in repeats that are either 9 mm apart or 18mm apart, or some other multiple of 9 mm.
  • the seat can further comprise a valve connected to one or both of the two interface ports, such as a three-way valve or a rotary valve; and/or further comprising a series of pumps (e.g., one-way miniaturized pumps) connected to one or both of the two interface ports.
  • a valve connected to one or both of the two interface ports, such as a three-way valve or a rotary valve; and/or further comprising a series of pumps (e.g., one-way miniaturized pumps) connected to one or both of the two interface ports.
  • one of the two interface ports is connected to a three-way valve, and the other interface port is connected to a first pump (e.g., syringe pump) for removing waste.
  • the three-way valve is configured to control flow between the interface port and the priming well, and flow between the interface port and a second pump (e.g., syringe pump).
  • FIG.62 showing the tubing behind the interface in this example.
  • Tube Holder Rack and Set Disclosed herein is a tube holder rack comprising a plurality of tube holders each configured to receive and hold a tube, and optionally the center-to-center distance between any two adjacent tube holders is between about 1.00 mm and about 1.25 mm (e.g., about 1.125 mm) or a multiple thereof. In one embodiment, the center-to-center distance between any two adjacent tube holders is about 2.25 mm, about 4.5 mm, about 9 mm, about 13.5 mm, about 18 mm, about 24 mm, or about 36 mm.
  • the tube holders can be separated from each other, or some or all of the tube holders can be connected.
  • the tube holder rack can further comprise one or more magnetic or magnetizable element, e.g., a permanent magnet or an electromagnet.
  • the tube holder rack can comprise 2, 3, 4, 6, 8, 12, 16, 24, 32, or 48 tube holders.
  • a tube holder rack set comprising at least two of the tube holder rack of any of the preceding embodiments, in which one is a sample tube holder rack and one is a product tube holder rack.
  • the product tube holder rack is distinguishable from the sample tube holder rack.
  • the product tube holder rack is distinguishable by the color, the shape, and/or the presence or absence of a letter, number, symbol, notch, or structure on the product tube holder rack.
  • An exemplary tube holder rack set is shown in FIG.65.
  • one or both of the product tube holder rack and the sample tube holder rack can comprise one or more magnetic or magnetizable element.
  • the product tube holder rack comprises one or more magnetic or magnetizable element while the sample tube holder rack does not.
  • the sample tube holder rack comprises one or more magnetic or magnetizable element while the product tube holder rack does not.
  • the assembly further comprises a securing means for fastening the housing to the seat, and the securing means optionally comprises one or more screws and optionally one or more clamps straddling the housing.
  • a securing means for fastening the housing to the seat
  • the securing means optionally comprises one or more screws and optionally one or more clamps straddling the housing.
  • FIG.63 the array interconnect subassembly shows interaction between the black valves and the filter arrays
  • FIG.64 shows the assembly placed on the base plate.
  • a chute comprising: a receiving section comprising a first (e.g., vertical) surface and an adjoining second (e.g., horizontal) surface, and the receiving section comprises a plurality of slits each spanning the first surface and the adjoining second surface, and optionally the slits are substantially parallel to each other, and/or optionally the angle between the first and second surfaces is between about 0 and 180 degrees, such as about 90 degrees; and/or a sliding section comprising an inclined sliding surface.
  • the length of the slit on the first surface is longer than the length of a pipette tip.
  • the slit can comprise an enlarged section near the top of the first surface.
  • the center-to-center distance between any two adjacent slits can be between about 1.00 mm and about 1.25 mm (e.g., about 1.125 mm) or a multiple thereof. In one embodiment, the center-to-center distance between any two adjacent slits about 2.25 mm, about 4.5 mm, about 9 mm, about 13.5 mm, about 18 mm, about 24 mm, or about 36 mm.
  • An exemplary chute is shown in FIG.68.
  • the chute has airflow limitations in that the air can only pass through the slits on the inside that are present to allow the pipettes to enter the ejection chamber, and the top of these slits strip off the pipette tips when the gantry is raised.
  • a base plate comprising the housing seat of any of the preceding embodiments mounted to the base plate, a recess for the tube holder rack of any of the preceding embodiments or the tube holder rack set of any of the preceding embodiments, the tube holder rack of any of the preceding embodiments or the tube holder rack set of any of the preceding embodiments, and/or the chute of any of the preceding embodiments.
  • the base plate further comprises a recess configured to hold a pipette tip rack, and/or the pipette tip rack.
  • the pipette tip rack holds 3 ⁇ 2 pipette tips (e.g., for a 6-well plate), 6 ⁇ 2 pipette tips (e.g., for a 12-well plate), 6 ⁇ 4 pipette tips (e.g., for a 24-well plate), 12 ⁇ 4 pipette tips (e.g., for a 48-well plate), 12 ⁇ 8 pipette tips (e.g., for a 96-well plate, at 9 mm spacing between wells), 24 ⁇ 16 pipette tips (e.g., for a 384-well plate, at 4.5mm spacing between wells), or 48 ⁇ 32 pipette tips (e.g., for a 1536-well plate, at 2.25 mm spacing between wells).
  • spacing between the wells has been referred to as“binary multiples” of 2.25 mm, i.e., ⁇ 1, ⁇ 2, ⁇ 4, ⁇ 8, ⁇ 16, ⁇ 32,
  • the base plate can further comprise an outflow manifold attached to the housing seat.
  • An exemplary base plate is shown in FIG.66 (no pipette tip rack shown) and in FIG.67 (showing the gantry for moving pipette tips and the chute for disposing the pipette tips).
  • the components are arranged in the following order: product tubes and rack, the seat with a filter array housing, sample tubes and rack, pipette tips and rack, and the chute. In operation, there would be a tube rack containing blood sample tubes behind the filter array, and a tube rack with empty product receiver tubes in front of the array.
  • FIG.69 is a bottom view of the base plate, showing an outflow manifold attached to the housing seat, and the baseplate (red) contains the motion methods, and the outflow manifold (grey) which is glued to the array interface on the top side of the instrument.
  • T. The Device [00509]
  • a device comprising the base plate of any of the preceding embodiments, and one or more pumps (e.g., syringe pumps) configured to control flow in and/or out of the filters.
  • the device comprises three or four syringe pumps.
  • the device can further comprise an inflow manifold connected to the one or more pumps, for example, three syringe pumps, and optionally the three pumps work in concert while engaged to three ports of the housing to control simultaneously the filtration rate and rate of flow at the fourth port of the housing.
  • the device can further comprise a controller, a processor, a port for accessing the controller and/or processor (such as a USB port), a means for wired or wireless internet connection, and/or a power supply.
  • the device can further comprise a dust cover, a front panel, a back panel, a bottom panel, and/or two side panels, defining a working chamber of the device.
  • the dust cover is transparent and/or comprises a magnetic interlock configured to sense whether the dust cover is closed.
  • the front panel can comprise a screen for operating the device, and the screen is optionally a touch screen.
  • the back panel can comprise an air filter, a fan configured to blow air out of the device through the air filter, and/or a vent hole.
  • the air filter is a HEPA or HEPA-like or HEPA-type filter, and the back panel comprises two or more fans configure to blow air out of the device through the air filter.
  • the back panel can further comprise a waste receptacle connected to the chute, or aligned with or engaged under the chute.
  • the back panel can further comprise an interface of the inflow manifold.
  • the back panel can further comprise a pass through grommet for a vacuum line.
  • the bottom panel can comprise an inflow ventilation port and a dust filter.
  • the outward air flow through the back panel is faster than the inward air flow through the inflow ventilation port of the bottom panel, and the vent hole of the back panel is configured to draw air into the device.
  • the two side panels can be removable.
  • the working chamber of the device can be a contained chamber during operation.
  • FIG.70 shows the inside, bottom view, of an exemplary device.
  • the master controller is at the back (green board), with a processor board connected on top of it, and the yellow power supply beside it.
  • the majority of the space is consumed by three large syringe pumps. All these components are contained within an inner frame which prevents damage from spills on top.
  • the inflow manifold that is visible through the back, and shown in FIG.71, is a valve arrangement that interconnects fluids to all the pump syringes.
  • FIG.72 shows the front and back views of an exemplary device.
  • all user interaction is through the touchscreen at the front.
  • the bottom has a ventilation port (inflow) with a dust filter.
  • the top at the back of the instrument the Q-bert eyes are two fans blowing air outward through a HEPA filter. That flow is twice as fast as air coming through the dust cover below, so some of it is made up by air coming in through back vent holes, up through the red baseplate Y axis slots, and through any leaks around the dust cover, making the working chamber a contained chamber during operation.
  • the Q-bert mouth is the ejection chute for the pipette tips to drop them into a waste receptacle behind the instrument.
  • USB ports for updating without internet access, or for storing log files onto a USB flash drive.
  • the two side panels are easily removable.
  • the ejection chute assembly has airflow limitations, the air can only pass through the slits on the inside that are present to allow the pipettes to enter the ejection chamber, and the top of these slits strip off the pipette tips when the gantry is raised.
  • the inflow manifold that is visible on the back and is a valve arrangement that interconnects fluids to all the pump syringes.
  • a method of filtering a liquid sample comprising: 1) picking up a liquid sample (e.g., in a pipette tip or a syringe) from a sample tube, and optionally the top portion of the pipette tip or syringe is filled with a filtration solution and the bottom portion is filled with the sample; 2) expelling the liquid sample into a pre-filtration port of the filter array housing on the device of any of the preceding embodiments; and 3) controlling the liquid flow in the pre-filtration chamber and the post-filtration chamber of each filter, such that the flows are substantially anti-parallel to each other, and the flow rate entering one post-filtration port is less than the flow rate exiting the other post-filtration port, thereby drawing fluid flow across the filter, optionally drawing an undesired component in the liquid sample across the filter into the post-filtration chamber to be removed, and enriching a desired component in the pre-filtration chamber, optionally the flow rate in the post-filtration chamber is
  • the method can further comprise: 4) applying a flow such that the desired component is lifted off the filter, optionally the flow is applied across the filter from the post-filtration chamber to the pre-filtration chamber or the flow is created by the difference in flow speeds between the post-filtration chamber and the pre-filtration chamber.
  • the method can further comprise drawing the desired component into the pipette tip or syringe. In one embodiment, the method can further comprise delivering the desired component into a product tube. In a further embodiment, the method further comprises ejecting the pipette tip into the chute.
  • FIG.73 is a cross section that shows the fluidic path and components.
  • the blood sample is mixed by the user with pre-filtration buffer (PFB) in the tubes on the right where the pipette tips pick it up after priming the array.
  • the filtration buffer is what the filter is primed with, and the pre- filtration buffer is used to dilute the blood prior to filtering.
  • three pumps work in concert while engaged to three ports of the housing to control simultaneously the filtration rate and rate of flow at the forth port of the housing.
  • the filtration buffer (AviWash fluid) flows into the filter from the pipette tip from above, expelling the sample into the top chamber of the filter housing, while simultaneously AviWash flows into the bottom chamber from the solenoid valve on the left side, while simultaneously a larger flow of solution is drawn into waste from the bottom on the right side.
  • the flows are such that the forth port (top left) will have only a small rate of flow into the top chamber, preventing cells from escaping into the “recovery well” (top left port which opens into the large well of the filter housing).
  • the filtration rate, across the filter membrane is about 25 ⁇ L/sec.
  • the solenoid valve connects on its other ports to a syringe pump and to the“sink,” which is the priming location for the pipette tips, seen here as the funnel structure to the right of the array.
  • the waste port connects to a syringe pump.
  • the pipette tip is inserted into a DiTi tool on the gantry above, then a tube travels to a third syringe pump. All of these fluidics on this side of the syringe pumps are referred to as“outflow side.”
  • the outflow manifold is shown here in white, it is glued to the array interface, in black, which the chip array seats into.
  • the seal between the array and its interface is formed by tiny O-rings.
  • the inflow side connects to the inflow manifold pictures earlier, which selects which solutions are being pulled into the syringes and keeps waste streams isolated from clean solution and from sanitizing solution.
  • the device further comprises one or more accessary units, such as a monitor unit for the liquid level of one or more containers (e.g., bottles) connected to the inflow manifold.
  • the monitor emits a signal, such as sound and/or light, when the liquid levels goes below and/or above a reference level. This can warn the user to replenish the liquid or stop filling the one or more containers.
  • the housing shown in FIG.74 When the housing shown in FIG.74 is used (in a so-called BlueSift mode), the basic operation is relatively unchanged as compared to FIG.73.
  • the top of the housing in this case has an extra port which will feed into an atrial chamber over a small pore filter which is used only to distribute perfusion of the buffer through the C port across the entire filtration area. In so doing, it will create a cross-flow to the filtration which provides additional driving force to deplete the RBCs and platelets and plasma components of the blood through the filter below.
  • the C tip can be pre-filled with PFB solution which will break up the rouleaux, and backfilled with the usual wash buffer used in filtration.
  • the blood is introduced from the S tip and is depleted as it traverses the membrane, avoiding need for any additional washing.
  • This can deplete sufficiently to perform single-pass filtration, where the sample ends up in the reservoir end, or it can still be used in the same mode used now where sample is brought back to the pipette tip and dispensed to a product tube. It also allows slower outflow from the Sample pipette and provide better concentrating effect on the cells, where WBC’s become more concentrated as the pass through the filter.
  • a final capability this affords is to provide continuous flow filtration of the sample, for a very large volume of blood. Examples Example 1
  • a silicon chip of dimensions (1.8 cm by 1.8 cm x 500 micron) was used to fabricate a filtration area of 1 cm by 1 cm by 50 micron with slots having dimensions from about 0.1 micron to about 1000 microns, preferably from about 20 to 200 microns, preferably from about 1 to 10 microns, more preferably 2.5 to 5 microns.
  • the slots were vertically straight with a maximum tapered-angle of less than 2%, preferably less than about 0.5% with an offset distance between neighboring columns of the filter slots were 1 to 500 microns, preferably from 5to 30 microns.
  • Manufacturing included providing a silicon chip having the above referenced dimensions and coating the top and bottom of the silicon chip with a dielectric layer.
  • a cavity along the bottom portion of the chip was then created.
  • the cavity was formed by removing an appropriate cavity pattern from the dielectric layer, and then etching the silicon chip generally following the pattern, until desired thickness is reached.
  • the chip was re-oxidized to coat the contoured region.
  • a filter pattern was then removed from the dielectric layer coating the top of the silicon chip in substantial alignment (above) with the cavity.
  • the silicon chip was etched (e.g., via deep RIE or ICP processes) at the above referenced angles starting at the pattern created along the top of the chip until the silicon layer has been etched through.
  • the dielectric layer from the top and bottom were then removed.
  • throughbores referred to as slots, were created. It is also possible to create these slots using laser cuts to bore though materials, including but not limited to silica or polymers such as plastic.
  • a filter chip made as described in Example 1 was placed on a ceramic heating plate in an oven and heated at 800 degrees Celsius for 2 hours in oxygen containing gas (e.g. air). The heating source was then turned off the chips are slowly cooled overnight. This results in a thermally grown layer on the surface of the chip.
  • oxygen containing gas e.g. air
  • a nitride layer could also be deposited onto the filter surface.
  • An oxide layer is put on the surface of the chip by low-pressure chemical vapor deposition (LPCVD) in a reactor at temperatures up to ⁇ 900o C.
  • the deposited film is a product of a chemical reaction between the source gases supplied to the reactor. The process is typically performed on both sides of the substrate at the same time to form a layer of Si3N4.
  • Polyvinylpyrrolidone (PVP) and polyvinyl alcohol (PVA) filter coatings are preferred.
  • Filter chips made by the method of Example 1 were coated with either PVP or PVA.
  • the chips were pre-treated as follows: The filter chips were rinsed with deionized water and then immersed in 6N nitric acid. The chips were placed on a shaker for 30 minutes at 50 degrees Celsius. After acid treatment, the chips were rinsed in deionized water.
  • PVP coating chips were immersed in 0.25% polyvinylpyrrolidone (K-30) at room temperature until the chips were ready for use. Chips were then rinsed with deionized water and dried by pressurized air.
  • K-30 polyvinylpyrrolidone
  • the chips were stored in water prior to coating.
  • 0.25% PVA (Mn 35,000-50,000) solution dissolve the PVA in water under slow heating to 80 degrees Celsius and gentle stirring.
  • To coat the chips were immersed in a hot PVA solution and heated for 1-2 hours. The chips were then rinsed in deionized water and dried by pressurized air.
  • Bovine serum albumin (BSA) filter coating The Bovine serum albumin (BSA) filter coating.
  • the chips were pre-treated as follows: The filter chips were rinsed with deionized water and then immersed in 95% ethanol for 10 seconds at room temperature and then were rinsed again in deionized water.
  • filter chips were immersed in a solution of DBE-814 (a PEG solution containing polysiloxane from Gelest, Morrisville, PA) in 5% methylene chloride. The immersed chips were heated at 70 degrees Celsius for 3 hours under vacuum. After the incubation, the PEG- coated chips were rinsed in deionized water and dried by pressurized air.
  • DBE-814 a PEG solution containing polysiloxane from Gelest, Morrisville, PA
  • Figure 13 shows a process flow chart for enriching fetal nucleated cells from maternal blood samples. The whole process comprises the flowing steps:
  • the blood sample may be transferred to a centrifuge tube.
  • the sample does not have to be but can be washed before addition to the automated unit.
  • (3) The process starts with a volume of blood sample 10 mls (range of 3-40 ml) in a tube(s).
  • Fluidic level sensing step is used to determine the exact volume of the blood sample in the tube to be processed.
  • Another fluidic level sensing step is applied to determine what the volume of the“un- aggregated” cell suspension is present in the tube.
  • Figure 14 provides a schematic diagram showing the microfiltration process.
  • the simplified process steps include the following:
  • Test sample (coming from the first step of the procedure in [Example 9]) is loaded into the 45 mL loading reservoir.
  • Combined Reagent PBS lacking calcium and magnesium containing: 5 millimolar EDTA, 2% dextran (molecular weight from 70 to 200 kilodaltons), 0.05 micrograms (range of 0.01 to ugs) per milliliter of IgM antibodies to glycophorin A, and approximately 1-10 x 10 9 pre-coated magnetic beads are manually added to the sample tubes.
  • the Rare Cell Isolation Automated System has control circuits for automated processing steps, and plugs into a 110 volt outlet.
  • the tubes containing the samples are placed in a rack of a Rare Cell Isolation Automated System.
  • the tubes are automatically rotated in the Automated System rack for 30 minutes (range between 5 and 120 minutes).
  • the tubes are then allowed to stand upright while a second rack that has a magnet field, which is automatically positioned next to the tube rack. It is also possible to have other types of magnetic fields including but not limited to electromagnetic fields.
  • the tubes are held in the upright position for 30 minutes (range of 5-120 minutes) so that the aggregated RBCs can settle to the bottom of the tube and WBC-magnetic bead aggregates are attracted to the side of each tube that is adjacent to the magnet. After the cells are allowed to settle, the supernatant volume is determined by the automated system using a light transmission-light sensor transparency measuring device.
  • the transparency measuring device consists of bars that each have a collated light source (the number of bars corresponds to the number of tubes) that can be focused on a sample tube, and a light detector that is positioned on the opposite side of the tube.
  • the light source uses a laser beam that emits light in the infrared range (780 nanometers) and has an intensity greater than 3 milli-watts.
  • the light from the source is focused through the sample tube, and at the other side of the sample tube the light detector having an intensity measurement device records the amount of light that has passed through the sample (the laser output measurement).
  • the bars having the low wattage laser sources and light detectors move upward from a level at the bottom of the tubes.
  • the laser output measurement is zeroed.
  • the vertical movement of the bar stops.
  • the bar then moves to find the exact vertical point at which the transmitted light equals the threshold value. In this way the vertical point position of the aggregated cell/cell supernatant interface is determined.
  • the fluid handling unit moves to a preset location and uses a capacitive sensing routine to find the level of the bar (corresponding to the level of the interface). Using this data, the fluid handling accurately removes the supernatant from the fluid container. The supernatant is automatically dispensed directly into the loading reservoir of the filtration unit.
  • the filtration chamber comprises an antechamber (604) and a postfiltration subchamber (605) separated by a single filter (603).
  • the microfabricated filter measuring 1.8 cm by 1.8 cm and having a filtration area of approximately 1 cm by 1 cm.
  • the filter has approximately 94,000 slots arranged in a parallel configuration as shown in Figure 2 with the slots having a taper of one to two degrees and dimensions of 3 microns x 100 microns, within a 10% variation in each dimension.
  • the filter slots can have dimensions of 1-10 microns by 10-500 microns with a vertical taper of 0.2 to 10 degrees depending on the target.
  • the thickness of the filter is 50 microns (range of 10-200 microns).
  • the filter is positioned in a two piece filtration chamber with the top half (antechamber) being an approximately rectangular filtration antechamber that tapers upward with a volume of approximately 0.5 milliliters.
  • the bottom post-filtration subchamber is also approximately circular and tapers toward the bottom, also having a volume of approximately 0.5 milliliters.
  • the filter covers essentially the entire bottom area of the (top) antechamber and essentially the entire top area of the (bottom) post-filtration subchamber.
  • the filtration unit comprises a“frame” having a loading reservoir (610), a valve controlling the flow of sample form the loading reservoir into the filtration chamber (“valve A”, 606), and separate ports for the outflow of waste or filtered sample (the waste port, 634) and for the collection of enriched rare cells (the collection port, 635).
  • the post-filtration subchamber (605) comprises a side port (632) that can be used for the addition of buffer, and an outlet that can engage the waste port during filtration for the outflow of waste (or filtered sample).
  • the antechamber (604) comprises an inlet that during filtration can engage the sample loading valve (valve A, 606) and during collection of enriched cells, can engage the collection port (635).
  • the filtration chamber (comprising the antechamber (604), post-filtration subchamber (605), and side port (632)) resides in the frame of the filtration unit.
  • valve A During filtration, valve A is open, and the outlet of the post-filtration subchamber is aligned with the waste port, allowing a flow path for filtering sample from the loading reservoir through the filtration chamber and to the waste.
  • a syringe pump draws fluid through the chamber at a flow rate of from about 10 to 500 milliliters per hour, depending upon the process step.
  • the side port (632) and waste port (634) of the filtration unit Prior to dispensing the appropriate volume of supernatant from each tube into the loading reservoir of the filtration unit, the side port (632) and waste port (634) of the filtration unit are closed, and valve A (606) is opened (see Figure 23). (When the filtration unit is in the loading/filtering position, the filtration chamber does not engage the collection port (635)). With the side port of the filtration unit open, the unit is filled with PBE from the side port until the buffer reaches the bottom of the sample reservoir. The side port is then closed, and the blood sample supernatant is loaded into the loading reservoir.
  • the waste port (634) of a filtration unit is opened, and, using a syringe pump connected through tubing to the waste port, sample supernatant is drawn into and through the filtration chamber.
  • sample goes through the chamber, the larger cells stay in the top chamber (antechamber) and the smaller cells go through the filter into the lower chamber (post-filtration subchamber) and then through the waste port to the waste. Filtering is performed at a rate of approximately 2-100 milliliters per hour.
  • Valve A (606) is then closed and the side port (632) is opened. Five to ten milliliters of buffer are added from the side port (632) using a syringe pump connected to tubing that is attached to the waste port (634) to wash the bottom post-filtration subchamber. After residual cells have been washed from the post- filtration subchamber (605), the bottom (post-filtration) subchamber is further cleaned by pushing air through the side port (632).
  • the filter cartridge is then rotated approximately 180 degrees within the filtration unit, so that the antechamber (604) is below the post-filtration subchamber (605).
  • the outlet of the post-filtration subchamber disengages from the waste port and, as the post-filtration subchamber becomes positioned above the antechamber, the“outlet” becomes positioned at the top of the inverted filtration chamber, but does not engage any openings in the filtration unit, and thus is blocked.
  • the antechamber rotates to the bottom of the inverted filtration unit, so that the antechamber inlet disengages from valve A, and instead engages the collection port at the bottom of the filtration unit.
  • the side port does not change position. It is aligned with the axis of rotation of the filtration chamber, and remains part of, and a functional port of, the post-filtration subchamber. As a result of this rotation, the filtration chamber is in the collection position.
  • the post-filtration subchamber having a side port but now closed off at its outlet, is above the antechamber.
  • the antechamber“inlet” is aligned with and open to the collection port.
  • the enriched rare cells can be analyzed microscopically or using any of a number of assays, or can be stored or put into culture.
  • Magnets of dimensions 9/16x1.25x1/8”, (Forcefield (Fort Collins, Co) NdFeB block, item #27, Nickel Plate, Br max 12,100 Gauss, Bh max 35 MGOe) were used to test the magnetic field strength.
  • the strongest field could be used to capture magnetic beads that were coated with antibodies that specifically bound white blood cells, and improve the removal of white blood cells from a blood sample compared to commercially available magnetic cell separation unit MPC-1 (Dynal, Brown Deer, WI).
  • Magnets were attached in several configurations and orientations to a polypropylene stand designed to hold a 50 milliliter tube, as depicted schematically in Figure 9.
  • the magnetic field in the right, center, and left of the tube was measured by Gauss meter (JobMaster Magnets (Randallstown, MD) Model GM1 using probe model PT-70, Cal # 373).
  • Gauss meter JobMaster Magnets (Randallstown, MD) Model GM1 using probe model PT-70, Cal # 373).
  • Leukocytes carry diagnostic information about the health of immune system and are the primary samples analyzed by flow cytometry and other cell analyzers.
  • leukocytes are first stained with a fluorescently labeled monoclonal antibody, and then the labeled leukocytes are separated from the erythrocytes.
  • separation of blood cells is performed by density gradient centrifugation, and lately, lysis of erythrocytes has become a routinely used method.
  • FICOLL TM HYPAQUE TM density gradient centrifugation exploits the density difference between mononuclear cells from other elements in blood fluid to perform this separation (Boyum A. Scand J Clin Lab Invest (1968) 21 (Suppl 97):77–89). Different cell populations are distributed in the ficoll solution after centrifugation in different layers based on their density. Thus mononuclear cells can be purified by collecting cells in that particular layer.
  • the BD Vacutainer® (Becton Dickinson, Franklin Lakes, NJ) CPTTM Cell Preparation Tube with Sodium Citrate simplifies the FICOLL HYPAQUE method, and it combines a blood collection tube containing a citrate anticoagulant with a FICOLL HYPAQUE density fluid and a polyester gel barrier that separates the two liquids.
  • a blood collection tube containing a citrate anticoagulant with a FICOLL HYPAQUE density fluid
  • polyester gel barrier that separates the two liquids.
  • internal studies have shown that as many as 7% of the leukocytes are lost even during careful centrifugation steps (data not shown) and the mononuclear cell band may get disturbed due to sample sources or centrifugation process; thus desired purity can not be achieved even with the CPT tubes (Product information on BD Vacutainer® CPT TM Cell Preparation Tube with Sodium Citrate).
  • lysis reagents may produce artifacts when used to isolate leukocytes (Macey et al., Cytometry (1999) 38:153–160). The presence of free hemoglobin after erythrocytes lysis may also alter leukocytes’ property by stimulating them to release certain cytokines (McFaul et al., Blood (1994) 84:3175– 3181).
  • Membrane filters are applied widely in sample cleanup as they can remove particles or molecules based on size.
  • classical filter membranes do not have homogeneous and precisely controlled pore sizes, so the resolving power of this separation is limited and provides only quantitative results.
  • particles retained by the filter are rarely recovered in high yield.
  • filter membranes used in preparation of RNA from whole blood retain leukocytes on top of the filter, while erythrocytes pass through.
  • the leukocytes are lysed on the filter without being recollected and the RNA is retained on the filter membrane (Applied Biosystems, Instruction Manual: LeukoLOCK TM Total RNA Isolation System; Life Technologies).
  • the filter chips and cartridges were manufactured by AVIVA Biosciences (San Diego, CA).
  • the microfabricated filters were made from silicon wafer with channels micro-etched on the chip.
  • the filter cartridge has valves connected to sample reservoir, wash reservoir, and a syringe pump that controls fluid in and out of the cartridge as shown in Figure 25.
  • Forty devices in two batches (30 in the first batch and 10 in the second batch) were evaluated on performance of leukocyte isolation from healthy donor whole blood. Mainly recovery of leukocyte and subpopulations after filtration, robustness of the filtration process, and cell sustainability after filtration were carefully assessed.
  • Cartridge is recommended for single use; however, it was discovered to be reusable in continuous runs with washing in between. (Reuse was limited to the same donor blood to avoid contamination.)
  • the cartridge was first primed with a proprietary wash buffer, AVIWash-P and then diluted whole blood (10 ⁇ l or 50 ⁇ l labeled with CD45-PerCP or Multitest TM reagent diluted to 250 ⁇ l) was introduced into the upper filter chamber. Buffer or sample solutions were pulled through the filter chip by a syringe pump attached to the lower exit chamber of the device at a speed of either 0.33 or 0.18 ml/min. This was followed by two washing steps: rinsing top of the filter and washing bottom of the filter. Finally, 2 ml of elution buffer was added to the filter cartridge and a 3-ml syringe was used to collect leukocytes that were retained on top of the filter membrane (Figure 32). The collected leukocytes were transferred to a BD Trucount TM Absolute Counting Tube (cat.340334) for flow cytometer analysis.
  • a proprietary wash buffer 10 ⁇ l or 50 ⁇ l labeled with CD45-PerCP or Multitest TM
  • Each blood sample was also tested on an ABX Micros 60 Hematology Analyzer (Horiba ABX) to obtain total leukocyte counts (WBC), erythrocyte counts (RBC), and percent of lymphocytes, monocytes, and granulocytes.
  • WBC total leukocyte counts
  • RBC erythrocyte counts
  • ABX counts were used as reference numbers in evaluating recovery of total leukocyte and its three subpopulations from the filtration device.
  • Lysing (BD Biosciences, cat.349202) solution. Lyse No Wash sample was stained and lysed in Trucount Absolute Counting Tube and Lyse Wash sample was transferred to the Counting Tube after washing.
  • Leucocytes viability after filtration was tested with BD TM Cell Viability Kit (BD Biosciences, cat.349480).
  • Apoptosis test (Annexin V FITC, BD Biosciences, cat.556547) was also performed on leukocytes recovered from filtration to test sustainability of the cells.
  • T cells were defined as CD3+ lymphocyte
  • NK cells were defined as CD16+CD56+ lymphocyte
  • FIG. 26 shows dot plots for FSC versus SSC and FL3 versus SSC for the same blood sample prepared following Lyse No Wash procedure, Lyse Wash procedure, and the filtration procedure.
  • the Lyse No Wash sample is substantially contaminated with red cell debris, as can be seen in the dot plot where they represent 91% of the total events acquired.
  • red cell debris are removed through centrifugation and only 13% of the events shown in the dot plot are from debris.
  • Leucocytes recovered from the filtration process contain the smallest percentage of background particles, 4% of the total events; showing that red blood cells are effectively separated from leukocytes. [00572] None or minimum leukocyte cell loss resulted from the filtration process. Leucocyte counts in each sample were calculated with reference to the BD TruCount internal standard counting beads and the overall recovery was based on the ratio of this result to the complete blood count obtained from ABX hematology analyzer. Figure 27 shows the comparison of recovery results for the total leukocytes, three major leukocyte populations and three lymphocyte subpopulations (T, B, and NK cells). A total of 10 filter cartridges were tested on leukocyte recovery with 10 different donors’ blood with each sample run in triplicate on the filter.
  • the filter gives on average 98.6% ⁇ 4.4% recovery of total leukocyte compared to 100.2% ⁇ 6.0% from LNW and 86.2% ⁇ 7.8% from LW.
  • the recovery of cells after filtration did not have bias among lymphocyte, monocyte, and granulocyte as compared to blood lysis method.
  • fresh blood samples were stained with Multitest reagent to investigate the recovery of subpopulations of lymphocyte, T, B, and NK cells.
  • the microfabricated filter evaluated here is capable of performing fast, simple whole blood separations with high leukocytes recovery without introducing bias among the leukocyte subpopulations.
  • the filter removes erythrocytes, platelets, plasma proteins, and unbound staining reagent. This gentle filtration process produces very clean stained leukocytes for cytometric analysis without any apparent damage to leukocytes.
  • the current filter cartridge is capable of processing the number of cells that are typically required in a flow assay. Its application in flow cytometry sample preparation will help in method standardization, saving labor and material, and minimizing hands-on operation.
  • Isolation of leukocytes from other components in whole blood is a very important step in flow cytometry cell analysis.
  • Routinely used methods, FICOLL HYPAQUE density gradient centrifugation and red cell lysis have shown their limitations in applications.
  • Reported here are the evaluation results of a microfibricated filtration device in blood separation, which potentially provides a new way to prepare stained clean live leukocytes for flow cytometric analysis.
  • the microfabricated filter evaluated here is capable of performing fast, simple whole blood separations with high leukocytes recovery without introducing bias among the leukocyte subpopulations.
  • the filter removes erythrocytes, platelets, plasma proteins, and unbound staining reagent.
  • FIG. 33 An exemplary embodiment of a filtration chamber is depicted in Figure 33, which has an antechamber and a post-filtration subchamber formed on both sides of a filter by two separate housing parts.
  • the depth of the antechamber is 400 ⁇ m.
  • An embodiment of an antechamber having a depth of about 200 ⁇ m or less is also contemplated.
  • the two housing parts may be bound by laser.
  • liquid glue may be used to bond the two housing parts.
  • the top housing part is 34.0 mm x 7.9 mm, squared on the inflow side (small port) and rounded on the outflow side (with the large collection well).
  • the outflow receiving well holds 300 ⁇ L, has a filtration area of 150 ⁇ 150 mm 2 and the antechamber holds approximately 65 ⁇ 6 ⁇ L of fluid (depending on glue thickness).
  • the volume may be ⁇ 30 ⁇ L.
  • the inflow port has a 2.4 mm target that funnels down to 1.1 mm port (to engage and seal 19 guage tube or pipette tip or robotic injector tip).
  • the depth of the post-filtration subchamber is non-uniform, starting at 500 ⁇ m on the right for inflow, and ending at 700 ⁇ m on the left for the outflow (to correct partially for the increasing concentration of effusate containing the waste cells).
  • the perimeter of the bottom housing part contains a tall well which is meant to prevent contamination of the instrument when in use in the case of accidental overflow of blood on the device or accidental dispensing of the blood outside the inflow port.
  • the largest dimensions at the overflow well are 37.7 mm ⁇ 11.6 mm.
  • the ports are sized to engage and seal pipes that are 1.1 mm in diameter (19 guage tube) and are spaced about 29.1 mm apart (about 29.0 mm after shrinkage).
  • the post- filtration subchamber is about 400 ⁇ m wider than the antechamber to retain any residual glue between the housing parts.
  • the top housing part engages the bottom housing part not only on the horizontal contact surfaces but also for about >1 mm around the perimeter where the quasi-vertical side-walls meet, with a little extra clearance at the corners.
  • pulse width, pulse height, pulse profile, and duty time will be optimized to recover the leukocytes and rare cells without damage while maximizing removal of red cells, plasma, and platelets.
  • FIG. 35 An exemplary embodiment of an automated system is depicted in Figure 35, which has a filtration chamber directly connected to a flow cytometer.
  • the syphon picks up the sample cells, preferably a 10 ⁇ to 100 ⁇ dilution of whole-blood, or any other mixed cell sample, using environmental pressure as the passive pump.
  • Pumps 1, 2, and 3 are metered pumps with programmable flow rates that produce the filtration rates.
  • Pump 4 is that which normally produces the concentrated flow (focused flow) of a normal flow cytometer. The flow cell is pumped by vacuum pressure at its distal end.
  • a pre-filter above the cell flow chamber
  • SS filter a commercially available SS filter that is coated with our non-stick surface and which only serves to provide directional flow of solution across the filtering chamber as the sample flows through.
  • the second filter is a slotted filter as provided in the present invention, also coated to be non-stick to cells. Plasma, red blood cells, platelets, and unbound markers are removed through the slot filters by the waste pump.
  • FIG. 36 An exemplary embodiment of a high-rinse capacity filtration chamber is depicted in Figure 36.
  • the high-rinse capacity filtration chamber has two clean buffer entry points (1 and 3) to not only wash away the erythrocytes as they pass through the bottom filter, but to also add clean buffer from above to push more cells through the filter and enable a higher flow rate from the feed pump into the recovery chamber.
  • a pulsatile flow would be preferred where pumps 1 and 2 will alternate between same speed and higher waste outflow, in a coordinated manner with pump 3 alternating between different rates of pump 2 - pump 1 and 0. When pump 3 is at 0 flow rate, pumps 1 and 2 will flow at the same rate.
  • the bottom filter is a slotted filter and the top filter may be any common filter that will retain its flatness in the low flow conditions and that may be coated with a non-stick surface as needed.
  • the top filter could, for example, be a stainless steel sheet or a polyimide sheet with holes of any shape which are approximately 0.05 to 2 microns in diameter.
  • the top filter may be supported by structures on the buffer distribution chamber above it to maintain its flatness during filtration.
  • the recovery pump is imaginary (atmospheric pressure) and its flow rate may be calculated by pump 4 - pump 2 + pump 1 + pump 3.
  • the filtering pump (of the slotted filter on the bottom) is imaginary (controlled by other pumps working in tandem) and its flow rate may be calculated by pump 2 - pump 1.
  • FIG. 37 An exemplary embodiment of two filtration chambers in tandem is depicted in Figure 37.
  • the two filtration chambers are in fluid connection between the two filters overlapping each other, i.e., the antechamber.
  • Example 15
  • FIG. 38 An exemplary embodiment of a filtration chamber with multiple output ports is depicted in Figure 38. Two or more filters in tandem with slot widths of increasing size for each filter may be enclosed in a filtration chamber. It may also be possible to use a single, longer filter with multiple output ports on the bottom to remove sequentially larger cells along the path through the top chamber.
  • Example 16
  • a Silicon wafer was bonded to a glass wafer that was to act as a sacrificial carrier, then was thinned, masked, and etched to produce a continuous filter on the entire surface of the wafer, using the following steps.
  • the bonding compound was spin-coated to a uniform thickness onto a sacrificial glass wafer and the silicon wafer was pressed onto the sacrificial wafer to eliminate bubbles during curing and the glue was baked to cure.
  • the attached silicon wafer was then thinned by CMP until its thickness across its entire surface was 40 to 60 ⁇ m, and specifically 55 ⁇ m to 60 ⁇ m in thickness.
  • a dielectric layer such as silicon dioxide was then depositioned onto the silicon wafer to function as a hard mask.
  • a polymer mask layer (soft mask) was then layered on top of the hard mask by spin-coating method, and solidified on a hot-plate.
  • the soft mask was then pattered across its entire surface using a projection mask such that the entire surface was cured by ultraviolet light except for the repeating rectangular areas that would become the slots.
  • the uncured soft mask material and the exposed hard mask under it were etched away.
  • the wafer was then deep-etched using deep reactive ion etching, DRIE, process according to the Bosch method. This process removed the soft mask and etched the patterned slots through the wafer and was continued to remove some of the underlying wafer bonding compound between the two wafers.
  • the mask sizing and DRIE process were configured such that the resulting slots were 2.8 ⁇ m wide by 55-60 ⁇ m deep by 50 ⁇ m long and repeating over the entire surface of the wafer every 9 ⁇ m along its short axis and every 70 ⁇ m along its long axis.
  • the perimeter of the wafer had an un-etched ring area of 5mm from the edge which resulted in a stronger perimeter edge that could be used for handling later.
  • the wafer was then placed into a plasma-enhanced vapor deposition chamber and TiN was depositioned onto its entire surface.
  • the liberated filter wafer was rinsed well in methanol then placed into a vacuum oven to dry.
  • the wafer was then bonded to a plastic handling ring as well as to one side of the injection- molded plastic filter body housings that had also been deposition coated with TiN.
  • the housings were snapped apart retaining the bonded segments of filter, and assembled to the second half of the molded filter housings, also deposition-coated with TiN, to produce ready-to-use filters.
  • Example 17
  • erythrocytes RBC
  • PLT thrombocytes
  • WBC leukocytes
  • PLTs PLTs are easily activated, forming clots that often render samples unusable. Lysis or gradient centrifugations are commonly used to remove RBCs and PLTs, but these have serious limitations including poor recovery rates and damage to target cells. In addition to having a cytosolic effect, lysis may damage rare cells that express the same anion exchanger membrane protein as RBCs.
  • the resulting alkalinization of the cytosol activates carbonic anhydrase in red blood cells (RBC) and other cells, which in turn enhances the anion exchanger activity and further burdens the cell with chloride anion in the futile effort to correct the cell’s pH imbalance, ultimately resulting in osmotic lysis.
  • RBC red blood cells
  • this lysis method has been useful for debulking blood of its erythrocytes, and producing a population for study which is enriched in nucleated cells, however the cytosolic alkalinization also modifies many other events in the cells, ultimately changing homeostasis.
  • the cells of clinical relevance are usually sick cells or remodeled and dedifferentiated cells, such as stem cells and tumor cells, that express higher levels of anion exchanger than mature leukocytes.
  • lysis has been problematic, resulting in selective loss of those cells of highest interest (e.g., Resnitzky and Reichman, 1978, Blood, 51(4):645).
  • typical lab practice is to sample about 10-fold the amount of blood that is needed for analysis, and keep sufficient safety stock to be able to repeat the procedure where necessary.
  • the samples may contain very rare cells or cells that are so sensitive to lysis that often the samples are wasted.
  • the physical characteristics of blood cells are used to parse and recover total nucleated cells (TNC) in a blood sample without centrifugation.
  • the RedSiftTM Cell Processor uses a micro- machined, chemically engineered membrane that allows blood plasma, PLTs, and RBCs to pass through while all nucleated cells are retained on the membrane.
  • TNCs were enriched from 10 to 250 ⁇ L of whole blood with minimal user interaction, no centrifugation, and no harsh chemical treatments to produce 80 to 500 ⁇ L of sample containing 90 to 99% of TNCs with less than 1% RBCs.
  • Low count, unfixed, and labeled tumor cells were spiked into blood and recovered with high efficiency, demonstrating potential use in recovering circulating tumor cells (CTC), fetal cells from maternal blood, or for minimal residual disease monitoring (MRD).
  • CTC circulating tumor cells
  • MRD minimal residual disease monitoring
  • the system in this example used micromachined filters to automate cell preparation and provide samples enriched for total nucleated cells.
  • the RedSift Cell Processor system can handle any blood volume as small as 10 ⁇ L and as much as 3 million nucleated cells per track, with four tracks per filter array.
  • the cells are separated by a gentle technique that does not lyse cells or liberate cytosolic contents and RNA into the sample.
  • Peripheral blood and bone marrow were collected from 39 healthy donors and aliquots of each sample were used up to 72 hours after collection. The 39 samples represent consequent data in a validation set, no runs were removed within the sequence. On some aliquots, samples were enriched for TNC using RedSift method and compared to lysis method (VersaLyse, Beckman Coulter). In some experiments, cells were stained using fluorescent biomarkers (Becton Dickinson, or eBioscience). Samples were not fixed prior to staining, and were assayed immediately after staining. Tumor cell lines (ATCC) were cultured in DMEM with F12 supplement and 10% BSA (Thermo Fisher Scientific).
  • FIG.39 compares the Ficoll method with the lysis method.
  • FIG.40 on the left is a graphical display of process flow using RedSift Cell Processor for tissue preparation, illustrating RBC and platelets passing through filter while retaining up to 3 million nucleated cells above filter using antiparallel flow filtration.
  • Top right Recovery efficiencies (as a percent of whole blood, ⁇ SE) using a range of starting volumes of whole blood.
  • the RedSift Cell Processor works with peripheral blood, bone marrow, etc.; removes RBC, PLT, and plasma soluble compounds; cause no exposure to harsh chemicals; requires no centrifugation; is amenable to multiple downstream analysis; has configurable input volume down to 20 ⁇ L; has configurable output volume up to 1mL; generates isolated cells ready for flow cytometry, NGS, ISH, and QPCR etc.; and/or provides robust and repeatable automated cell preparation.
  • FIG.41 shows cell subpopulations were elucidated by flow cytometry in one sample.
  • Plots are in sets of two where left plot represents data from 100 ⁇ L of filtered blood, right plot represents dilution matched data from 100 ⁇ L of lysed blood. Except for determination of NK cells, all plots show side scatter on Y axis and fluorescence emission of each biomarker on X axis.
  • Panel A CD45 determination showing total nucleated cells. The CD45 region from top plots was selected as a data gate for the bottom two plots as well as for monocytes quantification in panel D. In bottom plots, the CD45-gated data was subdivided to show subpopulation ratios.
  • Panel B Red Blood cells (CD235a positive) make up about half the population of remaining cells (top). Note that the blood sample had many rouleaux as may be evidenced in the Versa Lyse sample where each cluster represents an increasing number of multicellular stacks. In this sample platelets (CD41a positive were removed equally well by both methods (bottom). Panels C and D: Assessment of T (CD3 positive), B (CD19 positive), and NK cells was done using only CD45 positive cells from the lymphocytes gate (lym in panel A). Note that in NK cell determination, NK cells are indicated in the third quadrant (CD16/CD56 on X axis), whereas the first quadrant are T-cells (CD3 on Y axis) and the second quadrant are NK(T). Monocytes (CD14 positive) were assessed from the overall CD45 positive population. Counts within each outlined region of interest are indicated below each plot.
  • FIG.42 shows filtered cells are amenable to cell culture.
  • Day 4 culture of spiked cancer cells recovered from whole blood.
  • Three tumor cell lines were harvested at 75-85% confluency, and equal aliquots were either directly filtered (control), or were spiked into whole peripheral blood then filtered (RS Filter). The filtration product was replaced into culture, and observed for growth at day 4 after filtration.
  • RS Filter filtered peripheral blood then filtered
  • This example shows that RedSift filters are able to recover >80% of all nucleated cells from small blood samples, while reducing RBC counts by 3 orders, and removing unbound PLT. Nucleated cells from blood samples are not damaged or modified or selectively removed by the filters.
  • CTC circulating tumor cells
  • MRD minimal residual disease
  • anuclear cells in blood greatly outnumber nucleated cells and present significant challenges to the study of the nucleated cells, for example, erythrocytes can absorb excitation or emission wavelengths in fluorescence studies, and their shape promotes rouleaux formation which can sequester the cells of interest; platelets also have a tendency to be activated by physical handling and cause aggregation that can sequester and damage the cells of interest, and these all contain the greatest content of RNA and other markers that increase background noise in many assays.
  • the cells of clinical relevance are usually sick cells or remodeled and dedifferentiated cells such as stem cells, tumor cells, that express higher levels of anion exchanger than mature leukocytes.
  • lysis has been problematic, resulting in selective loss of those cells of highest interest.
  • cytosolic alkalization from dissolved ammonia in lysis buffers can activate carbonic anhydrase and many other cellular processes, ultimately changing homeostasis.
  • Another common method for rare cell enrichment is to employ high osmolality solutions to produce density gradient which, under centrifugation, is able to separate cells based on their density.
  • an automated technology was used for the depletion of erythrocytes, thrombocytes, and plasma markers from, initially, small volumes of blood, using a micromachined membrane filter.
  • Small counts (10 to 1000 estimated from dilution) of tumor cell lines BT474 (breast cancer), DLD1 (colorectal cancer), and K562 (myelogenous leukemia) and other cell types were spiked into aliquots of blood.
  • the technology is amenable to use of beads for initial negative depletion of common nucleated cells by magnetic beads and has a recovery capacity of a few to as much as 3 million cells per specimen.
  • Tumor cell lines alone that were run through this automation process then seeded for cell culture demonstrated growth rates indistinguishable from those seeded in similar counts in a regular cell passage.
  • depletion of leukocytes with magnetic beads and of anuclear cells by filtration were demonstrated to handle larger blood volumes.
  • the filtration system may be used for automated recovery of nucleated cells or cell clusters from blood and other fluid samples without use of harsh chemicals or centrifugation, removing a common barrier for emerging approaches.
  • the RedSift Cell Processor system can handle any blood volume as small as 10 ⁇ L and as much as 3 million nucleated cells per pass. With four filtration lanes per filter array, the cell processor can recover 25-30 million nucleated cells per hour. The cells are separated by a gentle technique that does not lyse cells, nor does it liberate cytosolic contents and RNA into the sample; and configurable input and output volumes can remove centrifugation steps in cell preprocessing.
  • various carcinoma cell lines including K562 (myelogenous leukemia), DLD-1 (colorectal tumor), BT474 (breast carcinoma), and A549 (lung tumor), were cultured in DMEM with F12 supplement and 10% BSA (Thermo Fisher Scientific). Aliquots of cells were counted on a microscope using a hemocytometer, and counts were confirmed on a CBC instrument (Sysmex) to determine cell density per aliquot.
  • Peripheral blood was collected from healthy donors and aliquots of each sample were used up to 72 hours after collection. Blood counts were done on a CBC instrument. Some aliquots were enriched for TNC using RedSift method to determine efficiency of recovery of TNC’s. Enrichment is performed on RedSift Cell Processor, an automated microfluidics platform that recovers total nucleated cells in 15 minutes.
  • carcinoma cells were stained using Calcein-AM-loaded fluorescent biomarker (Becton Dickinson, or eBioscience). These unfixed marked carcinoma cells were then assayed immediately after staining to determine cell counts using a CBC instrument. Aliquots of the marked carcinoma cells were spiked into 50 ⁇ L whole blood in in quantities of 10 to 1000 cells then filtered on RedSift system. Additional aliquots of same quantities were spiked into the same volume of whole blood and left unfiltered. Finally, aliquots of 1000 cells were spiked into 50 ⁇ L of PBS as controls. All test aliquots were assayed by flow cytometry (Beckman Coulter, FC500) to determine counts of marked spiked carcinoma cells. [00621] FIG.43 is a graphical display of process flow using RedSift Cell Processor for tissue preparation, illustrating RBC and platelets passing through filter while retaining up to 3 million nucleated cells above filter using antiparallel flow filtration.
  • FIG.44 shows K562 leukemia cell line was spiked into buffer (top left), or whole peripheral blood buffered in EDTA (top right), Streck (bottom left) or Heparin (bottom right) then filtered prior to measuring calcein fluorescence in the spiked tumor cells. Filtration did not reduce the tumor cell counts.
  • FIG.45 shows filtered cells are amenable to cell culture.
  • Various cancer cells from equal aliquots that were not spiked or filtered (Control) or were spiked into whole peripheral blood then recovered using RedSift method (RS Filtered) were imaged after 4 days in culture.
  • FIG.46 shows K562 cells were spiked in graded quantities from 1000 to 12 cells into buffer (top) or into whole blood (bottom). Both sets of samples were filtered by RedSift system and resulting scatter grams were recorded by flow cytometry.
  • FIG.47 counts from recovery experiments in FIG.46 are plotted by quantity of Spiked K562 cells. Recovery percent represents counts recovered over counts spiked into buffer or into blood then filtered.
  • BT474 breast carcinoma
  • DLD1 colonal tumor
  • A549 lung carcinoma
  • RedSift filters are able to recover 80-97% of all nucleated cells from small blood samples, while reducing red blood cell (RBC) counts by more than 3 orders, and removing unbound platelets (PLT). Small counts of cancer cells introduced into the blood sample were recovered in high efficiency, undamaged, and allow subsequent culturing of the recovered cells. This may prove useful for recovery of rare cells including CTCs, stem cells or fetal cells from blood. Thus, the RedSift system removes user-dependent variance and facilitates standardization across multiple sites for recovery of rare cells.
  • RBC red blood cell
  • PHT unbound platelets
  • erythrocytes red blood cells, RBC
  • the RBC are so much more populous than the leukocytes (white blood cells, WBC) or other rare nucleated cells (RC) in the blood that any signal that is captured is met with at least a thousand times more noise from the RBCs, often entirely obscuring visualization of or shielding the cells of interest.
  • WBC white blood cells
  • RC rare nucleated cells
  • thrombocytes platelets, PLT
  • WBCs platelets
  • Flow cytometry is quickly replacing many older microscopic imaging based diagnostics, where cells may be sampled 10-30 thousand per second compared to automated microscopic imaging capabilities of less than a thousand per minute. While microscopic observation has no recourse for eliminating the noise contributed by RBCs in a sample, Flow cytometry allows the configuration of a discrimination threshold that defines how large a cell must be, as it flies through the measurement area, to be counted as a cell. This allows the experimenter to ignore counting RBC’s, however it does not eliminate the other effects of having RBC’s present in the sample, namely the shielding effect (obscuring), and the dimming effect
  • experimenters employ a number of techniques for selectively reducing the counts of RBCs in the sample, thereby increasing the proportion of total nucleated cells (TNC) and hence improving signal to noise ratio of the measurements.
  • the more common techniques include density gradient, osmotic swelling, membrane permeation, and aggregation/flocculation.
  • Density-gradient-based separation of cells is performed by a gentle but very long centrifugation at about 300-600g with the cells layered (very carefully to avoid mixing)) over a sugar or starch-based media.
  • the RBCs being of highest density, drop fastest, the lymphocytes stratify above the RBCs, and the platelets and granulocytes remain at the top of the tube.
  • These samples are very clean since the sticky hemoglobin and even more sticky RNA molecules that are packed inside the RBC’s remain packaged in the RBCs and do not interfere with subsequent biomarker binding.
  • This technique is often disfavored because it only effectively isolates lymphocytes and then only those which are not trapped in rouleaux.
  • the centrifugation must spin down without breaking otherwise the sample will randomize with the stirring, and once the centrifuge has stopped, the sample must be handled very carefully to not stir it before collecting the lymphocytes.
  • the sample is simply centrifuged at higher g to produce a buffy coat of WBC, there is still a great many cells lost to rouleaux, and the proximity of the buffy coat to the RBC layer makes it impossible to extract the WBC’s without a very small amount of RBC, and even a small amount of the RBC layer will still greatly outnumber the counts of WBCs in the buffy coat.
  • Permeation based separation may be used for flow cytometry analyses, where saponification of the cell membranes allows WBC to shrink only a small amount until their nucleus limits the shrinking, but the enucleated RBCs may shrink quite considerably, making them easier to exclude from the measurements by size discrimination threshold, as well as allowing much of the hemoglobin to leak out into the interstitial spaces so it may be removed by centrifugation (“wash”) prior to performing the measurements. This method does, however release hemoglobin and into the interstitial space, which is then difficult to remove. Often a double-wash technique is performed in an attempt to further improve signal to noise ratio.
  • Aggregation/flocculation involves inducing the RBCs to aggregate so that they will precipitate as heavier large particles in the blood, leaving the plasma and free WBC’s floating above the aggregated RBCs. This is a lossy technique as well, probably resulting in many WBCs trapped within the aggregates.
  • Lysis has over the years become a method of choice for many laboratories.
  • the majority of lysis techniques employ a buffered solution of ammonium chloride.
  • Ammonium remains in approximate equilibrium with ammonia when in solution, and ammonia, being a neutral gas, easily transverses the membrane of all cells and establishes its equilibrium inside the cells, and in so doing it consumes H+, liberating OH- inside the cells.
  • RBC While most highly differentiated cells have little recourse to correct their intracellular pH, RBC’s are specifically equipped to buffer their intracellular milieu as a byproduct of their CO2 buffering system. They employ a large amount of carbonic anhydrase to convert CO2 to bicarbonate, consuming OH-.
  • WBCs are protected by their low content of carbonic anhydrase and bicarbonate-chloride exchanger proteins, but they too will eventually also overload with ammonium chloride, hence lysis buffers must be washed from the cells with a centrifugation step after RBC lysis is complete, otherwise they must be higher osmolality to protect WBCs until they can be measured or fixed.
  • Lysis has its drawbacks.
  • the resulting alkalization changes many reactions including changes in oxidative processes.
  • an alternative method is provided for recovering the total nucleated cells content of blood (TNC) without damaging the cells. Since it is a low contact filtration based method, it is expected to be free of many of the known problems of other methods for RBC removal and TNC enrichment.
  • the subpopulation content of major nucleated cell types from blood using RedSift Cell Processor is compared to different lysis methods.
  • each of the lysis reagents which were all supplied as 10x concentrated stock, were diluted to 1x using filtered and deionized water.
  • the 1x lysis reagents were triturated to guarantee good mixing.
  • a stock mixture of antibodies was prepared containing CD3-FITC and CD16/56-PE (BD Simultest, Cat. #340042), CD19-PE-CF594 (BD Cat. #562294), CD235- APC (BD Cat. #551336), and CD45-APC-Cy7 (BD Cat. #557833).
  • RedSift Cell Processor To prevent uptake of bubbles, an additional 25 ⁇ L of blood (total 125uL) was delivered into a cytometry tube that itself contained 125uL of Pre-Filtration Buffer (PFB).
  • the buffer functions to immediately break up rouleaux and prevent further aggregation of cells without employing EDTA.
  • the tube containing the 50% diluted blood was placed onto the RedSift Cell processor, and the“h200” procedure was run. Under automation, 200 ⁇ L of the 50% blood mixture was processed through a single lane of a RedSift filter, and 800uL of Eluent containing the WBCs was collected into a new flow cytometry tube.
  • the eluted WBCs solution was incubated for 15 minutes with appropriate antibody mix for cell staining, then fixed by adding paraformaldehyde to a final concentration of 0.5% w/v. After at least 10 minutes in the presence of paraformaldehyde at ambient temperature, the sample was diluted to 1.0mL using AVIwash buffer, the same buffer that is used during filtration. AVIwash is a supplemented PBS buffer without EDTA and without fixative. Since RedSift Cell Processor completed the separation of the cells in about 10 minutes, the final fixed, diluted sample was put aside until all the lysis samples were completed so that all samples could be run in sequence on an FC500 Flow Cytometer (Beckman Coulter).
  • Lysis was performed with three different lysis reagents: VersaLyseTM (Beckman Coulter, cat. #A09777), FACS LyseTM (Becton Dickinson, cat. #349202), and BD Pharm LyseTM (Becton Dickinson, cat. #555899). Since two of the three lysis buffer options contain a fixative, the blood sample was pre-stained with the antibodies prior to lysis. This also served to reduce the number of centrifugation steps necessary, and hence reduced the losses related to centrifugation. For each of the buffers, two 100 ⁇ L aliquots of blood were started, each stained with a different biomarker mix.
  • the mixture was diluted with 900 ⁇ L of each of the buffers to provide a complete set of two 1mL final volume samples per lysis reagent, and the lysis was allowed to continue for a further 15 minutes prior to recording results on a flow cytometer.
  • the doublets of lysed samples one sample was centrifuged for one minute, at ambient temperature, at 500g RCF, then the pellet was quickly resuspended into PBS buffer to wash away any remaining reagent prior to running through a flow cytometer as a Lyse-Wash sample.
  • each Lyse-Wash sample was washed three times into PBS to guarantee as much cleaning and removal of reagents and of RBCs and PLTs.
  • each sample of the doublets was fixed with paraformaldehyde (0.5% w/v), for 10 minutes in ambient temperature, after completion of the lysis.
  • the final set of samples included one cytometry tube each for RedSift, and two samples for each of the three lysis reagents, where one set was Lyse-No-Wash (i.e., measured while still in the lysis reagent) and the other set was Lyse-Wash (i.e., the set that were centrifuged and resuspended in PBS to wash out the lysis buffer). All the lysis samples were obtained from the same blood tube, and all at the same time.
  • CBC complete blood cell counts
  • FIG.49 shows the relative ratios of major cell populations after filtering on the RedSift system for a typical case.
  • the top left panel is forward-scatter of the blue laser (FS) on X and side-scatter of the blue laser (SS) per detection event, showing good separation between the major populations.
  • FS blue laser
  • SS blue laser
  • CD235 positive cells are presumed to be RBC, illustrating that only 5% of the RBC remain after RedSift filtration, representing 4 to 5 orders of depletion of RBC from the sample.
  • the non-binding cells, CD235-negative, from this dataset were then redisplayed in the bottom right panel showing SS and CD45 binding affinity.
  • 78% were CD45-positive, representing the leukocytes (WBC) as 74% of all recovered cells.
  • the WBC population had well defined clusters of what is presumed to be lymphocytes (below), granulocytes (above), and monocytes (middle).
  • the CD45-negative population represented 21% of this population, or about 20% of all recovered cells.
  • the CD45-negative gated population from the CD235-negative population was separated based on SS and CD41 binding affinity in the bottom left panel. This shows that what was expected to be only Cd41-positive PLT, there were 3% of cells remaining that were not RBC, not WBC, and not PLT. From these data, the recovered cells from the sample, after filtering, contained 74% WBC, 5% RBC, 20% PLT, and 0.6% unidentified cells. This represents 4 to 5 orders of depletion of RBC, and almost 3 orders of depletion of PLT compared to normal blood populations expected from healthy donors. This donor sample was initially assayed for complete blood cell counts and determined to contain, per nanoliter, 4.24 WBC, 5,250 RBC, and 367 PLT.
  • RedSift filtration was compared to multiple lysis methods in a flow cytometry analysis of multiple subpopulations.
  • the subpopulations analysis is shown in FIG.50, depicting the flow of analysis using the RedSift filtered aliquot.
  • Top left panel shows SS against FS for the entire population of cells.
  • the subpopulations are less distinct in the larger total population of cells sampled.
  • the entire dataset was displayed in the top center panel showing CD235 binding against SS to illustrate RBC counts in the aliquot. In this case, RBC depletion was 22%, still about 4 orders of depletion.
  • the CD235-negative subpopulation was then further analyzed in the top right panel showing CD45 binding against SS.
  • the WBC population was further subdivided into lymphocytes, monocytes, and granulocytes.
  • the WBC group overall made up 64% of the CD235-negative cells, or 50% of the total recovered cells, and the WBC population itself consisted of 64% granulocytes, 11% monocytes, and 20% lymphocytes.
  • CD45 CD235-negative cells
  • Platelets and other CD45-negative cells comprised 35% of the CD235-negative cells, or 27% of the recovered cells.
  • This donor sample had the following complete blood cell counts, per nanoliter, 4.73 WBC, 5,130 RBC, and 206 PLT.
  • the lymphocytes subpopulation was itself then further subdivided into CD19 against SS (bottom left panel of FIG.50) to assess the B cells subpopulation, and CD3 against SS (bottom center panel) to assess the T cells subpopulation, and CD16/CD56 combination against CD3 to assess NK cells (bottom right panel).
  • the lymphocytes subpopulation was comprised of 11% B cells, 65% T cells, and 19% NK cells. As a percent of total WBC population, this represents 2% B cells, 13% T cells, and 4% NK cells. This donor had a high proportion of NK cells.
  • FIG.51 to FIG.56 show the same plots as in FIG.50, but one plot type per figure, showing side-by-side effects of different lysis reagents.
  • the top three panels in each figure show results from the Lysis technique, without centrifugation, and the bottom three panels show the same lysis techniques but washed three times by centrifugation to remove debris from the lysis. Note that in the case of RedSift the wash steps are unnecessary since the RBC are removed intact, without dumping their contents into the sample.
  • These figures show, as labelled, VersaLyse in the left panels, FACS-Lyse in the center panels, and Pharm Lyse in the right panels.
  • FIG.51 illustrates the differing effects of lysis reagents in FS against SS plots.
  • Lysis there was greater spread in the plots with Lysis than with RedSift.
  • One exception is the FACS-Lyse, Wash sample (bottom center panel) which had little spread, however the washing removed the majority of the cells.
  • the FACS-Lyse sample Prior to the wash step, the FACS-Lyse sample (top center) showed good separation of the subpopulations, however all lysis plots have cells shifted far to the right on the FS scale, consistent with swelling of the cells.
  • FIG.52 shows the differing effects of lysis reagents in CD235 binding against SS.
  • the lysis methods were generally unable to remove the entire content of RBC from the samples, leaving 25-59% RBC in the sample, or about 3 orders of depletion.
  • the RBC within the sample clustered into a large smear consistent with cell swelling.
  • the lysis-resistant cells were not washed out in VersaLyse and Pharm Lyse samples; however FACS-Lyse had proportionally good removal of RBC by the wash after lysis, although a large portion of all cells was lost in the wash.
  • RedSift system did not show a smear of RBC’s, but did show the spread in SS which is symptomatic of their flattened morphology.
  • SS flattened morphology.
  • the RedSift sample there is visible evidence of a doublets cluster and possibly triplets cluster, also typical of rouleaux formation. The cells from RedSift showed good separation.
  • FIG.53 shows the differing effects of lysis reagents in CD45 binding against SS.
  • the lysis samples did not remove as many free PLT as RedSift, as inferred from the CD45-negative population.
  • Pharm Lyse did not appear to deplete PLT (top right panel), and PLT were unable to be washed out after VersaLyse (bottom left panel).
  • the FACS-Lyse reagent resulted in lower proportion of granulocytes (56% compared to 66%) and higher proportion of lymphocytes (29% versus 21%); no attempt was made to elucidate whether FACS-lyse had removed granulocytes or whether all other methods had lost lymphocytes.
  • FIG.54 to FIG.56 utilized the lymphocytes subpopulation to show, respectively, CD19- binding, assaying B cells, CD3-binding, assaying T cells, and CD16+CD56 binding, assaying NK cells.
  • FIG.56 is plotted against CD3 to discriminate NK cells from NK(T) cells which also bind CD3.
  • the distribution of NK cells is considered to be the summation of NK and NK(T) cells.
  • the breakdown of the WBC subpopulations has been extrapolated from FIG.51 to FIG.56 and is shown in FIG.57 in a nested doughnut plot for comparison of the pre-wash state, i.e., initial recovery.
  • the left doughnut chart shows the subpopulation recovery from each method as a percent of total WBC for, from outer ring to inner ring, RedSift, VersaLyse, FACS-Lyse, and Pharm Lyse methods.
  • the right doughnut shows the same samples in the same order, but breaks them down as a percent of total
  • FIG.58 shows the same doughnut plot for just the lysis samples; showing side-by-side the Lysed samples and the lysed then washed samples to highlight the effect of the centrifugation based cell washing method.

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Abstract

La présente invention concerne un logement pour un ensemble de filtres comprenant : une première surface (par exemple, supérieure), une seconde surface (par exemple, inférieure), et une périphérie, qui sont conçues pour loger (par exemple, renfermer) un ensemble de filtres comprenant une pluralité de filtres ; et pour chaque filtre de l'ensemble, au moins deux orifices de pré-filtration sur la première surface qui sont raccordés à une chambre de pré-filtration du filtre, et au moins deux orifices de post-filtration sur la seconde surface qui sont raccordés à une chambre de post-filtration du filtre. La présente invention concerne également un siège pour le logement, l'ensemble logement/siège, une plaque de base comprenant l'ensemble, un dispositif comprenant la plaque de base, et un procédé d'utilisation du dispositif pour filtrer un échantillon.
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WO2020146723A1 (fr) * 2019-01-10 2020-07-16 Massachusetts Institute Of Technology Analyse fonctionnelle de cellules cancéreuses
WO2021100620A1 (fr) * 2019-11-20 2021-05-27 ソニーグループ株式会社 Kit d'isolation de particules
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