EP1931800A2 - Systemes et methodes d'enrichissement d'analytes - Google Patents

Systemes et methodes d'enrichissement d'analytes

Info

Publication number
EP1931800A2
EP1931800A2 EP06803736A EP06803736A EP1931800A2 EP 1931800 A2 EP1931800 A2 EP 1931800A2 EP 06803736 A EP06803736 A EP 06803736A EP 06803736 A EP06803736 A EP 06803736A EP 1931800 A2 EP1931800 A2 EP 1931800A2
Authority
EP
European Patent Office
Prior art keywords
analyte
sample
cells
cell
blood
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP06803736A
Other languages
German (de)
English (en)
Other versions
EP1931800A4 (fr
Inventor
Ravi Kapur
Mehmet Toner
Lotien Richard Huang
Tom Barber
Bruce Carvalho
Darren Gray
Ulysses Balis
John Walsh
Michael Grisham
Ron Tompkins
Martin Schmidt
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
General Hospital Corp
Artemis Health Inc
Original Assignee
General Hospital Corp
Artemis Health Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US11/228,462 external-priority patent/US20070059680A1/en
Priority claimed from US11/229,336 external-priority patent/US20070059781A1/en
Priority claimed from US11/229,332 external-priority patent/US20070059719A1/en
Priority claimed from US11/229,328 external-priority patent/US20070059718A1/en
Priority claimed from US11/229,037 external-priority patent/US20070059774A1/en
Priority claimed from US11/228,454 external-priority patent/US20070059716A1/en
Application filed by General Hospital Corp, Artemis Health Inc filed Critical General Hospital Corp
Publication of EP1931800A2 publication Critical patent/EP1931800A2/fr
Publication of EP1931800A4 publication Critical patent/EP1931800A4/fr
Withdrawn legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/80—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving blood groups or blood types or red blood cells
    • 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
    • B01L3/502761—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 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/543—Immunoassay; Biospecific binding assay; Materials therefor with an insoluble carrier for immobilising immunochemicals
    • G01N33/54366—Apparatus specially adapted for solid-phase testing
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/06—Fluid handling related problems
    • B01L2200/0647—Handling flowable solids, e.g. microscopic beads, cells, particles
    • B01L2200/0668—Trapping microscopic beads
    • 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
    • B01L2300/0809—Geometry, shape and general structure rectangular shaped
    • B01L2300/0816—Cards, e.g. flat sample carriers usually with flow in two horizontal directions
    • 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
    • B01L2400/00—Moving or stopping fluids
    • B01L2400/04—Moving fluids with specific forces or mechanical means
    • B01L2400/0403—Moving fluids with specific forces or mechanical means specific forces
    • B01L2400/043—Moving fluids with specific forces or mechanical means specific forces magnetic forces
    • 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
    • B01L2400/04—Moving fluids with specific forces or mechanical means
    • B01L2400/0475—Moving fluids with specific forces or mechanical means specific mechanical means and fluid pressure
    • B01L2400/0487—Moving fluids with specific forces or mechanical means specific mechanical means and fluid pressure fluid pressure, pneumatics
    • 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
    • B01L2400/08—Regulating or influencing the flow resistance
    • B01L2400/084—Passive control of flow resistance
    • B01L2400/086—Passive control of flow resistance using baffles or other fixed flow obstructions
    • 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
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y15/00—Nanotechnology for interacting, sensing or actuating, e.g. quantum dots as markers in protein assays or molecular motors
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
    • B82Y—SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
    • B82Y30/00—Nanotechnology for materials or surface science, e.g. nanocomposites
    • 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
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/795—Porphyrin- or corrin-ring-containing peptides
    • G01N2333/805—Haemoglobins; Myoglobins
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/38—Pediatrics
    • G01N2800/385—Congenital anomalies
    • G01N2800/387—Down syndrome; Trisomy 18; Trisomy 13
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

Definitions

  • Analysis of specific cells can give insight into a variety of diseases. These analyses can provide non- invasive tests for detection, diagnosis and prognosis of diseases, thereby eliminating the risk of invasive diagnosis. For instance, social developments have resulted in an increased number of prenatal tests. However, the available methods today, amniocentesis and chorionic villus sampling (CVS) are potentially harmful to the mother and to the fetus. The rate of miscarriage for pregnant women undergoing amniocentesis is increased by 0.5-1%, and that figure is slightly higher for CVS.
  • Some non-invasive methods have already been developed to diagnose specific congenital defects. For example, maternal serum alpha-fetoprotein, and levels of unconjugated esrriol and human chorionic gonadotropin can be used to identify a proportion of fetuses with Down's syndrome, however, these tests not one hundred percent accurate. Similarly, ultrasonography is used to determine congenital defects involving neural tube defects and limb abnormalities, but is useful only after fifteen weeks' gestation.
  • fetal cells represent a small number of cells against the background of a large number of maternal cells in the blood which make the analysis time consuming and prone to error.
  • the invention relates to a system comprising one or more size-based separation modules adapted to increase a concentration of a first analyte in a sample by at least 10,000 fold, wherein the first analyte has an initial concentration in the sample of less than 1 x 10-3 analytes/ ⁇ L and an analyzer optionally comprising a computer executable logical for analyzing the first analytes in a medium enriched with the first analyte.
  • the analyzer further comprises a microscope, a microarray, or cell counter.
  • the computer executable logic detects a color change in the presence of fetal hemoglobin, globin ⁇ , globin e, GPA, i-antigen, CD46, selectins, CD45 or a combination thereof. ⁇ m
  • the analyzer comprises dual scanning capabilities. 5 In some embodiments, the computer executable logic images the first analytes.
  • the computer executable logic analyzes the fetal cells to determine sex of a fetus, trisomy, or a chromosomal abnormality in one or more of the fetal cells.
  • one or more of the size-based separation modules comprise a two-dimensional array 0 of obstacles that directs the first analyte deterministically in a first direction and a second analyte having a hydrodynamic size smaller than the first analyte in a second direction.
  • two or more of the size-based separation modules are fluidly coupled in parallel with one another.
  • the system is adapted for high-throughput analysis of at least 10 mL of the fluid 5 sample per hour.
  • the system further comprises one or more capture regions fluidly coupled to the separation regions that selectively capture the first analyte or a second analyte from the fluid sample.
  • the system comprises one or more capture modules, wherein one of the capture modules comprises a two-dimensional array of obstacles.
  • capture module obstacles are coupled to antibodies. Such antibodies selectively bind a red blood cell, a white blood cell, a fetal blood cell, a fetal nucleated blood cell, a cancer cell, an epithelial cell, or stem cell, a progenitor cell, a foam cell, or a platelet over a second analyte in a sample.
  • the antibodies are selected from the group consisting of: anti-CD71, anti-CD36, anti-carbohydrates, anti-selectin, anti-CD451, anti-GPA, anti-antigen-I, and anti-EpCaM. 5
  • the fluid sample is a maternal blood sample and the first analyte is a nucleated fetal red blood cell.
  • the fluid sample is a blood sample and the first analyte is selected from the group consisting of: an epithelial cell, an endothelial cell, a progenitor cell, a stem cell, a foam cell, or a cancer cell.
  • the sample is a blood sample and is less than 5 mL. 0 In some embodiments, the fluid sample is a blood sample derived from a female who is in less than 12 weeks of gestation.
  • a gap between obstacles in the size-based separation modules or the capture modules is less than 1000 microns.
  • the system further comprises a reservoir containing magnetic particles.
  • the 5 reservoir is fluidly coupled to the size-based separation modules or the capture modules.
  • the present invention provides systems comprising a separation module adapted for removal of more than 99.5% of enucleated cells from a blood sample and retention of more than 99% of nucleated cells from a blood sample.
  • the system further comprising an analyzer fluidly coupled to said separation module adapted to analyze one or more of the nucleated cells and a database for storing data from 0 analysis.
  • the present invention further provides systems useful for the enrichment of analytes, for example, cells of selected types, in samples, and methods for analyzing the condition of a patient based on analysis of the analytes in r ⁇ _ _ __ ⁇ e4ntfc ⁇ r ⁇ 5Fs&ri ⁇ plelJ'"Mr
  • analytes for example, cells of selected types, in samples, and methods for analyzing the condition of a patient
  • the invention includes embodiments wherein said first analyte is selected from the group consisting of a red blood cell (RBC), a fetal RBC, a trophoblast, a fetal fibroblast, a white blood cell (WBCs), an infected WBC, a stem cell, an epithelial cell, an endothelial cell, a stem cell, a cancer cell, a viral cell, a bacterial cell, and protozoan, and further embodiments wherein said cell type is found in vivo at a concentration of less than 1 x 10-3 cells/ ⁇ L.
  • the gaps between obstacles in said first enrichment region of the system is at most
  • the system comprises one or more second enrichment regions comprising, wherein said second enrichment regions captures said first analyte or said second analyte, and wherein said second enrichment region is in fluid communication with said first enrichment region.
  • said one or more first enrichment regions are adapted to retain at least 99% of said first analyte. In related embodiments, said one or more first enrichment regions are adapted to increase concentration of said first analyte by at least a factor of 100,000.
  • the invention also relates to a method for identifying a characteristic associated with a condition in a patient comprising obtaining a plurality of control samples, obtaining a plurality of case samples, applying each of said samples to a device comprising a plurality of obstacles that deflect a first analyte from said sample in a direction away from a second analyte of said blood sample wherein said first analyte and said second analyte have a different hydrodynamic diameter, analyzing said first analyte from said samples to determine a characteristic of said first analyte, and performing an association study based on said characteristic.
  • said characteristic is the presence or absence of said first analyte, and in other embodiments, said characteristic is the number of said first analyte. In various embodiments contemplated, said characteristic is the morphology of said first analyte, the genotype of said first analyte, the proteome of said first analyte, the RNA composition of said first analyte, and/or the level of gene expression of said first analyte.
  • said plurality of control samples comprises at least 100 control samples.
  • said plurality of case samples comprises at least 100 case samples.
  • said control samples and case samples are blood samples. Also contemplated are embodiments wherein each blood sample comprises less than 100 mL of blood.
  • the invention contemplates embodiments wherein said analyte is a cell type, and in particular embodiments, said analyte is an epithelial cell, a cancer cell, or a fetal cell.
  • the present invention relates to methods for detecting biohazard analytes, including but not limited to bacteria, protozoa, viral pathogens, and toxins, in environmental and other samples.
  • the invention relates to methods for detecting a biohazard analyte in a sample wherein said biohazard analyte is found at a concentration less than 1 x 10-3 analytes/ ⁇ L of a sample comprising applying the sample to an enrichment device/module, and analyzed said enriched biohazard analyte.
  • the enrichment device can, in some embodiments, comprise a two-dimensional array of obstacles that deterministically direct the biohazard analyte(s) in a first direction and one or more non-biohazard analytes in a second direction.
  • the enrichment device includes a two-dimensional array of obstacles that selectively captures the biohazard analytes.
  • ⁇ G ⁇ p/bItlvelXMia ⁇ ies : llffii''alElpabove are preferably less than 1000 microns, 500 microns, 100 microns, 50 microns, or 10 microns.
  • the enrichment device is adapted to retain at least 99% of said biohazard analyte. In some embodiments, the enrichment is adapted to enrich said biohazard analyte by a factor of at least 10,000.
  • the invention contemplates embodiments wherein the enrichment device has specificity of at least 98% and sensitivity of at least 98%, such that the concentrator can
  • biohazard analyte is a pathogen selected from the group consisting of: a bacterium, a protozoan, and a virus. More specifically, in embodiments of the invention said biohazard analyte is a pathogen selected from the group consisting of: Yersinia pestis, Bacillus anthracis,
  • a biohazard analyte is a cell type or a toxin.
  • said sample is a water sample, an air sample, a plant or animal sample or a soil sample.
  • said sample is a fluid sample.
  • the invention further comprises methods that include the step of liquefying a sample to convert it to a fluid sample.
  • the invention contemplates methods wherein said enrichment removes at least 99% of a second analyte from the sample.
  • the invention relates to methods of identifying fetal abnormality from a maternal blood sample by delivering a maternal blood sample from a pregnant female to an analyzer adapted for capturing an image of one or more fetal cell enriched from said blood sample; analyzing signals from one or more nucleic acid probes that bind fetal nucleic acids; analyzing said signals; and generating a diagnostic output according based on said analyzing step.
  • probes can be specific to a chromosome, such as, e.g., X chromosome, Y chromosome, chromosome 21, chromosome 13 and chromosome 18.
  • analyzing comprises determining number of said probe signals, determining size of said probe signals, determining shape of said probe signals, determining aspect ratio of said probe signals, or determining distribution of said probe signals. In some embodiments, analyzing comprises capturing an image of a fetal nucleated red blood cell obtained from the maternal blood sample; inputting probe intensities for a plurality of nucleic acid probes that bind fetal nucleic acids of interest; analyzing the probe intensities; and generating a diagnostic output according to results of the analysis. In one embodiment, the probes are specific to a chromosome.
  • the chromosome is selected from the group consisting of: X chromosome, Y chromosome, chromosome 21, chromosome 13 and chromosome 18.
  • the analyzing step comprises determining the number of the probes.
  • the invention relates to a computer program product that detects a condition of a fetus comprising of computer code that detects fetal nucleated red blood cell (friRBC) in a sample; computer code that receives probe intensities from one or more nucleic acid probes that bind fetal nucleic acids of interest; computer code that analyzes the intensities received; computer code that generates a call according to results of analyzing the probe intensities; and a computer readable medium that stores the computer codes.
  • the computer readable medium is a memory, hard drive, floppy disk, CD-ROM, flash memory, or tape.
  • the probes are specific to a chromosome.
  • the chromosome is selected from the gfoi ⁇ p Y chromosome, chromosome 21, chromosome 13 and chromosome 18.
  • the probes are colorimetric probes. In one embodiment, the probes are fluorescent probes.
  • the invention provides a kit for prenatal testing comprising a size-based separation module adapted to isolate one or more cells of a first cell type from a maternal blood sample wherein said first cell type is found in vivo in a pregnant female at a concentration of less than 1% of all blood cells, and a set of instructions for analyzing said one or more enriched cells to make a prenatal diagnosis.
  • kits also comprise one or more reagents (in vials or containers).
  • reagents can be selected from the group consisting of: a PCR reagent, a lysis reagent, a nucleic acid probe, and a labeling reagent.
  • a labeling reagent is a FISH reagent or FISH probe.
  • the FISH probe selectively binds a chromosome selected from the group consisting of X chromosome, Y chromosome, chromosome 13, chromosome 18, and chromosome 21.
  • the kit can also include a microarray.
  • a size-based separation module can include a two-dimensional array of obstacles that deterministically direct said one or more cells of a first cell type in a first direction and one or more cells of a second cell type in a second direction.
  • first cell type can be a fetal cell.
  • second cell type is an enucleated red blood cell or a platelet.
  • a size-based separation module can retain more than 99% of said first cell types and remove more than 99% of said enucleated red blood cells.
  • a size-based separation module can be fluidly coupled to an array of obstacles, wherein said obstacles are coupled to an antibody is selected from the group consisting of an anti-CD71, anti-CD36, anti-selectin, anti-GPA, anti-CD45, and anti-antigen i.
  • the fetal diagnosis can be for sex of a fetus, the existence trisomy 13, trisomy 18, trisomy 21 (Down's Syndrome), Turner Syndrome (damaged X chromosome), Klinefelter Syndrome (XXY) or another irregular number of sex or autosomal chromosomes, or the existence of a condition selected from the group consisting of WoIf- Hirschhorn syndrome (4p-), Cri-du-chat (5p-), Williams syndrome (7ql 1.23), Prader-Willi syndrome (15ql 1.2-ql3), Angehnan syndrome (15ql 1.2-ql3), Miller-Dieker syndrome (17pl3.3), Smith-Magenis syndrome (17pl 1.2), DiGeorge and Velo-cardio-facial syndromes (22ql 1.2), Kallman syndrome (Xp22.3), Steroid Sulfatase Deficiency (STS) (Xp22.3), X-Linked Ichthiosis (Xp22.3), and Retinoblast
  • the invention relates to a method for diagnosing an animal for a condition by obtaining a fluid sample from the animal, enriching a first analyte having a concentration of less than 1 x 10 -3 analytes/ ⁇ L from said sample by a factor of at least 10,000 fold; and analyzing one or more enriched first analytes to determine a condition in said animal. Enrichment is preferably performed using one or more size-based separation modules.
  • a size-based separation module comprises a two-dimensional array of obstacles that creates a deterministic flow path for a first analyte from the fluid sample and a second deterministic path for a second analyte from the fluid sample, wherein the first analyte has a different hydrodynamic size than the second analyte.
  • the first path leads to a first outlet and the second path leads to a second outlet.
  • the methods herein can also include the step of analyzing one or more enriched first analytes to determine the condition in the animal.
  • the first analyte is a cancer cell, a fetal cell, or a pathogen.
  • the animal is a domesticated animal.
  • the domesticated animal is selected from the group consisting of: a cow, a chicken, a pig, a horse, a fish, a rabbit, a dog, a cat, and a goat.
  • the first analyte is a cancer cell.
  • the first analyte is a fetal cell.
  • the first analyte is a pathogen.
  • the pathogen is a bacterium, a virus, or a if"" " '' plotozoanr ' tf'SoSle'emWiiffieiltsJ'Oie analyzing step comprises performing DNA analysis.
  • the analyzing step comprises performing RNA analysis.
  • the analyzing step comprises performing protein analysis.
  • the fluid sample is a blood sample.
  • the method further comprises of the step of applying a reagent to the sample 5 wherein the reagent increases the size of the first analyte by at least 10%.
  • applying a reagent step occurs prior to applying the sample to an array of obstacles.
  • applying a reagent step occurs simultaneous to applying the sample to an array of obstacles.
  • the reagent comprises a quantum dot, an antibody, a phage, an aptamer, a fluorophore, an enzyme or a bead.
  • the reagent comprises a bead. 0
  • the analyzing step involves counting the number of enriched first analytes.
  • the condition is a sex of a fetus of the animal. In some embodiments, the condition comprises a microbial infection of the animal. In some embodiments, the condition comprises cancer.
  • the first outlet is fluidly coupled to one or more capture regions comprising a plurality of obstacles that selectively captures the first analyte. In some embodiments, the plurality of obstacles that selectively captures is coupled to one 5 or more binding moieties that selectively bind red blood cells, fetal cells, cancer cells, or epithelial cells. In some embodiments, the capture moieties comprise of an antibody or fragment thereof.
  • the present invention also relates to business methods in which screening services and diagnostics for analyzing the condition of a fetus are provided.
  • the invention relates to a business method for a business to provide fetal screening service comprising obtaining a blood sample from a mammal who is or has been 0 pregnant; screening the blood sample to identify a fetal cell from a fetus of said mammal; analyzing the fetal cell to determine a condition of said fetus; and providing a report on the condition in exchange for a service fee.
  • the business conducts the service.
  • said business licenses a CLIA laboratory to perform said analyzing step.
  • the invention also includes embodiments in which said report is performed for a health care provider or a 5 health insurance company.
  • the screening is performed in a fluid system adapted to separate said fetal cell from maternal cells by directing said cells in different directions by size.
  • the fetal condition determined is selected from the group consisting of: trisomy 13, trisomy 18, trisomy 21 (Down Syndrome), Turner Syndrome (damaged X chromosome), Klinefelter Syndrome 0 (XXY), and other conditions in which an irregular number of sex or autosomal chromosomes are present.
  • said condition is selected from the group consisting of: Wolf-Hirschhorn (4p-), Cri-du-chat (5p-), Williams syndrome (7ql l.23), Prader-Willi syndrome (15qll.2-ql3), Angelman syndrome (15ql l.2-ql3), Miller-Dieker syndrome (17pl3.3), Smith-Magenis syndrome (17pl l.2), DiGeorge and Velo-cardio-facial syndromes (22ql 1.2), Kallman syndrome (X ⁇ 22.3), Steroid Sulfatase Deficiency (STS) (Xp22.3), X-Linked 5 Ichthiosis (Xp22.3), and Retinoblastoma (13ql4).
  • the invention also relates to business methods for a business to provide a diagnostic comprising commercializing a diagnostic for conducting a prenatal screen for a genetic defect in a fetus, wherein said diagnostic analyzes maternal blood.
  • said business manufactures said diagnostic.
  • said diagnostic is manufactured from a polymer material. In certain embodiments the diagnostic is 0 disposable.
  • the diagnostic product analyzes maternal blood by separating fetal nucleated red blood cells (fnRBCs) from maternal enucleated red blood cells.
  • said diagnostic detects genetic "" embodiments, business methods wherein said genetic abnormalities are detected using a label that binds nucleic acids are included.
  • the label is a fluorescence label or a colorimetric label.
  • the invention also relates to business methods for isolating fetal cells from maternal blood which is conducted in exchange for a fee or a cross license.
  • Such business method involves obtaining a blood sample of a mammal (e.g., a human) who is or has been pregnant with a fetus; and enriching from the blood sample one or more fetal cells. This service can be performed in exchange for a fee or a cross license.
  • Figure 1 illustrates one embodiment of a size-based separation module.
  • Figure 2 illustrates one embodiment of a size-based separation module with three separate analytes each of a different hydrodynamic size flowing through it.
  • Figure 3 illustrates one embodiment of a size-based separation module with bypass obstacles having a cheese wedge shape.
  • Figure 4 illustrates one embodiment of a plurality of size-based separation modules in parallel with one another.
  • Figure 5 is a table illustrating separation capabilities of one embodiment of the size-based separation module.
  • Figure 6 is a picture illustrating cells captured by the capture module.
  • FIGS 7A-7C illustrate various embodiments of the capture module.
  • Figure 8 illustrates one embodiment of the capture module.
  • FIGS 9A-9D illustrate various aspects of the detection module.
  • Figures 10A-B illustrate embodiments of the business methods described herein.
  • Figures 1 IA-I IF illustrate an exemplary size-based separation module of the invention.
  • Figures 12A-F illustrate typical histograms generated by hematology analytes from a blood sample generated by the device.
  • FIGS 13A-13D illustrate various embodiments of the size-based separation module.
  • Figures 14A-14D illustrate various embodiments of the size-based separation module.
  • Figures 15A-15B illustrate cell smears of the product and waste fractions.
  • Figures 16A-16F illustrate cell smears of the product and waste fractions.
  • Figure 17 illustrates trisomy 21 pathology in an isolated fetal nucleated red blood cell.
  • Figures 18A-18D illustrate an exemplary mask employed to fabricate a size-based separation module.
  • Figures 19A-19G illustrate exemplary SEMs of a size-based separation module.
  • Figures 20A-20D illustrate one embodiment of a mask employed to fabricate a size-based separation module.
  • Figures 21A-21F illustrate exemplary SEMs of a size-based separation module.
  • Figures 22A-22F illustrate exemplary SEMs of a size-based separation module.
  • Figures 23A-23D illustrate mask and portions of a size-based separation module.
  • Figures 24A-24S illustrate exemplary SEMs of a size-based separation module.
  • Figures 25A-25C illustrate an exemplary size-based separation module.
  • the present invention provides systems, apparatuses, and methods for isolation, separation and enrichment of rare analytes (e.g., organisms, cells, and cellular components) from a sample, a fluid sample, or more preferably a whole blood sample.
  • rare analytes e.g., organisms, cells, and cellular components
  • Table 1 illustrates examples of various cell types and their concentrations and average sizes in blood in vivo.
  • the apparatus(es) herein are used for separating or enriching analytes or cell from a fluid mixture wherein said analytes or cells are at a concentration of less than 1 x 10-3, 1 x 10-4, 1 x 10-5, 1 x 10-6, or 1 x 10-6 cells/ ⁇ L of a fluid sample. In some, embodiments, the apparatus(es) herein are used for separating or enriching analytes or cells from a fluid mixture wherein said analytes or cells are at a concentration of less than 1:100, 1:1000, 1:10,000, 1:100,000, 1,000,000, 1:10,000,000 or 1:100,000,000 of all cells in a sample.
  • the present invention provides systems and apparatuses for separating and enriching one or more cells from a blood sample.
  • fetal cells can be enriched or separated by the systems and methods herein from a maternal blood sample.
  • sample Collection/Preparation The systems and methods herein involve obtaining one or more samples from a source to be analyzed.
  • a sample can be obtained from a water source, food, soil, air, animal, etc. If a solid sample is obtained (e.g., tissue sample or soil sample) such solid sample can be liquefied or solubilized prior to subsequent enrichment and/or analysis. If a gas sample is obtained, it may be liquefied or solubilized as well.
  • a sample when derived from an animal, it is preferably derived from a mammal, or more preferably from a human.
  • fluid samples derived from an animal include, but are not limited to, whole blood, sweat, tears, ear flow, sputum, lymph, bone marrow suspension, lymph, urine, saliva, semen, vaginal flow, cerebrospinal fluid, brain fluid, ascites, milk, secretions of the respiratory, intestinal and genitourinary tracts, and amniotic fluid.
  • a fluid sample derived from an animal is a blood sample.
  • the animal When analyzing a fluid sample from an animal, the animal can be, for example, a domesticated animal, such as a cow, a chicken, a pig, a horse, a rabbit, a dog, a cat, and a goat.
  • the animal is a human and the blood sample is a whole blood sample.
  • Blood samples derived from an animal can be used, for example, to screen/diagnose that animal for a condition, or when derived from a pregnant animal to perform prenatal screen.
  • the systems herein contemplate obtaining a blood sample from a pregnant human to screen a fetus for a condition or abnormality.
  • a fluid sample can be obtained from an animal using any technique known in the art. For example, for drawing blood, a syringe or other vacuum suction device may be used.
  • a fluid sample such as blood is preferably drawn into an evacuated tube or bag.
  • a fluid sample obtained from an animal is directly applied to the apparatus(es) herein, while in other embodiments, the sample is pre-treated or processed prior to being delivered to an apparatus of the invention.
  • blood drawn from an animal can be treated with one or more reagents prior to delivery to an apparatus of the invention or it maybe collected into a container that is preloaded with such reagent(s).
  • Reagents that are contemplated herein include but are not limited to, a stabilizing reagent, a preservative, a fixant, a lysing reagent, a diluent, an anti-apoptotic reagent, an anti-coagulation reagent, an anti-thrombotic reagent, magnetic property regulating reagents, a buffering reagent, an osmolality regulating reagent, a pH regulating reagent, and/or a cross-linking reagent.
  • less than 50 mL, 40 mL, 30 mL, 20 mL, 10 mL, 9 mL, 8 mL, 7 mL, 6 mL, 5 mL, 4 mL, 3 mL, 2 mL, or 1 mL of a fluid sample (e.g., blood) are obtained from the animal.
  • 1-50 mL, 2-40 mL, 3-30 mL, or 4-20 mL of blood are obtained from an individual.
  • more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 100 mL of a fluid sample are obtained from the animal.
  • samples are obtained at successive time intervals and applied to the a ⁇ paratus(s) herein for further analysis.
  • the systems and methods herein allow enrichment, separation and analysis of rare cells (e.g., fetal cells, epithelial cells, or cancer cells) from a blood sample of less than 10 mL, 5 mL or 3 mL.
  • rare cells e.g., fetal cells, epithelial cells, or cancer cells
  • the systems and methods herein can be used to enrich rare cells from larger volumes of blood such as those greater than 20 mL, 50 mL, or 100 mL. Any one of the above functions can occur within, for example, less than 1 day, or 12, 10, 11, 9, 8, 7, 6, 5, 4, 3, 2, hours or less than 60, 50, 40, 30, 20, or 10 minutes.
  • a blood sample can be obtained from a pregnant mammal or pregnant human within 24, or more preferably 20, 16, 12, 8, or more preferably 4 weeks of gestation. In other embodiments, screening and detecting fetal cells can occur after pregnancy has terminated.
  • a blood sample is combined with a lysate that selectively lyses one or more cells or components in the blood sample, e.g., fetal cells or components of a blood cell.
  • a maternal blood sample comprising fetal cells can be combined with water or another osmolality regulating agent to selectively lyse the fetal cells prior to separation and enrichment of the cellular components of the fetal cells by the systems herein.
  • a blood sample is applied to the system herein within 1 week, 6 days, 5 days, 4 days, 3 days, 2 days, 1 day, 12 hrs, 6 hrs, 3 hrs, 2 hrs, or 1 hr from when the blood is obtained.
  • a blood sample is applied to a system herein upon withdrawal from an animal.
  • the sample is applied to the systems herein at a temperature of 4-37°C. II.
  • the present invention involves enrichment of rare analytes from a sample.
  • the rare analytes are cells or cellular components.
  • rare cells include, but are not limited to, platelets, white blood cells, fetal nucleated red blood cells from maternal blood, epithelial cells, endothelial cells, progenitor cells, cancer cells, rumor cells, bacteria, viruses, protozoan cells and chimera thereof.
  • cellular components include, but are not limited to, mitochondria, a ribozyme, a lysosome, endoplasmic reticulum, a golgi, a protein, protein complexes and nucleic acids. Such separation is preferably made according to size.
  • a sample of the present invention can be a solid, gaseous, or liquid sample. Solid samples are preferably sol ⁇ bilized or liquefied prior to performing an enrichment step.
  • Enrichment can be performed using one or more of the methods and apparatuses known in the art, and in particular those disclosed in International Publication Nos. 2004/029221 and 2004/113877, U.S. Publication No. 2004/0144651, U.S. Patent Nos. 5,641,628, 5,837,115 and 6,692,952, and U.S. Application Nos. 60/703,833, 60/704,067, 60/668,415, 10/778,831, 11/071,679, and 11/146,581, all of which are incorporated herein by reference for all purposes.
  • enrichment or separation of analytes occur using one or more size-based separation modules (e.g., sieves, matrixes, electrophoretic modules); and optionally one or more capture modules (e.g., an affinity-based separation module, antibodies, and magnetic beads).
  • size-based separation modules e.g., sieves, matrixes, electrophoretic modules
  • capture modules e.g., an affinity-based separation module, antibodies, and magnetic beads.
  • Size based separation modules can separate analyte(s) from a fluidic sample based on the hydrodynamic sizes of analytes in the sample.
  • a size-based separation module comprises one or more two-dimensional arrays of obstacles which form an array of gaps.
  • Arrays of obstacles are preferably two- dimensional and can have obstacles/gaps which are preferably staggered.
  • the arrays are configured such that fluid passing through a gap in an array is divided unequally into subsequent gaps.
  • An angle of deflection can be, for example, at least 10, 20, 30, 40, 50, 60, or 70% of pitch.
  • a separation module can be adapted to deflect ⁇ nalyt ⁇ B$hStlMiaFgWiiiiii S'cIiMal size away from the array of obstacles and into a bypass channel.
  • a size-based separation module comprises more than 10, 100, 1,000, 10,000 or 100,000 obstacles.
  • the array can have, for example, more than 2, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 400, 600, 800, or 1000 rows of obstacles.
  • either gaps, obstacles, or both may be of mesoscale (less than 1 mm in one direction).
  • Figure 1 illustrates an exemplary size-based separation module.
  • Obstacles (which may be of any shape) are coupled to a flat substrate to form an array of gaps.
  • a transparent cover or lid may be used to cover the array.
  • the obstacles form a two-dimensional array with each successive row being staggered from the one above and below. Average fluid flow is designated by the field array.
  • arrays of obstacles are designed to allow passage and processing of at least 1 mL, 2 mL, 5 mL, 10 mL, 20 mL, 50 mL, 100 mL, 200 mL, or 500 mL of fluid sample per hour.
  • the flow of sample into a size-based separation module can be aligned at a small angle (flow angle) with respect to a line-of-sight of the array.
  • a size-based separation module can be coupled to an infusion pump to perfuse the sample through the obstacles.
  • the size-based separation modules herein can be configured such that analytes (e.g., cells) having a hydrodynamic size larger than a critical size migrate along the line-of-sight in the array, whereas those having a hydrodynamic size smaller than the critical size follow the flow in a different direction.
  • Hydrodynamic size of an analyte depends in part on the analyte's physical dimensions, osmolarity of the fluid medium, and the analyte's shape and deformability.
  • Figure 2 illustrates this embodiment; a first path A is the deterministic path for a first analyte having a first hydrodynamic size.
  • a second path which is more tortuous within the obstacles is the deterministic path for a second analyte having a hydrodynamic size smaller than said first analyte.
  • the second analyte is seen to flow more in the average flow direction through the array than the first analyte. It follows a deterministic path B.
  • a third analyte which has a hydrodynamic size smaller than both the first and second analytes, travels in path C, which is exclusively within the array of obstacles and the average fluid path.
  • one or more arrays obstacles are fluidly coupled in series or in parallel.
  • more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, or 100 separation modules are fluidly coupled in parallel.
  • Preferably about 10-20 of such modules are fluidly coupled in parallel.
  • Fluidly coupling more than one separation module in parallel allows for high-throughput analysis of the sample assayed (e.g., more than 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 mL of a fluid sample per hour, or more preferably more than 5 mL of fluid sample per hour).
  • Figure 3 illustrates one embodiment of multiplexing.
  • two arrays of obstacles are disposed side- by-side, e.g., as mirror images.
  • the critical size of the two arrays may be the same or different.
  • the arrays may be arranged such that the major flux flows to the boundary of the two arrays, to the edge of each array, or a combination thereof.
  • Such a duplexed array may also contain a central region disposed between the two arrays to collect particles above the critical size or to alter the sample (e.g., through buffer exchange, reaction, or labeling).
  • the central region or bypass channel is disposed within obstacles shaped like cheese wedges to prevent backflow.
  • Putting multiple arrays on one device in parallel increases sample-processing throughput, and allows for parallel processing of multiple samples or portions of the sample for different fractions or manipulations. It also increases the flow rate of fluid being processed by the separation module.
  • outlets may or may not be fluidly connected. For example, when the plurality of arrays has the 1
  • multiplexing is achieved by placing a plurality of duplex arrays on a single device.
  • a plurality of arrays, duplex or single, may be placed in any possible three- dimensional relationship to one another.
  • a multiplex device comprises two or more arrays of obstacles fluidly coupled in series. For example, an output from the major flux of one device may be coupled to an input of a second device. Alternatively, an output from the minor flux of one device may be coupled to an input of the second device.
  • multiple arrays are employed to separate an analyte over a wide size range.
  • a device can have three arrays fluidly coupled in series, but any other number of arrays may be employed.
  • the cut-off size in the first array is larger than the cut-off in the second array (adjacent and downstream from the first array), and the first array cut-off size is smaller than the maximum pass- through size of the second array. The same is true for any subsequent array.
  • the first array will deflect (remove) analytes that may clog the second array.
  • the second array will deflect (and remove) analytes that may clog the third array.
  • devices of the invention may include bypass channels that remove output from an array. Although described here in terms of removing particles above the critical size, bypass channels may also be employed to remove output from any portion of the array.
  • a separation module preferably has specificity greater than 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or 99.95% for separating an analyte of interest from a fluid sample (especially a fetal cell or epithelial cell).
  • a separation module preferably has sensitivity greater than 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or 99.95% for separating an analyte of interest from a fluid sample (especially a fetal cell or epithelial cell).
  • an analyte of interest can be concentrated from an initial concentration of less than 5, 2, 1, 5 x 10-1, 2 x 10 -1, 1 x 10 -1, 5 x 10 -2, 2 x 10 -2, 1 x 10 -2, 5 x 10 -3, 2 x 10 -3, 1 x 10 -3, 5 x 10 -4, 2 x 10 -4, 1 x 10 -4, 5 x 10 -5, 2 x 10 -5, 1 x 10 -5, 5 x 10 -6, 2 x 10 -6, 1 x 10 -61, 5 x 10 -7, 2 x 10 -7, or 1 x 10 -7 analytes/ ⁇ L fluid sample.
  • me separation module can separate an analyte (e.g., cell) that is less than 1% of all analytes in a sample or less than 1%, 0.5%, 0.2%, 0.1%, 0.05%, 0.02%, 0.01%, 0.005%, 0.002%, 0.001%, 0.0005%, 0.0002%, 0.0001%, 0.00005%, 0.00002%, 0.00001%, 0.000005%, 0.000002%, or 0.000001% of all analytes (e.g., cells) in a sample (e.g., a blood sample derived from an animal such as a human).
  • a sample e.g., a blood sample derived from an animal such as a human
  • the separation module herein can increase the concentration of such analytes of interest by transferring them from the fluid sample to an enriched sample (sometimes in a new fluid medium, such as a buffer).
  • the new concentration of the analytes in the enriched sample can be at least 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, 200,000, 500,000, 1,000,000, 2,000,000, 5,000,000, 10,000,000, 20,000,000, 50,000,000, 100,000,000, 200,000,000, 500,000,000, 1,000,000,000, 2,000,000,000, or 5,000,000,000 fold more concentrated than in the original sample.
  • 0 Inlets/Outlets can be at least 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, 200,000, 500,000, 1,000,000, 2,000,000, 5,000,000, 10,000,000, 20,000,000, 50,000,000, 100,000,000, 200,000,000, 500,000,000, 1,000,000,000, 2,000,000,000, or 5,000,000,000 fold more concentrated than in the original sample.
  • a single array of obstacles comprises two or more outlets.
  • An example of such an array is are disposed as mirror images of one another. Each array thus has a first inlet for delivering a sample and a second inlet for delivering a reagent such as a buffer to the array. Each array also has a first outlet for waste (undesirable products) and a second outlet for product (analytes of interest).
  • a size-based separation module includes a first outlet for removal of larger analytes which are directed away from the average direction of flow and a second outlet for removal of smaller analytes, which flow through the array of obstacles in the average direction of flow. Additional outlets can be provided to collect fractions during various points in the separation procedure. Furthermore, in some embodiments, more than one inlet is contemplated for a single two dimensional array.
  • the inlets can provide additional samples and/or reagents, including for example, a stabilizing reagent, a preservative, a f ⁇ xant, a lysing reagent, a diluent, an anti- apoptotic reagent, labeling reagent, an anti-coagulation reagent, an anti-thrombotic reagent, a buffering reagent, an osmolality-regulating reagent, a pH-regulating reagent, a stabilizer, a PCR reagent, a washing solution, and/or a cross-linking reagent.
  • a stabilizing reagent including for example, a stabilizing reagent, a preservative, a f ⁇ xant, a lysing reagent, a diluent, an anti- apoptotic reagent, labeling reagent, an anti-coagulation reagent, an anti-thrombotic reagent, a buffering reagent,
  • cells of interest e.g., fetal cells
  • a fluid sample comprising the cellular components of the cells of interest can pass over the separation module.
  • Cellular components of interest can be separated from other cells in a blood sample based on size using the methods disclosed herein or known in the art.
  • the device When a lysing regent is delivered to a separation device simultaneously with a sample, or when a sample is first mixed with a lysing reagent and then delivered to the separation devices herein the device may be configured to defied/separate one or more cellular organelles such as, for example, a nucleus, a mitochondria, a ribozyme, a lysosome, an endoplasmatic reticulum or a golgi.
  • a maternal blood sample is mixed with a lysing reagent that selectively lyses fetal nucleated red blood cells.
  • Such lysing reagent can be, for example, water or any other agent known in the art to selectively lyse fetal cells.
  • the blood sample is then delivered to a device herein that selectively deflects all or substantially all other analytes from the blood sample, thus enriching the concentration of organelles (e.g., nuclei) of the fetal red blood cells.
  • organelles e.g., nuclei
  • the lysing reagent is delivered in a second inlet along with the blood sample. In this embodiment, lysing occurs on the device concurrently with the separation.
  • one or more analyte(s) may be contacted with binding moieties (e.g., magnetic beads), that selectively bind the agents and increase their size (hydrodynamic size). Unbound analytes and unbound binding moieties may be removed based on their smaller size (e.g., via the "waste" outlet), while the bound analytes may be deflected and removed based on size from a different outlet.
  • binding moieties e.g., magnetic beads
  • Unbound analytes and unbound binding moieties may be removed based on their smaller size (e.g., via the "waste" outlet), while the bound analytes may be deflected and removed based on size from a different outlet.
  • Device configuration and/or geometry may also be designed in various manners.
  • circular inlets and outlets may be used. (See Figure 4 as an example of circular inlets.)
  • An entrance region devoid of obstacles is then incorporated into the design to ensure that blood cells are uniformly distributed when they reach the region where the obstacles are located.
  • the outlet is designed with an exit region devoid of obstacles to collect the exiting cells uniformly without damage.
  • a bypass channel is characterized as having a channel wider than the average gap between obstacles.
  • a bypass channel has a width equal to or larger than the largest component (largest cell) separated from the sample.
  • a bypass channel in a separation module can have a width greater than 50, 60, 70, 80, 90, 100, 110, t> _ ⁇ ⁇ ⁇
  • a main channel has a width of less than 100, 90, 80, 70, 60, 50,
  • a bypass channel can also be characterized by the obstacles that surround it or form its outer edges. Such obstacles are preferably adapted to prevent backflow or turbulence of larger cells or analytes that have reached the bypass channel.
  • bypass channel obstacles have a straight edge parallel to the main channel and flow direction.
  • a bypass channel obstacle has a cross section in the shape of a cheese wedge, wherein the pointed end of the wedge is directed downstream. (See Figure 3)
  • a single bypass channel is used, and one or more stages (arrays) share the bypass channel.
  • multiple bypass channels are used.
  • each of a plurality of stages can have its own bypass channel.
  • larger analytes e.g., fetal cells, epithelial cells, tumor cells
  • the bypass channel can be fluidly connected to an outlet, thus allowing for collection of multiple fractions from a sample.
  • Bypass channels can also be designed to maintain constant flux through a device, remove an amount of flow so the flow in the array is not perturbed, or increase the amount of flow in certain regions.
  • portions of the boundaries of arrays may be designed to generate unique flow patterns (e.g., flow-feeding, flow extracting, etc.).
  • each array thus has a maximum pass-through size that is several times larger than the cut-off size. This result may be achieved using a combination of larger gaps and smaller bifurcation ratio e.
  • the e is at most 1/2, 1/3, 1/10, 1/30, 1/100, 1/300, or 1/1000.
  • obstacle shape may affect the flow profile in the gap; however, the obstacles can be compressed in the flow direction, in order to make the array short.
  • Single stage arrays may include bypass channels as described herein.
  • Shape of obstacles Dimensions and geometry of obstacles in a size-based separation module may be uniform or may vary to form uniform or non-uniform patterns.
  • obstacles may have cylindrical, moon shape, or square cross sections.
  • obstacles are cylindrical, such that the obstacle has a round cross-section.
  • Obstacles preferably have a diameter (longest cross sectional length) of between 4-40 microns, 5-30 microns, 6-20 microns, or 7-10 microns.
  • a separation obstacle has a diameter of more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, or 50 microns.
  • a separation obstacle has a diameter of less than 100, 90, 80, 70, 60, 50, 40, 30, 20, or 10 microns.
  • the distance between obstacles may also vary. In some embodiments, the distance between obstacles is at least 10, 25, 50, 75, 100, 250, 500, or 750 ⁇ m.
  • the distance between the obstacles is at most 1000, 750, 500, 250, 100, 75, 50, or 25 ⁇ m.
  • the diameter, width, or length of the obstacles may be at least 5, 10, 25, 50, 75, 100, or 250 ⁇ m and at most 500, 250, 100, 75, 50, 25, or 10 ⁇ m.
  • the height of obstacles can also vary but preferably is equal to or greater than the height of the largest analyte being separated.
  • separation obstacles have a height ranging from 10-500 microns, 20-200 microns, 30-100 microns, or 40-50 microns.
  • separation obstacles have a height less than 1500, 1000, 500, 400, 300, 200, 100, 90, 80, 70, 60, 50, 40, 30, 20, or 10 microns.
  • a separation module has a first separation region adapted to separate an analyte (rare cell) from a fluid sample, wherein the analyte has a hydrodynamic size greater than 20, 19, 18, 17, 16, 15, 14, 13, P 1 iy y Finicron. More preferably a separation module has a first separation region adapted to separate an analyte from a fluid sample, wherein the analyte has a hydrodynamic size greater than 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, or 4 microns. More preferably a separation module has a first separation region adapted to separate an analyte from a fluid sample, wherein the analyte has a hydrodynamic size greater than 10, 9, 8, 7, or 6 microns.
  • a separation module has a first separation region and a second separation region wherein the first separation region is adapted and configured to separate an analyte with a hydrodynamic size of at least 15, 20, 25, 30, 35, or 40 microns or greater, and the second separation region is adapted to separate an analyte with a hydrodynamic size of at least 10, 15, 20, 25, 30, or 35 microns or greater wherein the critical size of the first region is greater than the critical size of the second region.
  • the first and second separation regions can be in fluid communication (fluidly coupled) with one another, such that the second separation region is downstream and in series with the first separation region.
  • the separation module can also comprise a third separation region adapted to separate components having a hydrodynamic size of at least 5, 10, 15, 20, 25, or 30, microns or greater wherein the critical size of the second region is greater than the critical size of the first region.
  • the third separation region is fluidly coupled to said second separation region and is downstream of it.
  • the separation module can optionally comprise additional regions as described above, each of which separates smaller and smaller components from a sample.
  • a separation module is adapted to direct analytes in a sample having a hydrodynamic size (e.g., diameter) of 15 microns or greater in a direction away from the flow direction of smaller components and into a main channel; a second separation region adapted to direct components in a sample having a hydrodynamic size (e.g., diameter) of 7.5 microns or greater in a direction away from the flow direction of smaller components and into a main channel; and a third separation region adapted to direct components in a sample having a hydrodynamic size (e.g., diameter) of 5 microns or greater in a direction away from the flow direction of smaller components and into a main channel.
  • the above embodiment is especially useful for separating red blood cells from a blood sample.
  • a separation module can be adjusted to separate smaller or larger components from a liquid sample.
  • a separation module can be configured to separate all components that have a dimension greater than 4 microns (e.g., fetal nucleated RBCs, nucleated RBC, and WBC).
  • a separation module is adapted to separate nucleated cells in a blood sample from non- nucleated cells.
  • a separation device can be used to concentrate a cell type or component of interest out of a fluid sample (e.g., a blood sample, urine sample, or other bodily samples) wherein the cell type or component of interest is found in vivo at a concentration of less than 50, 40, 30, 20, or 10% of all blood cells, or more preferably less than 9, 8, 7, 6, 5, 4, 3, 2, or 1% of all blood cells, or more preferably less than 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, or 0.1% of all blood cells, or more preferably less than 0.09, 0.08, 0.07, 0.06, 0.05, 0.04, 0.03, 0.02, or 0.01% of all blood cells, or more preferably less than 0.009, 0.008, 0.007, 0.006, 0.005, 0.004, 0.003, 0.002, or 0.001% of all blood cells, or more preferably less than 0.0009, 0.0008, 0.0007, 0.0006, 0.0005, 0.0004, 0.0003, 0.0002,
  • a size-based separation device can be used for separating one or more cell types from a mixed cell population (e.g., whole blood) with increased efficiency.
  • a size-based separation device preferably retains after separation >50%, >60%, >70%, >80%, >90%, >91%, >92%, >93%, > P r ii:: , i ⁇ -5 ;1 ' r ⁇ %s' >99%, >99.9% of all nucleated cells from a whole blood sample, or more preferably more than >50%, >60%, >70%, >80%, >90%, ⁇ 91%, >92%, >93%, >94%, ⁇ 95%, >96%, _ ⁇ 97%, > 98%, ⁇ 99%, >99.9% of all nucleated fetal red blood cells from a maternal blood sample.
  • the above devices can retain after separation >50%, >60%, >70%, >80%, >90%, ⁇ 91%, ⁇ 92%, ⁇ 93%, >94%, >95%, > 96%, >97%, >98%, >99%, >99.9% of all epithelial cells from a blood sample or >50%, >60%, >70%, >80%, > 90%, ⁇ 91%, ⁇ 92%, >93%, >94%, ⁇ 95%, >96%, >97%, ⁇ 98%, >99%, >99.9% of all cancer cells from a blood sample.
  • the separation module herein can also remove ⁇ 95%, >96%, >97%, ⁇ 98%, >99%, > 99.9% of all unwanted analytes (e.g., red blood cells and platelets) from a fluid sample, such as for example whole blood.
  • Figure 8 illustrates some examples of specificity and sensitivity achieved by one embodiment of the size- based separation modules herein.
  • any or all of the above steps can occur with minimal dilution of the product.
  • desired analytes of interest are retained and separated into a solution that is less than 50, 40, 30, 20, 10, 9.0, 8.0, 7.0, 6.0, 5.0, 4.5, 4.0, 3.5, 3.0, 2.5, 2.0, 1.5, 1.0, or 0.5 fold diluted from the original sample.
  • any or all of Hie above steps occur while the desired product is concentrated.
  • enriched analytes of interest maybe at least 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10,000, 100,000, 500,000 or 1,000,000 fold more concentrated in the final enriched solution than in the original sample.
  • a 10 times concentration increase of a first cell type out of a blood sample means that the ratio of first cell type/all cells in a sample is 10 times greater after the sample was applied to the apparatus herein.
  • Such concentration can take a fluid sample (e.g., a blood sample) of greater than 10 mL or 20 mL total volume comprising rare components of interest, and it can concentrate such rare component of interest into a concentrated solution of less than 5 mL total volume.
  • a fluid sample e.g., a blood sample
  • concentration can take a fluid sample (e.g., a blood sample) of greater than 10 mL or 20 mL total volume comprising rare components of interest, and it can concentrate such rare component of interest into a concentrated solution of less than 5 mL total volume.
  • reagents are added to a sample, to selectively or non-selectively increase the hydrodynamic size of analytes within the sample.
  • This modified sample is then delivered through an obstacle array of the present invention. Because the analytes are swollen and have an increased hydrodynamic size, it will be possible to use obstacle arrays with larger and more easily manufactured gap sizes.
  • the steps of swelling and size-based enrichment are performed in an integrated fashion on a device.
  • Suitable reagents include any hypotonic solution, e.g., de-ionized water, 2% sugar solution, or neat non-aqueous solvents.
  • Other reagents include beads, e.g., magnetic or polymer, that bind selectively (e.g., through antibodies or avidin-biotin) or non-selectively.
  • reagents are added to the sample to selectively or non-selectively decrease the hydrodynamic size of the analytes within the sample.
  • a non-uniform decrease in particle size in a sample will increase the difference in hydrodynamic size between analytes.
  • nucleated cells are separated from enucleated cells by hypertonically shrinking the cells. The enucleated cells can shrink to a very small particle, while the nucleated cells cannot shrink below the size of the nucleus.
  • Exemplary shrinking reagents include hypertonic solutions.
  • affinity functionalized beads are used to increase the volume of particles of interest relative to the other particles present in a sample, thereby allowing for the operation of an obstacle array with a larger and more easily manufactured gap size.
  • fluids may be driven through a device either actively or passively.
  • Fluids may be pumped using electric field, a centrifugal field, pressure-driven fluid flow, an electro-osmotic flow, direction of the field will be parallel to the walls of the channel that contains the array. Separation by Capture
  • the systems herein can optionally include one or more capture modules.
  • a capture module enriches an analyte (e.g., cell) of interest from a fluid sample by restricting or inhibiting its migration or movement or by complexing it with capture moiety.
  • the capture module utilizes affinity based separation though affinity based separation is only optional.
  • a capture module herein is highly specific and selective.
  • a capture module preferably has specificity greater than 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or 99.95% for separating an analyte of interest (e.g., a fetal cell or epithelial cell) from a fluid sample.
  • an analyte of interest e.g., a fetal cell or epithelial cell
  • a capture module preferably has sensitivity greater than 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or 99.95% for separating an analyte of interest (e.g., a fetal cell or epithelial cell) from a fluid sample.
  • an analyte of interest e.g., a fetal cell or epithelial cell
  • an analyte of interest can be separated (e.g., concentrated) by a capture module from an initial concentration of less than 5, 2, 1, 5 x 10-1, 2 x 10 -1, 1 x 10 -1, 5 x 10 -2, 2 x 10 -2, 1 x 10 -2, 5 x 10 -3, 2 x 10 -3, 1 x 10 -3, 5 x 10 -4, 2 x 10 -4, 1 x 10 -4, 5 x 10 -5, 2 x 10 -5, 1 x 10 -5, 5 x 10 -6, 2 x 10 -6, 1 x 10 -61, 5 x 10 -7, 2 x 10 -7, or 1 x 10 -7 analytes/ ⁇ L fluid sample.
  • a capture module can separate an analyte (e.g., cell) that is less than 1% of all analytes in a sample or less than 1%, 0.5%, 0.2%, 0.1%, 0.05%, 0.02%, 0.01%, 0.005%, 0.002%, 0.001%, 0.0005%, 0.0002%, 0.0001%, 0.00005%,
  • an analyte e.g., cell
  • a capture module can increase the concentration of such analytes of interest by at least 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000, 10,000, 20,000, 50,000, 100,000, 200,000, 500,000, 1,000,000, 2,000,000, 5,000,000, 10,000,000, 20,000,000, 50,000,000, 100,000,000, 200,000,000, 500,000,000, 1,000,000,000, 2,000,000,000, or 5,000,000,000 fold of their original sample concentrations.
  • a capture module comprises a channel with an array of obstacles.
  • the obstacles can be of one or more shapes.
  • the array is preferably two-dimensional, and the obstacles can be uniform or nonuniform in their order.
  • the array comprises a two-dimensional uniform array of staggered obstacles. Examples of capture modules are disclosed in International Publication No. 2004/029221 and U.S. Patent
  • capture obstacles of the present invention can have various shapes and forms to increase their surface area and/or contact time with a sample.
  • shape and size of obstacles can vary depending on the analyte being captured, sample concentration etc. The larger the analyte being captured by the capture module, the higher the capture obstacles will be.
  • the height of an obstacle is less than 1500, 1400, 1300, 1200, 1100, 1000, 900, 800, 700, 600, 500, 400, 300, 200, or 100 microns. In some embodiments, the height of an obstacle is more than 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, or 500 microns.
  • the size of the gap between obstacles will vary depending on the size of obstacle that is being captured. In some embodiments, the gap between obstacles is less than 50, 40, 30, 20, or 10 microns. In some ⁇ n m _ ⁇
  • I-" CeiSboclililnililllaip Utffefn'ffiieles is less than 10, 9, 8, 7, 6, 5, 4, 3, or 2 fold the hydrodynamic size of the analyte of interest.
  • the gap between obstacles is less than the hydrodynamic size of the analyte(s) of interest.
  • analytes of interests are trapped between obstacles.
  • the present invention contemplates arrays having gaps both wider than the analyte(s) of interest and narrower than the analytes of interest.
  • restricted gaps are dispersed either uniformly or non-uniformly throughout the array of obstacles.
  • a restricted gap is uniforrnally dispersed throughout an array of obstacles.
  • the diameter of each obstacle is less than 1500, 1400, 1300, 1200, 1100, 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 90, 80, 70, 60, 50, 40, 30, or 20 microns. In other embodiments, the diameter of each obstacle is more than 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 microns.
  • obstacles in a capture array are adapted to selectively (and optionally reversibly) bind one or more component of a fluid sample either reversibly or non-reversibly.
  • An obstacle can include, for example, one or more capture moieties having an affinity for selected cell(s) or component(s) in a fluid sample.
  • capture moiety can comprise an antibody that can specifically bind a cell or component of interest, e.g., fetal cells, red blood cells, white blood cells, platelets, epithelial cells, cancer cells, endothelial cells, or other rare cells.
  • a capture moiety comprises of an antibody (or fragment thereof) that specifically binds red blood cells or epithelial cells.
  • Such antibodies include, for example anti-CD71 and anti- EpCAM, respectively. In preferred embodiments, such antibodies are monoclonal. Other antibodies that can be included in capture moieties include, but are not limited to, anti-CD235a, anti-CD36, anti-selectins, anti- carbohydrates, anti-CD45, anti-GPA, and anti-antigen i.
  • Figure 6 illustrates an embodiment of the present invention wherein fetal cells are bound to obstacles coupled with a binding moiety (anti-CD71).
  • Figure 7A illustrates a path of a first analyte through an array of posts wherein an analyte that does not specifically bind to a post continues to migrate through the array, while an array that does bind a post is captured by the array.
  • Figure 7B is a picture of antibody coated posts.
  • Figure 7C illustrates coupling of antibodies to a substrate (e.g., obstacles, side walls, etc.) as contemplated by the present invention.
  • a capture module can have multiple regions, each of which selectively binds different cell(s) and/or component(s) of interest.
  • a system comprising a multi-region capture module will include two or more capture regions fluidly coupled to one another in series.
  • a system can comprise a plurality of separation modules fluidly coupled in parallel to increase the amount of sample being simultaneously analyzed.
  • a first cell type from a mixed cell population e.g., blood
  • a mixed cell population e.g., blood
  • the surface coating of the capture module is preferably designed to minimize nonspecific binding of cells. For example, at least 99%, 98%, 95%, 90%, 80%, or 70% of cells or analytes not capable of binding to the binding moiety are not bound to the surfaces of the capture module.
  • the selective binding in the capture module results in the separation of a specific analyte (e.g., living cell population) from a mixture of cells.
  • Obstacles are present in the device to increase surface area for analytes (e.g., cells) to interact with while in the chamber containing the obstacles so that the likelihood of binding is increased.
  • the flow conditions are such that analyte cells are very gently handled in the device without the need to deform mechanically in order to go in between the obstacles.
  • Positive pressure or negative pressure pumping or flow from a column of fluid may be employed to transport cells into and out of the microfluidic devices of the invention (e.g., capture modules).
  • IF 1 '- C T/ iiyijiMy ; -'tlii ⁇ illtS(fs ' 'Ulein retain at least 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%,
  • a capture module comprises more than 10, 100, 1,000, 10,000 or 100,000 obstacles.
  • the array can have, for example, more than 2, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 400, 600, 800, or 1000 rows of obstacles.
  • the capture module involves the use of magnetic particles, magnetic fields, and/or magnetic devices/components of devices for purposes of separating and/or enriching one or more analytes.
  • Magnetic particles of the present invention can come in any size and/or shape.
  • a magnetic particle has a diameter of less than 500 nm, 400 nm, 300 nm, 200 nm, 100 run, 90 nm, 80 nm, 70 nm, 60 nm or 50 nra
  • a magnetic particle has a diameter that is between 10-1000 nm, 20-800 nm, 30-600 nm, 40-400 nm, or 50-200 nm.
  • a magnetic particle has a diameter of more than 10 nm, 50 nm, 100 nm, 200 nm, 500 nm, 1000 nm, or 5000 nm.
  • the magnetic particles can be dry or suspended in a liquid. Mixing of a fluid sample with a second liquid medium containing magnetic particles can occur by any means known in the art including those described in U.S. Ser. No. [Not Assigned], entitled “Methods and Systems for Fluid Delivery,” filed September 15, 2005.
  • an analyte in a sample e.g., analyte of interest or not of interest
  • a sample e.g., analyte of interest or not of interest
  • Figure 8 illustrates an embodiment of this capture mechanism wherein a first analyte is coupled to antibodies that specifically bind the first analyte and wherein the antibodies are also coupled to nano-beads.
  • the 5 first analyte-nanobead complex When a mixture of analytes comprising the first analyte-nanobead complex and a second analyte are delivered into a magnetic field, the 5 first analyte-nanobead complex will be captured while other cells continue to migrate through the field. The first analyte can then be released by removing the magnetic field.
  • the magnetic field can be external or internal to the devices herein.
  • An external magnetic field is one whose source is outside a device herein (e.g., container, channel, obstacles) contemplated herein.
  • An internal magnetic field is one whose source is within a device contemplated herein. 0
  • a magnetic particle can be coupled to a binding moiety that selectively binds such analyte.
  • binding moieties include, but are not limited to, polypeptides, antibodies, nucleic acids, etc.
  • a binding moiety is an antibody that selectively binds to an analyte of interest (such as a red blood cell, a cancer cell, or an epithelial cell). Therefore, in some embodiments a 5 magnetic particle may be decorated with an antibody (preferably a monoclonal antibody) selected from the group consisting of: anti-CD71, anti-CD45, anti-EpiCAM, or any other antibody disclosed herein.
  • Magnetic particles may be coupled to any one or more of the devices herein prior to contact with a sample or may be mixed with the sample prior to delivery of the sample to the device(s).
  • the systems herein include a reservoir containing a reagent (e.g., magnetic particles) 0 capable of altering a magnetic property of the analytes captured or not captured.
  • the reservoir is preferably fiuidly coupled to one or more of the devices/modules herein.
  • a magnetic reservoir is n _
  • a magnetic reservoir is coupled to a capture module.
  • reagents include agents that oxidize or reduce transition metals, reagents that oxidize or reduce hemoglobin, magnetic beads capable of binding to the analytes, or reagents that are capable of chelating, oxidizing, or otherwise binding iron, or other magnetic materials or particles.
  • the reagent may act to alter the magnetic properties of an analyte to enable or increase its attraction to a magnetic field, to enable or increase its repulsion to a magnetic field, or to eliminate a magnetic property such that the analyte is unaffected by a magnetic field.
  • Desirable particles are those that have surface chemistry that can be chemically or physically modified, e.g., by chemical reaction, physical adsorption, entanglement, or electrostatic interaction.
  • Capture moieties can be bound to magnetic particles by any means known in the art. Examples include chemical reaction, physical adsorption, entanglement, or electrostatic interaction. The capture moiety bound to a magnetic particle will depend on the nature of the analyte targeted. Examples of capture moieties include, without limitation, proteins (such as antibodies, avidin, and cell-surface receptors), charged or uncharged polymers (such as polypeptides, nucleic acids, and synthetic polymers), hydrophobic or hydrophilic polymers, small molecules (such as biotin, receptor ligands, and chelating agents), carbohydrates, and ions.
  • proteins such as antibodies, avidin, and cell-surface receptors
  • charged or uncharged polymers such as polypeptides, nucleic acids, and synthetic polymers
  • hydrophobic or hydrophilic polymers such as small molecules (such as biotin, receptor ligands, and chelating agents), carbohydrates, and ions.
  • capture moieties can be used to specifically bind cells (e.g., bacterial, pathogenic, fetal cells, fetal blood cells, cancer cells, and blood cells), organelles (e.g., nuclei), viruses, peptides, proteins, carbohydrates, polymers, nucleic acids, supramolecular complexes, other biological molecules (e.g., organic or inorganic molecules), small molecules, ions, or combinations (chimera) or fragments thereof.
  • specific examples of capture moieties for use with fetal cells include anti-CD71, anti-CD36, anti-selectins, anti-GPA, anti-carbohydrates, and holotransferrin.
  • the capture moiety is fetal cell specific.
  • a magnetic property of an analyte may be used to effect an isolation or enrichment of the analyte relative to other constituents of a sample.
  • the isolation or enrichment may include positive selection by using a magnetic field to attract the desired analytes to a magnetic field, or it may employ negative selection to attract an analyte not of interest. In either case, the population of analytes containing the desired analytes may be collected for analysis or further processing.
  • the device used to perform the magnetic separation may be any device that can produce a magnetic field (e.g., any of the devices or reservoirs described herein).
  • a MACS column is used to effect separation of the magnetically altered analyte. If the analyte is rendered magnetically responsive by the reagent (e.g., using any reagent described herein), it may bind to the MACS column, thereby permitting enrichment of the desired analyte relative to other constituents of the sample.
  • separation may be achieved using a device, preferably a rnicrofluidic device, which contains a plurality of magnetic obstacles.
  • a device preferably a rnicrofluidic device, which contains a plurality of magnetic obstacles.
  • an analyte in the sample is modified to be magnetically responsive (e.g., through a reagent that enhances an intrinsic magnetic property of the analyte or by binding of a magnetically responsive particle to the analyte)
  • the analyte may bind to the obstacles, thereby permitting enrichment of the bound analyte.
  • negative selection may be employed.
  • the desired analyte may be rendered magnetically unresponsive, or an undesired analyte may be bound to a magnetically responsive particle.
  • an undesired analyte or analytes will be retained on the obstacles whereas the desired analyte will not, thus enriching the sample for the desired analyte.
  • « l IL I / 'l-. May ⁇ t ⁇ W ' gi ⁇ lilM'SiI'Mvice can be fabricated with either hard or soft magnetic materials, such as, but not limited to, rare earth materials, neodymium-iron-boron, ferrous-chromium-cobalt, nickel-ferrous, cobalt- platinum, and strontium ferrite. Portions of the device may be fabricated directly out of magnetic materials, or the magnetic materials may be applied to another material.
  • hard magnetic materials can simplify the design of a device because they are capable of generating a magnetic field without other actuation.
  • Soft magnetic materials enable release and downstream processing of bound analytes simply by demagnetizing the material.
  • the application process can include cathodic sputtering, sintering, electrolytic deposition, or thin-film coating of composites of polymer binder-magnetic powder.
  • a preferred embodiment is a thin film coating of micromachined obstacles (e.g., silicon posts) by spin casting with a polymer composite, such as polyimide-strontium ferrite (the polyimide serves as the binder, and the strontium ferrite as the magnetic filler).
  • an electrically conductive material is micropatterned on the outer surface of an enclosed microfiuidic device.
  • the pattern may consist of a single, electrical circuit with a spatial periodicity of approximately 100 microns.
  • the magnetic particles can be disposed uniformly throughout a device or in spatially resolved regions.
  • magnetic particles may be used to create structure within the device. For example, two magnetic regions on opposite sides of a channel can be used to attract magnetic particles to form a "bridge" linking the two regions.
  • the invention features analytical devices for the enrichment of analytes such as bacteria, viruses, fungi, cells, cellular components, viruses, nucleic acids, proteins, protein complexes, carbohydrates, and fragments or combination (chimera) thereof.
  • the devices may be used to effect various manipulations on analytes in a sample. Such manipulations include enrichment or concentration of a particle, including size-based fractionation, or alteration of the particle itself or the fluid carrying the particle.
  • the devices are employed to enrich rare analytes (rare cells) from a heterogeneous mixture or to alter a rare analytes, e.g., by exchanging the liquid in the suspension or by contacting an analyte with a reagent.
  • Such devices allow for a high degree of enrichment with limited stress on cells, e.g., reduced mechanical lysis or intracellular activation of cells.
  • the devices of the invention may be employed with any analytes whose size allows for separation in a device of the invention.
  • Devices of the invention may be employed in concentrated samples, e.g., where analytes are touching, hydrodynamically interacting with each other, or exerting an effect on the flow distribution around another analyte.
  • the method can separate white blood cells from red blood cells in whole blood from a human donor. Human blood typically contains ⁇ 45% of cells by volume. Cells are in physical contact and/or coupled to each other hydrodynamically when they flow through the array.
  • the methods of the invention may involve separating from a sample one or more analytes based on a magnetic property of the one or more analytes.
  • the sample is treated with a reagent that alters a magnetic property of the analyte.
  • the alteration may be mediated by a magnetic particle.
  • the particle e.g., a magnetic particle
  • desired analytes e.g., rare cells such cells, or bacterial cells
  • the analyte or analytes of interest may then bind to the surfaces of the device.
  • desired analytes are retained in the device through size-, shape- or deformability-based mechanisms.
  • negative selection is employed, where the desired analyte is not bound by the magnetic particles.
  • Any of the embodiments may use a MACS column for retention of an analyte (e.g., an analyte bound to a magnetic particle).
  • positive selection it is desirable that at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% of the analytes are retained in the device.
  • the surfaces of the device are desirably designed to minimize nonspecific binding of non-target analytes.
  • non-target analytes are not retained in the device.
  • the selective retention in the device can result in the separation of a specific analyte population from a mixture, e.g., blood, sputum, urine, and soil, air, or water samples.
  • Capture moieties may be bound to the magnetic particles to affect specific binding of the target analyte.
  • the magnetic particles may be disposed such as to only allow analytes of a selected size, shape, or deformability to pass through the device. Combinations of these embodiments are also envisioned.
  • a device may be configured to retain certain analytes based on size and others based on binding.
  • a device may be designed to bind more than one analyte of interest, e.g., in a serial, parallel, or interspersed arrangement of regions within the device or where two or more capture moieties are disposed on the same magnetic particle or on adjacent particles, e.g., bound to the same obstacle or region.
  • multiple capture moieties that are specific for the same analytes e.g., anti-CD71 and anti-CD36
  • Magnetic particles may be attached to obstacles present in the device (or manipulated to create obstacles) to increase surface area for analytes to interact with to increase the likelihood of binding.
  • the flow conditions are typically such that the analytes are very gently handled in the device to prevent damage.
  • Positive pressure or negative pressure pumping or flow from a column of fluid may be employed to transport analytes into and out of the microfluidic devices of the invention.
  • the device enables gentle processing, while maximizing the collision frequency of each analyte with one or more of the magnetic particles.
  • the target analytes interact with any capture moieties on collision with the magnetic particles.
  • the capture moieties can be co-localized with obstacles as a designed consequence of the magnetic field attraction in the device.
  • analytes are retained based on an inability to pass through the device, e.g., based on size, shape, or deformability.
  • Captured analytes can be released by demagnetizing the magnetic regions retaining the magnetic particles.
  • the demagnetization can be limited to selected obstacles or regions.
  • the magnetic field can be designed to be electromagnetic, enabling turn-on and turn-off off the magnetic fields for each individual region or obstacle at will.
  • the analytes can be released by disrupting the bond between the analyte and the capture moiety, e.g., through chemical cleavage or interruption of a noncovalent interaction.
  • some ferrous particles are linked to a monoclonal antibody via a DNA linker; the use of DNAse can cleave and release the analytes from the ferrous particle.
  • an antibody fragmenting protease e.g., papain
  • Increasing the sheer forces on the magnetic particles can also be used to release magnetic particles from magnetic regions, especially hard magnetic regions.
  • the captured analytes are not released and can be analyzed or further manipulated while retained.
  • a device is configured to capture and isolate cells expressing the transferrin receptor from a complex mixture.
  • Monoclonal antibodies to CD71 receptor are readily available off-the-shelf covalently "'" ferrous doped polystyrene and ferroparticles or ferro- colloids (e.g., from Miltenyi and Dynal).
  • the mAB to CD71 bound to magnetic particles is flowed into the device.
  • the antibody coated particles are drawn to the obstacles (e.g., posts), floor, and walls and are retained by the strength of the magnetic field interaction between the particles and the magnetic field.
  • the particles between the obstacles and those loosely retained with the sphere of influence of the local magnetic fields away from the obstacles are removed by a rinse (the flow rate can be adjusted such that the hydrodynamic shear stress on the analytes away from the obstacles is larger than the magnetic field strength).
  • the device can be used for isolation and detection of blood borne pathogens, bacterial and viral loads, airborne pathogens solubilized in aqueous medium, pathogen detection in food industry, and environmental sampling for chemical and biological hazards.
  • the magnetic particles can be co-localized with a capture moiety and a candidate drug compound. Capture of a cell of interest can further be analyzed for the interaction of the captured cell with the immobilized drag compound. The device can thus be used to both isolate sub-populations of cells from a complex mixture and assay their reactivity with candidate drug compounds for use in the pharmaceutical drug discovery process for high throughput and secondary cell-based screening of candidate compounds.
  • receptor-ligand interaction studies for drug discovery can be accomplished in the device by localizing the capture moiety, i.e., the receptor, on a magnetic particle, and flowing in a complex mixture of candidate ligands (or agonists or antagonists).
  • the ligand of interest is captured, and the binding event can be detected, e.g., by secondary staining with a fluorescent probe.
  • This embodiment enables rapid identification of the absence or presence of known ligands from complex mixtures extracted from tissues or cell digests or identification of candidate drug compounds.
  • a size-based separation module(s) and capture module(s) are preferably fluidly coupled.
  • a first outlet from a separation module can be fluidly coupled to a capture module.
  • the average flow rate for a sample through the capture module can be the same or different than that in the separation module. In some embodiments, the average flow rate of a sample through the capture module is more than 1, 2, 3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100 mL/hour.
  • the separation module and capture module are integrated such that a plurality of obstacles acts both to deflect certain analytes according to size and direct them in a path different than the direction of analyte(s) of interest, and also as a capture module to capture, retain, or bind certain analytes based on size, affinity, magnetism or other physical property.
  • detection and/or analysis of enriched analytes can be performed in whole or in part by a person or an analyzer.
  • enriched analytes are cells
  • the cells may be permeablized or lysed prior to detection/analysis.
  • An analyzer of the present invention can be automated for high-throughput detection/analysis of enriched analytes (e.g., rare cells from blood or biohazardous analytes). Detection and analysis by an analyzer can occur in sequential steps or can be combined into one step. Preferably, detection and analysis occur in a single step.
  • An analyzer can include any sample analyzing device known in the art, such as, for example a microscope, a microarray, cell counter, etc.
  • An analyzer can further include one or more computers, databases, memory systems, and system outputs (e.g., a computer screen or printer).
  • an analyzer comprises a computer readable medium, e.g., floppy diskettes, CD-ROMs, hard drives, flash memory, tape, or other digital storage medium, with a program code comprising a set of instructions for detection or analysis to be performed on ⁇ nriUie$lrMjites' * . -J-.
  • computer executable logic or program code of an analyzer is stored in a storage medium, loaded into and/or executed by a computer, or transmitted over some transmission medium, such as over electrical wiring or cabling, through fiber optics, or via electromagnetic radiation.
  • the computer executable logic configures the microprocessor to create specific logic circuits, Preferably, the computer executable logic performs some or all of the tasks described herein including sample preparation, enrichment, detection and/or analysis.
  • an analyzer is fiuidly coupled to a size-based separation module or a capture module.
  • enriched analytes e.g., cells of interest
  • a cell sorting apparatus allows maintaining a plurality of analytes (e.g., cells) each at an addressable site. Examples of such embodiments are disclosed in US Patent No. 6,692,952, which is incorporated herein by reference for all purposes.
  • Such module can also include an actuator adapted to selectively release a cell from the addressable site.
  • an analyzer is configured to perform a detection step such as visualizing one or more analytes of interest. Visualization of analytes of interest can occur through a transparent cover or lid which covers obstacles in the size-based separation module and/or capture module.
  • an analyzer comprises a microscope, e.g., as a light microscope, bright field light microscope, fluorescence microscope, electron microscope, etc. (preferably fiuidly coupled to a capture module).
  • an analyzer has dual scanning capabilities (e.g., using a light microscope and a fluorescence microscope).
  • an analyzer provides a three-dimensional image of enriched analytes (including analytes of interest).
  • a computer code can detect all nucleated red blood cells, including fetal nucleated red blood cells in an enriched sample.
  • an analyzer comprises an imaging device such as a camera or video camera. Such imaging device can be used to, capture an image of analytes (including analytes of interest).
  • an imaging device can capture an image of one or more fhRBC obtained from a maternal blood sample. Any of the above may be controllable by computer executable logic that images and saves images of enriched analytes.
  • an analyzer is configured to perform an analysis step such as enumerating analytes of interest, e.g., cancer cells, endothelial cell, epithelial cells, etc.
  • an analyzer can include, for example, a cell counter. The number of analytes of interest detected in a sample can be used by the analyzer or user for making a diagnosis or prognosis of a condition, e.g., cancer).
  • an analyzer compares (and optionally stores) data collected with known data points.
  • an analyzer compares (and optionally stores) data collected from case samples and control samples and performs an association study.
  • an analyzer comprises a computer executable logic that detects probe signal from one or more probes that selectively bind enriched analytes, analytes of interest, or components thereof.
  • the computer executable logic also analyzes such signals for their intensity, size, shape, aspect ratio, and/or distribution. The computer executable logic can then general a call based on results of analyzing the probe signals.
  • probes whose signals can be detected/analyzed by an analyzer include, but are not limited to, fluorescence probes (e.g., for staining chromosomes such as X, Y, 13, 18 and 21 in fetal cells), chromogenic probes, indirect immunoagents (e.g., unlabeled primary antibodies coupled to secondary enzymes), quantum dots, or other probes that emit a photon.
  • an analyzer herein detects chromagenic probes, which can provide a significantly faster read time than fluorescent probes.
  • an analyzer comprises a computer executable logic that performs karyotyping, in situ hybridization (ISH) (e.g., florescence in situ P 1 Clyg ' ⁇ laliE fftfBif oHliiilffim situ hybridization (CISH), nanogold in situ hybridization (NlSR)), restriction fragment length polymorphism (RFLP) analysis, polymerase chain reaction (PCR) techniques, flow cytometry, electron microscopy, quantum dots, and nucleic acid arrays for detection of single nucleotide polymorphisms (SNPs) or levels of RNA.
  • ISH in situ hybridization
  • CISH florescence in situ P 1 Clyg ' ⁇ laliE fftfBif oHliiilffim situ hybridization (CISH), nanogold in situ hybridization (NlSR)
  • RFLP restriction fragment length polymorphism
  • PCR polymerase chain reaction
  • flow cytometry electron microscopy
  • FISH probes or other DNA probes may be used in analyzing a single cell or component of interest.
  • Methods for using FISH to detect rare cells are disclosed in Zhen, D.K., et al. (1999) Prenatal Diagnosis, 18(11), 1181 - 1185, Cheung, MC, (1996) Nature Genetics 14, 264 - 268, which are incorporated herein by reference for all purposes.
  • Methods for using CISH are disclosed in Arnould, L. et al British Journal of Cancer (2003) 88, 1587-1591; and US Application Publication No. 2002/0019001, which are incorporated herein by reference for all purposes.
  • an analyzer when analyzing fetal cells enriched from maternal blood, is configured to detect fetal cells or components thereof. In some embodiments, analysis of fetal cells or components thereof is used to determine the sex of a fetus; the presence/absence of a genetic abnormality (e.g., chromosomal/DNA/RNA abnormality); or one or more SNPs.
  • a genetic abnormality e.g., chromosomal/DNA/RNA abnormality
  • autosomal abnormalities that can be detected by an analyzer herein include, but are not limited to, Angleman syndrome (15ql 1.2-ql3), cri-du-chat syndrome (5 ⁇ -), DiGeorge syndrome and Velo-cardiofacial syndrome (22ql 1.2), Miller-Dieker syndrome (17pl3.3), Prader-Willi syndrome (15ql l.2-ql3), retinoblastoma (13ql4), Smith-Magenis syndrome (17pll.2), trisomy 13, trisomy 16, trisomy 18, trisomy 21 (Down's syndrome), triploidy, Williams syndrome (7qll.23), and Wolf-Hirschhorn syndrome (4p-).
  • sex chromosome abnormalities that can be detected by an analyzer herein include, but are not limited to, Kallman syndrome (Xp22.3), steroid sulfate deficiency (STS) (Xp22.3), X-linked ichthiosis (Xp22.3), Klinefelter syndrome (XXY); fragile X syndrome; Turner syndrome; metafemales or trisomy X; monosomy X, etc.
  • an analyzer detects analytes (e.g., cells) stained for an antigen selected from the group consisting of ⁇ and e globins, Glycophorin A (GPA), i-antigen, and CD35.
  • analytes e.g., cells
  • an antigen selected from the group consisting of ⁇ and e globins, Glycophorin A (GPA), i-antigen, and CD35.
  • an analyzer herein can detect cells stained with anti-6 or anti- ⁇ globin antibodies, or a combination thereof.
  • a combination of ⁇ and e globins has been found on 95-100% of fNRBC from 10-24 weeks gestation. Al Mufti et al., (2001) Haematologica 85, 357-362; Choolani et al., (2003) MoI. Hum. Reprod., 9, 227-235. The e- ⁇ combination, or ⁇ globin alone, has been shown to stain fNRBC. See Bohmer, (1998); Choolani et al., (2003); Christensen et al., (2005) Fetal Diagn. Ther.
  • Antibodies to both globins are known to those skilled in the art and can be obtained from various vendors. Staining can result in a binary score such as positive or negative or in various intensities indicating amount of antigen in the analytes.
  • an analyzer detects analytes (e.g., cells) stained for GPA and/or CD71.
  • GPA is present throughout the red blood cell lineage. Thus, it can be used for identifying nucleated red blood cells, regardless of their level of maturation. GPA is thought to be found exclusively on erythroid lineage cells, and is generally found on very few circulating cells, and its presence increases during pregnancy. FACS sorting has shown a combination of CD71 and GPA to be present on at least 0.15% of mononucleated cells during pregnancy. Price et al., (1991) Am. J. Obstet Gynecol., 165, 1713-1717; Sohda et al., (1997) Prenat. Diagn., 17, 743-752.
  • an analyzer is configured to detect probes specific to CD71 and GPA.
  • an analyzer detects analytes (e.g., cells) stained for antigen-i.
  • analytes e.g., cells
  • the i-antigens were first described in the 1950s using patient polyclonal sera. Subsequent data demonstrated that the two forms of the IP" IIm ⁇ g6n]L'Kto ⁇ il ⁇ weiS:!eitpiiisdLSiS ⁇ adult and fetal cells respectively. More recent structural evidence has defined these antigens as linear and branched repeats of N-acetyllactosamine.
  • the "i” structure arises from the action of two enzymes, ⁇ -l,3-N-acetyleglucosaminyltransferase and ⁇ -l,4-galactosyltransferase. Conversion of the "i" antigen to the "I” occurs via the enzyme, ( ⁇ -l,6-N-acetyleglucosaminyltransferase.
  • the genes and chromosomal loci for these enzymes have recently been identified. Yu et al., (2001) Blood, 98, 3840-3845. And more recently, antibodies for the i-antigens have been generated. Antibodies to antigen-i have been used in early work in the field on fetal cells.
  • an analyzer comprises a computer executable logic or computer program code that provides a set of instructions identifying/characterizing rare analytes, such as rare cells, in an enriched sample.
  • the code can further provide instruction for imaging such rare analytes and storing such images.
  • the computer executable logic directs a microscope to identify rare cells (e.g., fetal cells or epithelial cells).
  • the code can further provide a set of instructions for identifying a probe that selectively binds such rare cells or components thereof, e.g., an antibody that specifically binds to e globin, ⁇ globin, fetal hemoglobin, GPA, i-antigen, CD71, EpCAM, or a combination thereof.
  • a computer executable logic provides instructions to identify fetal nucleated red blood cells in a sample; identify and enumerate components of rare cells such as chromosomes; detect probes that specifically bind chromosome 13, 18, 21, X and/or Y; detect one or more single nucleotide polymorphisms (SNPs), detect mutations in genetic sequence; detect levels of mRNA; detect levels of microRNA; etc.
  • SNPs single nucleotide polymorphisms
  • the computer executable logic can also include code that detects and/or compares probe intensities e.g., from one or more nucleic acid probes that bind fetal nucleic acids of interest (e.g., chromosomes X, Y, 13, 18, or 21); and code that generates a call according to results of analyzing the probe intensities.
  • probe intensities e.g., from one or more nucleic acid probes that bind fetal nucleic acids of interest (e.g., chromosomes X, Y, 13, 18, or 21)
  • Figures 9A-D illustrate an embodiment of the present invention.
  • Figure 9A illustrates a computer coupled to a microscope which is coupled to a slide or cell arraying module. The microscope analyzes the cells on the slide or cell array.
  • Figure 9B illustrates cells as visualized by a bright field microscope.
  • Figure 9C illustrates an XXY cell.
  • Figure 9D illustrates an image of cells in a field of vision. It also illustrates various features of the code herein to detect various levels of intensities of probes.
  • an analyzer comprises computer executable logic that controls flow rate of a sample through one or more of the various modules herein. rV.
  • the devices/modules and methods herein can be used for various applications including, but not limited to, those already disclosed.
  • the systems and methods herein can be used to perform a prenatal diagnosis.
  • a peripheral blood sample from a pregnant animal preferably a human
  • the maternal blood sample is first enriched using one or more size-based modules to separate analytes in the blood sample that have a hydrodynamic size greater than 4 microns (e.g., fetal nucleated red blood cells and maternal white blood cells) from other analytes (e.g., enucleated red blood cells and platelets).
  • the enriched sample comprising the IP" ![5fet
  • the capture modules positively select (selectively and reversibly bind) the fetal blood cells over the white blood cells.
  • Such capture modules preferably do not use magnetic particles.
  • a capture module comprises one or more arrays of obstacles covered with anti-CD71 monoclonal antibody. Cell that are captured by such device are then subjected to genetic analysis using one or more FISH assay, PCR amplification, RNA analysis, DNA analysis, etc.
  • FISH assays are used to detect the presence or absence of aneuploidy.
  • DNA or KNA analysis is used to detect one or more SNPs or or mRNA levels in the enriched fetal cells.
  • An analyzer comprising computer executable logic that detect sand analyzes fetal cells can be used to automate the system.
  • the analyzer can further comprise a microscope or a microarray.
  • the systems and methods herein can be used to perform a cancer diagnosis.
  • a peripheral blood sample or other fluid sample can be obtained from an animal suspected or known for having cancer.
  • the sample can then be flowed through one or more size-based modules to separate analytes from the sample analytes that have a hydrodynamic size greater than 8, 10, 12, 14, 16, 18, or 20 microns.
  • enriched cells are one or more cells selected from the group consisting of: an infected WBC, a stem cell, a progenitor cell, an epithelial cell, an endothelial cell, an endometrial cell, a tumor cell, and a cancer cell.
  • the enriched analytes are optionally flowed through one or more capture modules as described herein.
  • Enriched cells can then be analyzed to determine, e.g., the number of epithelial cells in the sample, the number of endothelial cells in the sample, the ratio of epithelial/endothelial in the sample, the profile of all cells greater than the critical size, the migration pattern of all cells greater than the critical size, and the change in such characteristics based on at least a second sample obtained from the same animal at a different point in time.
  • analysis can involve applying the enriched cells into one or more capture modules that selectively capture cells in a particular size range or that selectively bind cells of interest (e.g., cancer cells expressing one or more cancer markers on their surface or epithelial cells).
  • enriched cells are further analyzed to determine the presence or absence of an intracellular cancer maker. Any of the embodiments herein can further involve the use of an analyzer to detect, enumerate, and analyze the cells.
  • Neoplastic conditions whose diagnosis or prognosis is contemplated by the present invention include those selected from the group consisting of: breast cancer, skin cancer, bone cancer, prostate cancer, liver cancer, lung cancer, brain cancer, larynx cancer, gallbladder cancer, pancreas cancer, rectum cancer, parathyroid cancer, thyroid cancer, adrenal cancer, neural tissue cancer, head cancer, neck cancer, colon cancer, stomach cancer, bronchi cancer, kidney cancer, basal cell carcinoma, squamous cell carcinoma, metastatic skin carcinoma, osteo sarcoma, Ewing's sarcoma, veticulum cell sarcoma, myeloma, giant cell tumor, small-cell lung tumor, gallstone tumor, islet cell tumor, primary brain tumor, acute and chronic lymphocyctic and granulocytic tumors, hairy-cell tumor, adenoma, hyperplasia, medullary carcinoma, pheochromocytoma, mucosal neuromas, interstitial ganglioneuromas hyperplastic cornea
  • a veterinary diagnosis can involve obtaining a fluid sample (e.g., a blood sample) from an animal, which is preferably domesticated.
  • a fluid sample e.g., a blood sample
  • domesticated animals include, but are not limited to, a cow, a chicken, a pig, a horse, a rabbit, a dog, a cat, and a dog, a cat, a fish, and a goat.
  • the sample is then enriched using one or more size-based modules to separate analytes from the sample analytes that have a unique hydrodynamic size, e.g., greater than 4, 6, 8, 10, 12, 14, 16, 18, or 20 microns or a hydrodynamic size range (e.g., 6-12 microns or 8-10 microns, etc.).
  • the enriched analytes may be optionally subjected to one or more additional enrichment steps prior to their analysis.
  • the enriched analytes are optionally flowed through one or more capture modules as described herein.
  • analytes enriched from a sample are fetal cells. Such cells can then be analyzed to determine sex of a fetus or a condition in the fetus.
  • analytes enriched from a sample are pathogens.
  • pathogens that can be enriched from the animal include, but are not limited to bacteria, viruses, and protozoa. (Of course such applications are not limited to domesticated animals and also apply to humans.)
  • the cells are analyzed using a detection/analyzer as contemplated herein.
  • a detection/analyzer as contemplated herein.
  • Such analyzer can perform gram positive tests, viral load test, FISH assay, PCR assays, etc. to determine to type of pathogen infection, its source, a therapy treatment, etc.
  • analytes enriched from a sample are epithelial cells or circulating cancer cells. Such cells can be further analyzed to determine the origin of a cancer affecting the animal, severity of the condition, effectiveness of a therapy treatment, etc. d. Biodefense
  • biohazardous material e.g., a biohazardous analyte
  • Biohazardous analytes include, but are not limited to, organisms that are infectious to humans, animals or plants (e.g. parasites, viruses, bacteria, fungi, prions, rickettsia); cellular components (e.g., recombinant DNA); and biologically active agents (e.g., toxins, allergens, venoms) that may cause disease in other living organisms or cause significant impact to the environment or community.
  • Biohazardous material can be detected using the methods and systems herein in, for example, a food sample, a water sample, an air sample, a soil sample, or a biological
  • a sample analyzed by the methods and systems herein can have biohazardous analytes that are less than 1%, 0.1%, 0.01%, 0.001%, 0.0001%, 0.00001%, or 0.000001%, of all analytes in the sample.
  • a biohazardous analyte can be at an initial concentration of less than 5, 2, 1, 5 x 10-1, 2 x 10 -1, 1 x 10 -1, 5 x 10 -2, 2 x 10 -2, 1 x 10 -2, 5 x 10 -3, 2 x 10 -3, 1 x 10 -3, 5 x 10 -4, 2 x 10 - 4, 1 x 10 -4, 5 x 10 -5, 2 x 10 -5, 1 x 10 -5, 5 x 10 -6, 2 x 10 -6, 1 x 10 -61, 5 x 10 -7, 2 x 10 -7, or 1 x 10 -7 biohazardous analytes/ ⁇ L fluid sample.
  • the sample is preferably solubilized or liquefied by any means known in the art.
  • the sample analyzed for biohazardous material is flowed through one or more of the size-based separation modules herein.
  • size-based separation module increases the concentration of the biohazardous
  • -Enriched analytes can be also optionally flowed through one or more of the capture modules described herein.
  • the analyzer optionally comprises a microscope, a microarray, a cell counter, reagents for performing a Gram test, reagents for performing a viral load analysis (e.g., PCR reagents), etc. e. Research
  • the systems and methods herein can further be utilized for. performing research.
  • the systems and methods herein are used to perform association studies based on data collected from a plurality of control samples and a plurality of case samples.
  • fluid samples e.g., blood samples
  • samples from each individual can then be enriched for a first or a plurality of analytes. Such analytes are then enumerated and/or characterized.
  • Data from the above steps is collected and subsequently used to perform an association study.
  • Data is preferably stored in an electronic database.
  • the association study can be performed using a computer executable logic for identifying one or more characteristics associated with case or control samples.
  • fluid samples obtained from individuals for an association study are blood samples.
  • the analytes enriched from such samples are ones that have a hydrodynamic size greater than 4 microns, or greater than 6, 8, 10, 12, 14, or 16 microns.
  • samples obtained from individuals are enriched for one or more cells selected from the group consisting of: a RBC, a fetal RBC, a trophoblast, a fetal fibroblast, a white blood cell (WBCs), an infected WBC, a stem cell, an epithelial cell, an endothelial cell, an endometrial cell, a progenitor cell, a cancer cell, a viral cell, a bacterial cell, and a protozoan.
  • cells that are enriched are those that are found in vivo at a concentration of less than 1 x 10 -1, 1 x 10 -2, or 1 x 10 -3 cells/ ⁇ L.
  • at least 99% of the cells of interest (those enriched) from the sample are retained. Enrichment for purposes of conducting an association study can increase the concentration of a first cell type of interest by at least 10,000 fold.
  • the enriched analytes are then analyzed to determine one or more characteristics.
  • characteristics can include, e.g., the presence or absence of the analyte in the sample, quantity of an analyte, ratio of two analytes (e.g., endothelial cells and epithelial cells), morphology of one or more analytes, genotype of analyte, proteome of analyte, RNA composition of analyte, gene expression within an analyte, microRNA levels, or other characteristic traits of the analytes enriched are subsequently used to perform an association study.
  • phenotypic conditions include but are not limited to cancer, endometriosis, infection (e.g., HIV, bacterial, etc.), inflammation, ischemia, trauma, fetal abnormality, etc.
  • kits for enriching analytes from a fluid sample can include, for example, one or more separation module, optionally coupled to capture module(s) adapted to enrich fetal cells from a maternal blood sample. for enriching the fetal cells.
  • one or more capture modules are fluidly coupled to the separation module(s). Preferably both separation and capture modules are on the same substrate.
  • the kits herein can further include a set of instructions for analyzing the enriched fetal cells for making a prenatal diagnosis.
  • Examples of 5 prenatal diagnoses that can be made by the kits herein include, but are not limited to, sex of a fetus, existence of trisomy 13, trisomy 18, trisomy 21 (Down Syndrome), Turner Syndrome (damaged X chromosome), Klinefelter Syndrome (XXY) or another irregular number of sex or autosomal chromosomes, or a condition selected from the group consisting of: Wolf-Hirschhorn (4p-), Cri-du-chat (5 ⁇ -), Williams syndrome (7ql 1.23), Prader-Willi syndrome (15ql l.2-ql3), Angelman syndrome (15qll.2-ql3), Miller-Dieker syndrome (17 ⁇ l3.3), Smith-Magenis 0 syndrome (17 ⁇ l 1.2), DiGeorge and Velo-cardio-facial syndromes (22ql 1.2), Kallman syndrome (X ⁇ 22.3), Steroid Sulfatase Deficiency (STS) (X ⁇ 22.3), X-Linked Ichthiosis (X
  • kits herein comprises one or more separation module, optionally coupled to capture module(s) adapted to enrich epithelial cells or cancer cells from a blood sample.
  • Such modules preferably have sensitivity and specificity greater than 98% or greater than 99%.
  • both separation and capture modules are 5 on the same substrate.
  • the kits herein can further include one or more labeling reagents for detection of cancer origin, cancer metastasis, effectiveness of treatment, prognosis, etc.
  • Such reagents can comprise an antibody that specifically binds a cell surface cancer marker.
  • the kits herein can further include a set of instructions for analyzing the enriched fetal cells for making a cancer diagnosis.
  • cancers that can be diagnosed using the methods herein include, but are not limited to, breast 0 cancer, skin cancer, bone cancer, prostate cancer, liver cancer, lung cancer, brain cancer, larynx cancer, gallbladder cancer, pancreas cancer, rectum cancer, parathyroid cancer, thyroid cancer, adrenal cancer, neural tissue cancer, head cancer, neck cancer, colon cancer, stomach cancer, bronchi cancer, kidney cancer, basal cell carcinoma, squamous cell carcinoma, metastatic skin carcinoma, osteo sarcoma, Ewing's sarcoma, veticulum cell sarcoma, myeloma, giant cell tumor, small-cell lung tumor, gallstone tumor, islet cell tumor, primary brain tumor, acute and 5 chronic lymphocyctic and granulocytic tumors, hairy-cell tumor, adenoma, hyperplasia, medullary carcinoma, pheochromocytoma, mucosal neuromas, interstinal ganglioneuromas hyperplastic corneal nerve tumor, mar
  • a diagnostic product can include, for example, one or more size-based separation modules, one or more capture modules, a detector, an analyzer, or a combination thereof. Diagnostic Services - Prenatal
  • the business methods herein contemplate providing a prenatal screening service. Such business contemplates obtaining a blood sample from a mammal whose fetus is to be diagnosed. In some 0 embodiments, the business can either draw blood from a patient (animal) that is pregnant or receive a blood sample derived from the pregnant patient. The business herein enriches fetal cells from the blood sample and performs one or more screening test on the fetal cells to determine a condition of the fetus.
  • the business method then provides a report on the condition in exchange for a service fee.
  • the report can be either provided directly to the patient being tested, a health care provider or insurance company of the patient, or the government.
  • the business licenses a CLIA laboratory to perform the enrichment and analysis step.
  • the business performs the enrichment step and licenses a third party (e.g., a CLIA lab) to perform the analysis step (e.g., genetic testing).
  • Figure 1OA illustrates one example of the business methods disclosed herein.
  • a blood sample e.g., 16-20 mL of blood
  • the business herein or the CLIA laboratory performs one or more of the following steps: (a) flowing the sample through a size-based separation module adapted to remove red blood cells and platelets from the sample; (b) flowing the sample through a capture module that is coupled to anti-CD71 antibodies and selectively binds red blood cells over white blood cells; (c) enriching the sample using magnetic beads (e.g., coated with CD71 to repeat the enrichment step conducted before); (d) arraying the enriched cells (e.g., on a cytospin 2D slide); (e) 0 adding to the enriched cells one or more FISH probes such as those that specifically bind the X and/or Y chromosomes; (f) using an analyzer/detection module to detect the
  • Figure 1OB illustrates another embodiment of the business methods disclosed herein.
  • a sample of 32-40 mL of blood is drawn from a pregnant woman.
  • the sample is flowed through an automated size-based separation module adapted to remove red blood cells and platelets from the sample.
  • the automated separation module is coupled to a delivery apparatus.
  • the sample is then flowed through a capture module coupled to anti-GPA antibodies.
  • the sample is then enriched using magnetic beads (e.g., coated with CD71 to repeat the enrichment step 0 conducted before).
  • the remaining enriched cells are arrayed on a cytospin 2D slide with FISH probes for chromosomes X, Y, 13, 18, and 21.
  • the FISH probes are then automatically read using an analyzer/detection module as described herein or preferably a multi-sepctral imaging system to identify and categorize nucleated RBC. Finally a report is generated for the patient tested, health care provider, or insurance diagnosing a fetus with presence or absence of a fetal abnormality. 5 Diagnostic Services - Oncology
  • the business methods herein contemplate providing an oncology screening service.
  • Fluid sample(s) e.g., blood
  • the business then performs one or more enrichment steps on the sample to enrich from the sample one or more cancer cells, tumor cells, epithelial cells, endothelial cells, or other cells that indicate the presence of a cancer.
  • the above cells can be 0 enriched from a fluid sample using any of the systems and methods disclosed herein.
  • cells can be further analyzed (e.g., enumerated, assayed for specific biomarkers, etc.) to determine if the patient has or does not have cancer, original of the cancer, effective therapy for the patient, metastasis of the cancer, etc.
  • the business methods herein contemplate providing an infection screening service.
  • a fluid sample e.g., urine or blood
  • the business can draw blood or obtain the sample from the patient (animal) directly.
  • samples are delivered to the business.
  • the business then performs a screening test on the sample to enrich from the sample one or more infected cells (e.g., infected white blood cells) or infectious organisms e.g., bacteria cells, viruses, or protozoans.
  • infectious organisms can be enriched by the business using the systems and methods disclosed herein.
  • circulating pathogens examples include, viruses (e.g., HIV, flu, SARS), bacteria (E. coli, H. influenza, S. pneumonia, M. meningitis, etc.), and protozoa (Plasmodium, Trypanosoma brucei, etc.).
  • viruses e.g., HIV, flu, SARS
  • bacteria E. coli, H. influenza, S. pneumonia, M. meningitis, etc.
  • protozoa Plasmodium, Trypanosoma brucei, etc.
  • the methods herein are used to separate and detect HIV infected cells in a blood sample.
  • a report generated by the business herein can be provided directly to the patient, or to a health care provider or insurance company of the patient. Diagnostic Products
  • a business method of the present invention commercializes a diagnostic product adapted to enrich one or more analytes from a fluid sample.
  • one business method herein contemplates selling one or more of the devices/modules herein either independently or optionally in a kit with one or more reagent(s) (e.g., labeling reagents) for the separation and optional analysis of fetal cells.
  • kit can include instructions for making a prenatal diagnosis.
  • Another business method herein contemplates selling one or more of the /modules herein either independently or optionally in a kit with one or more reagent(s) (e.g., labeling reagents) for the separation and optional analysis of circulating cancer cells.
  • kit can include instructions for making a cancer diagnosis.
  • Another business method herein contemplates selling one or more of the /modules herein either independently or optionally in a kit with one or more reagent(s) (e.g., labeling reagents) for the separation and optional analysis of circulating epithelial cells.
  • kit can include instructions for making a cancer diagnosis.
  • Another business method herein contemplates selling one or more of the /modules herein either independently or optionally in a kit with one or more reagent(s) (e.g., labeling reagents) for the separation and optional analysis of circulating endothelial cells.
  • kit can include instructions for making a cancer diagnosis.
  • a diagnostic product comprises one or more separation module(s) and optionally one or more capture module(s).
  • the diagnostic product can optionally include a detection/analysis tool (e.g., a computer code or software) for detecting a condition.
  • the business method herein manufactures the diagnostic tools. In some embodiments, the business method licenses a third party to manufacture the diagnostic tools. In any of the embodiments herein, the diagnostic tool is preferably manufactured from a polymer material and is optionally disposable.
  • a business method isolates one or more analytes from a sample using the systems and methods herein in exchange for a fee or a cross license.
  • the samples can be, for example, a blood sample or other bodily sample.
  • a CLIA lab or other third party entity provides blood samples to the business to isolate rare cells such as fetal cell, epithelial cells, or cancer cells from a blood sample using the systems and methods herein.
  • the business obtains blood samples from one or more individuals and separates form such blood samples one or more therapeutic blood components such as, for example, platelets, white Z W>P ⁇ feiPJi Such blood components can then be sold by the business for a fee.
  • Such blood product can have a research and/or a therapeutic purpose. VII. Manufacturing
  • SOI wafer consists of a 100 ⁇ m thick Si(IOO) layer atop a 1 ⁇ m thick SiO2 layer on a 500 ⁇ m thick Si(IOO) wafer.
  • the SOI wafers may be exposed to high-temperature vapors of hexamethyldisilazane prior to photoresist coating.
  • UV-sensitive photoresist is spin coated on the wafer, baked for 30 minutes at 90 0 C, exposed to UV light for 300 seconds through a chrome contact mask, developed for 5 minutes in developer, and post-baked for 30 minutes at 90 0 C.
  • the process parameters may be altered depending on the nature and thickness of the photoresist.
  • the pattern of the contact chrome mask is transferred to the photoresist and determines the geometry of Hie obstacles.
  • the etching is initiated.
  • SiO2 may serve as a stopper to the etching process.
  • the etching may also be controlled to stop at a given depth without the use of a stopper layer.
  • the photoresist pattern is transferred to the 100 ⁇ m thick Si layer in a plasma etcher. Multiplexed deep etching may be utilized to achieve uniform obstacles. For example, the substrate is exposed for 15 seconds to a fluorine-rich plasma flowing SF6, and then the system is switched to a fluorocarbon- rich plasma flowing only C4F8 for 10 seconds, which coats all surfaces with a protective fihn.
  • the exposure to ion bombardment clears the polymer preferentially from horizontal surfaces and the cycle is repeated multiple times until, e.g., the SiO2 layer is reached.
  • the substrate may be exposed to an oxygen plasma prior to surface modification to create a silicon dioxide layer, to which binding moieties may be attached.
  • the substrate may then be rinsed twice in distilled, deionized water and allowed to air dry.
  • Silane immobilization onto exposed glass is performed by immersing samples for 30 seconds in freshly prepared, 2% v/v solution of 3-[(2- aminoethyl)amino] propyltrimethoxysilane in water followed by further washing in distilled, deionized water.
  • the substrate is then dried in nitrogen gas and baked. Next, the substrate is immersed in 2.5% v/v solution of glutaraldehyde in phosphate buffered saline for 1 hour at ambient temperature. The substrate is then rinsed again, and immersed in a solution of 0.5 mg/mL binding moiety, e.g., anti-CD71, in distilled, deionized water for 15 minutes at ambient temperature to couple the binding agent to the obstacles. The substrate is then rinsed twice in distilled, deionized water, and soaked overnight in 70% ethanol for sterilization.
  • binding moieties may be immobilized onto the obstacles and the surfaces of the device. Simply physio-absorption onto the surface may be the choice for simplicity and cost.
  • Another approach may use self-assembled monolayers (e.g., thiols on gold) that are functionalized with various binding moieties. Additional methods may be used depending on the binding moieties being bound and the material used to fabricate the device. Surface modification methods are known in the art.
  • certain cells may preferentially bind to the unaltered surface of a material. For example, some cells may bind preferentially to positively charged, negatively charged, or hydrophobic surfaces or to chemical groups present in certain polymers.
  • the next step involves the creation of a flow device by bonding a top layer to the microfabricated silicon containing the obstacles.
  • the top substrate maybe glass to provide visual observation of cells during and after capture. Thermal bonding or a UV curable epoxy may be used to create the flow chamber.
  • the top and bottom may also be compression fit, for example, using a silicone gasket. Such a compression fit may be reversible.
  • Other IP Cpi ⁇ , ⁇ '(ilMM&f)g.,('e-Il &&fi ⁇ iing) are known in the art. The method employed may depend on the nature of the materials used.
  • the cell depletion device may be made out of different materials. Depending on the choice of the material different fabrication techniques may also be used.
  • the device may be made out of plastic, such as polystyrene, using a hot embossing technique. The obstacles and the necessary other structures are embossed into the plastic to create the bottom surface. A top layer may then be bonded to the bottom layer. Injection molding is another approach that can be used to create such a device.
  • Soft lithography may also be utilized to create either a whole chamber made out of ⁇ oly(demethylsiloxane) (PDMS), or only the obstacles may be created in PDMS and then bonded to a glass substrate to create the closed chamber.
  • PDMS ⁇ oly(demethylsiloxane)
  • Yet another approach involves the use of epoxy casting techniques to create the obstacles through the use of UV or temperature curable epoxy on a master that has the negative replica of the intended structure.
  • Laser or other types of micromachining approaches may also be utilized to create the flow chamber.
  • Other suitable polymers that may be used in the fabrication of the device are polycarbonate, polyethylene, and poly(methyl methacrylate).
  • metals like steel and nickel may also be used to fabricate the device of the invention, e.g., by traditional metal machining.
  • Three-dimensional fabrication techniques e.g., stereolithography
  • Other methods for fabrication are known in the art.
  • FIGS 1 IA-I IF show an exemplary size-based separation module of the invention, characterized as follows:
  • Device design multiplexing 14 array duplexes; flow resistors for flow stability
  • Device fabrication The arrays and channels were fabricated in silicon using standard photolithography and deep silicon reactive etching techniques. The etch depth is 150 ⁇ m. Through holes for fluid access are made using KOH wet etching. The silicon substrate was sealed on the etched face to form enclosed fluidic channels using a blood compatible pressure sensitive adhesive (9795, 3M, St Paul, MN).
  • the device was mechanically mated to a plastic manifold with external fluidic reservoirs to deliver blood and buffer to the device and extract the generated fractions.
  • An external pressure source was used to apply a pressure of 2.4 PSI to the buffer and blood reservoirs to modulate fluidic delivery and extraction from the packaged device.
  • Example 2 A silicon device multiplexing 14 single-stage array duplexes
  • Figures 13A-13D shows an exemplary device of the invention, characterized as follows.
  • Device fabrication The arrays and channels were fabricated in silicon using standard photolithography and deep silicon reactive etching techniques. The etch depth is 150 ⁇ m. Through holes for fluid access are made using KOH wet etching. The silicon substrate was sealed on the etched face to form enclosed fluidic channels using a blood compatible pressure sensitive adhesive (9795, 3M, St Paul, MN).
  • Device packaging The device was mechanically mated to a plastic manifold with external fluidic reservoirs to deliver blood and buffer to the device and extract the generated fractions.
  • An external pressure source was used to apply a pressure of 2.4 PSI to the buffer and blood reservoirs to modulate fluidic delivery and extraction from the packaged device.
  • FIG. 14A-14D shows a schematic of the device used to separate nucleated cells from fetal cord blood.
  • Device design multiplexing 10 array duplexes; flow rp ⁇ i ⁇ tnr ⁇ fr»r flnw ⁇ staW1itv.
  • J)giQ fibrifiatMii ⁇ llrSys and channels were fabricated in silicon using standard photolithography and deep silicon reactive etching techniques. The etch depth is 140 ⁇ m. Through holes for fluid access are made using KOH wet etching.
  • the silicon substrate was sealed on the etched face to form enclosed fluidic channels using a blood compatible pressure sensitive adhesive (9795, 3M, St Paul, MN).
  • Device packaging The device was mechanically mated to a plastic manifold with external fluidic reservoirs to deliver blood and buffer to the device and extract the generated fractions.
  • An external pressure source was used to apply a pressure of 2.0 PSI to the buffer and blood reservoirs to modulate fluidic delivery and extraction from the packaged device.
  • Nucleated cells from the blood were separated from enucleated cells (red blood cells and platelets), and plasma delivered into a buffer stream of calcium and magnesium-free Dulbecco's Phosphate Buffered Saline (14190-144, Invitrogen, Carlsbad, CA) containing 1% Bovine Serum Albumin (BSA) (A8412-100ML, Sigma-Aldrich, St Louis, MO) and 2 mM EDTA (15575-020, Invitrogen, Carlsbad, CA). Measurement techniques: Cell smears of the product and waste fractions (Figure 15A-15B) were prepared and stained with modified Wright-Giemsa (WGl 6, Sigma Aldrich, St. Louis, MO).
  • BSA Bovine Serum Albumin
  • Example 4 Isolation of Fetal Cells from Maternal blood The device and process described in detail in Example 1 were used in combination with immunomagnetic affinity enrichment techniques to demonstrate the feasibility of isolating fetal cells from maternal blood.
  • the nucleated cell fraction was labeled with anti-CD71 microbeads (130-046-201, Miltenyi Biotech Inc., Auburn, CA) and enriched using the MiniMACSTM MS column (130-042-201, Miltenyi Biotech Inc., Auburn, CA) according to the manufacturer's specifications. Finally, the CD71-positive fraction was spotted onto glass slides.
  • Measurement techniques Spotted slides were stained using fluorescence in situ hybridization (FISH) techniques according to the manufacturer's specifications using Vysis probes (Abbott Laboratories, Downer's Grove, IL). Samples were stained from the presence of X and Y chromosomes. In one case, a sample prepared from a known Trisomy 21 pregnancy was also stained for chromosome 21.
  • FISH fluorescence in situ hybridization
  • each device provides the number of stages in series, the gap size for each stage, ⁇ (Flow Angle), and the number of channels per device (Arrays/Chip).
  • ⁇ Flow Angle
  • Arrays/Chip the number of channels per device
  • This device includes five stages in a single array.
  • This device includes the stages, where each stage is a duplex having a bypass channel.
  • the height of the device was 125 ⁇ m.
  • Figure 18A shows the mask employed to fabricate a size-based separation device herein.
  • Figures 18B-18D are enlargements of the portions of the mask that define the inlet, array, and outlet.
  • Figures 19A-19G show SEMs of a size-based separation module herein.
  • This device includes the stages, where each stage is a duplex having -a bypass channel. "Fins" were designed to flank the bypass channel to keep fluid from the bypass channel from re-entering the array.
  • the chip also included on-chip flow resistors, i.e., the inlets and outlets possessed greater fluidic resistance than the array. The height of the device was 117 ⁇ m.
  • Figure 2OA shows the mask employed to fabricate a size-based separation module herein.
  • Figures 20B- 2OD are enlargements of the portions of the mask that define the inlet, array, and outlet.
  • Figures 21A-21F show SEMs of a separation module used in this example.
  • This device includes the stages, where each stage is a duplex having a bypass channel. "Fins" were designed to flank the bypass channel to keep fluid from the bypass channel from re-entering the array. The edge of the fin closest to the array was designed to mimic the shape of the array.
  • the chip also included on-chip flow resistors, i.e., the inlets and outlets possessed greater fluidic resistance than the array. The height of the device was 138 ⁇ m.
  • Figure 14A shows the mask employed to fabricate the device.
  • Figures 14B-14D are enlargements of the portions of the mask that define the inlet, array, and outlet.
  • Figures 22A-22F show SEMs of a device as described above.
  • This device includes the stages, where each stage is a duplex having a bypass channel.
  • "Fins” were optimized using Femlab to flank the bypass channel to keep fluid from the bypass channel from re-entering the array.
  • the edge of the fin closest to the array was designed to mimic the shape of the array.
  • the chip also included on-chip flow resistors, i.e., the inlets and outlets possessed greater fluidic resistance than the array.
  • the height of the device was 139 or 142 ⁇ m.
  • Figure 23A shows the mask employed to fabricate the device.
  • Figures 23B-23D are enlargements of the portions of the mask that define the inlet, array, and outlet.
  • Figures 24A-24S show SEMs of the above device.
  • Example 10
  • This device includes a single stage, duplex device having a bypass channel disposed to receive output from the ends of both arravs.
  • the obstacles in this device are elliptic " 11 rrUa « « mnH p i p rl in VpmUh EMfe" r c-ii
  • the height of the device was 152 ⁇ n.
  • Figure 13A shows the mask employed to fabricate the device.
  • Figures 13B-13D are enlargements of the portions of the mask that define the inlet, array, and outlet.
  • Figures 25A-25C show SEMs of the actual device.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Hematology (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Urology & Nephrology (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Biochemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Food Science & Technology (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Cell Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Genetics & Genomics (AREA)
  • Biophysics (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Virology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Fluid Mechanics (AREA)
  • Dispersion Chemistry (AREA)
  • Clinical Laboratory Science (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Sampling And Sample Adjustment (AREA)

Abstract

L'invention concerne, d'une part, au moins un module de séparation basé sur la taille conçu pour accroître d'au moins 10000 fois une concentration d'un premier analyte dans un échantillon, ledit premier analyte possédant une concentration initiale dans cet échantillon inférieure à 1 x 10 -3 analytes/µL, et, d'autre part, un appareil d'analyse conçu pour analyser lesdits premiers analytes dans un milieu enrichi. Cette invention a aussi pour objet des méthodes d'utilisation des modules de séparation dans l'identification d'une caractéristique associée à un trouble chez un patient, par exemple, une anomalie foetale.
EP06803736A 2005-09-15 2006-09-15 Systemes et methodes d'enrichissement d'analytes Withdrawn EP1931800A4 (fr)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US11/228,462 US20070059680A1 (en) 2005-09-15 2005-09-15 System for cell enrichment
US11/229,336 US20070059781A1 (en) 2005-09-15 2005-09-15 System for size based separation and analysis
US11/229,332 US20070059719A1 (en) 2005-09-15 2005-09-15 Business methods for prenatal Diagnosis
US11/229,328 US20070059718A1 (en) 2005-09-15 2005-09-15 Systems and methods for enrichment of analytes
US11/229,037 US20070059774A1 (en) 2005-09-15 2005-09-15 Kits for Prenatal Testing
US11/228,454 US20070059716A1 (en) 2005-09-15 2005-09-15 Methods for detecting fetal abnormality
PCT/US2006/036202 WO2007035585A2 (fr) 2005-09-15 2006-09-15 Systemes et methodes d'enrichissement d'analytes

Publications (2)

Publication Number Publication Date
EP1931800A2 true EP1931800A2 (fr) 2008-06-18
EP1931800A4 EP1931800A4 (fr) 2011-06-15

Family

ID=37889398

Family Applications (1)

Application Number Title Priority Date Filing Date
EP06803736A Withdrawn EP1931800A4 (fr) 2005-09-15 2006-09-15 Systemes et methodes d'enrichissement d'analytes

Country Status (6)

Country Link
EP (1) EP1931800A4 (fr)
JP (1) JP2009509143A (fr)
AU (1) AU2006292394A1 (fr)
CA (1) CA2622745A1 (fr)
IL (1) IL190090A0 (fr)
WO (1) WO2007035585A2 (fr)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB2427468B (en) * 2005-04-05 2011-03-02 Cellpoint Diagnostics Cell separation device and method for the detection of EpCAM positive cells
DE202015002650U1 (de) 2014-05-22 2015-05-06 Felix Checa Ayet Chirurgische Prothese zur Behandlung von Leistenbrüchen

Families Citing this family (26)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8158410B2 (en) 2005-01-18 2012-04-17 Biocept, Inc. Recovery of rare cells using a microchannel apparatus with patterned posts
CN103382434B (zh) 2005-01-18 2016-05-25 生物概念股份有限公司 利用含排列成图案的立柱的微通道分离细胞
US20090136982A1 (en) 2005-01-18 2009-05-28 Biocept, Inc. Cell separation using microchannel having patterned posts
US20070196820A1 (en) 2005-04-05 2007-08-23 Ravi Kapur Devices and methods for enrichment and alteration of cells and other particles
US7695956B2 (en) 2006-01-12 2010-04-13 Biocept, Inc. Device for cell separation and analysis and method of using
EP2589668A1 (fr) 2006-06-14 2013-05-08 Verinata Health, Inc Analyse de cellules rares utilisant la division d'échantillons et les marqueurs d'ADN
US20080050739A1 (en) 2006-06-14 2008-02-28 Roland Stoughton Diagnosis of fetal abnormalities using polymorphisms including short tandem repeats
US20080026390A1 (en) * 2006-06-14 2008-01-31 Roland Stoughton Diagnosis of Fetal Abnormalities by Comparative Genomic Hybridization Analysis
FR2931141B1 (fr) * 2008-05-13 2011-07-01 Commissariat Energie Atomique Systeme microfluidique et procede pour le tri d'amas de cellules et de preference pour leur encapsulation en continu suite a leur tri
EP2350652A2 (fr) * 2008-10-10 2011-08-03 Cnrs-Dae Systeme de classement de cellules
EP2421649B1 (fr) * 2009-04-23 2018-01-24 Dublin City University Dispositif d'essai à écoulement latéral pour la surveillance de la coagulation et procédé correspondant
SG184592A1 (en) * 2011-03-18 2012-10-30 Univ Singapore Isolating target cells from a biological fluid
AU2011277178B2 (en) 2010-07-16 2016-10-20 Stichting Vumc A method of analysing a blood sample of a subject for the presence of a disease marker
JP5626727B2 (ja) * 2010-09-21 2014-11-19 国立大学法人東京農工大学 微量血液からの白血球ポピュレーション解析法
CN103547920B (zh) 2011-03-18 2016-08-17 高等教育、科学研究及疾病护理协会 分析受试者的血液样品存在疾病标记物的方法
US20150064153A1 (en) 2013-03-15 2015-03-05 The Trustees Of Princeton University High efficiency microfluidic purification of stem cells to improve transplants
EP3608022A1 (fr) 2013-03-15 2020-02-12 The Trustees of Princeton University Procédés et dispositifs de purification à haut rendement
EP2971287B1 (fr) 2013-03-15 2019-08-14 GPB Scientific, LLC Traitement microfluidique intégré de particules
JP6403190B2 (ja) * 2013-08-06 2018-10-10 旭化成株式会社 マイクロ流路構造体及び粒子の分離方法
US10976232B2 (en) 2015-08-24 2021-04-13 Gpb Scientific, Inc. Methods and devices for multi-step cell purification and concentration
CN108473932B (zh) 2015-09-09 2022-07-15 集联健康有限公司 用于样品收集、稳定化和保存的系统、方法和装置
CN210383905U (zh) 2017-01-10 2020-04-24 集联健康有限公司 一种用于从受试者收集流体样品的装置以及运输套筒
CN111065399B (zh) 2017-09-01 2023-11-28 Gpb科学有限公司 使用微流体制备治疗活性细胞的方法
WO2020184500A1 (fr) * 2019-03-14 2020-09-17 株式会社カネカ Programme, procédé de création de modèle d'apprentissage, dispositif vestimentaire, dispositif de traitement d'informations et procédé de traitement d'informations
US20230364613A1 (en) 2020-09-29 2023-11-16 Nok Corporation Leukocyte trapping apparatus
CN116312809B (zh) * 2023-04-10 2023-08-29 杭州美赛生物医药科技有限公司 一种基于抗体偶联磁珠的细胞筛选方法

Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4508625A (en) * 1982-10-18 1985-04-02 Graham Marshall D Magnetic separation using chelated magnetic ions
US5715946A (en) * 1995-06-07 1998-02-10 Reichenbach; Steven H. Method and apparatus for sorting particles suspended in a fluid
WO1998010267A1 (fr) * 1996-09-04 1998-03-12 Technical University Of Denmark Systeme a microdebit pour separation et analyse de particules
WO2002030562A1 (fr) * 2000-10-10 2002-04-18 Aviva Biosciences Corporation Système à biopuce intégrée pour la préparation et l'analyse d'échantillons
US20020119482A1 (en) * 1996-07-30 2002-08-29 Aclara Biosciences, Inc. Microfluidic method for nucleic acid purification and processing
US20030134416A1 (en) * 2001-10-11 2003-07-17 Douglas Yamanishi Methods, compositions, and automated systems for separating rare cells from fluid samples
WO2004037374A2 (fr) * 2002-10-23 2004-05-06 The Trustees Of Princeton University Procede de separation continue de particules faisant appel a des reseaux d'obstacles alignes de maniere asymetrique par rapport a des champs

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6613581B1 (en) * 1999-08-26 2003-09-02 Caliper Technologies Corp. Microfluidic analytic detection assays, devices, and integrated systems
WO2004029221A2 (fr) * 2002-09-27 2004-04-08 The General Hospital Corporation Dispositif microfluidique pour la separation de cellules et utilisations de ce dispositif

Patent Citations (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4508625A (en) * 1982-10-18 1985-04-02 Graham Marshall D Magnetic separation using chelated magnetic ions
US5715946A (en) * 1995-06-07 1998-02-10 Reichenbach; Steven H. Method and apparatus for sorting particles suspended in a fluid
US20020119482A1 (en) * 1996-07-30 2002-08-29 Aclara Biosciences, Inc. Microfluidic method for nucleic acid purification and processing
WO1998010267A1 (fr) * 1996-09-04 1998-03-12 Technical University Of Denmark Systeme a microdebit pour separation et analyse de particules
WO2002030562A1 (fr) * 2000-10-10 2002-04-18 Aviva Biosciences Corporation Système à biopuce intégrée pour la préparation et l'analyse d'échantillons
US20030134416A1 (en) * 2001-10-11 2003-07-17 Douglas Yamanishi Methods, compositions, and automated systems for separating rare cells from fluid samples
WO2004037374A2 (fr) * 2002-10-23 2004-05-06 The Trustees Of Princeton University Procede de separation continue de particules faisant appel a des reseaux d'obstacles alignes de maniere asymetrique par rapport a des champs

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See also references of WO2007035585A2 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB2427468B (en) * 2005-04-05 2011-03-02 Cellpoint Diagnostics Cell separation device and method for the detection of EpCAM positive cells
DE202015002650U1 (de) 2014-05-22 2015-05-06 Felix Checa Ayet Chirurgische Prothese zur Behandlung von Leistenbrüchen

Also Published As

Publication number Publication date
AU2006292394A1 (en) 2007-03-29
EP1931800A4 (fr) 2011-06-15
CA2622745A1 (fr) 2007-03-29
WO2007035585A2 (fr) 2007-03-29
JP2009509143A (ja) 2009-03-05
IL190090A0 (en) 2008-08-07
WO2007035585A3 (fr) 2007-11-29

Similar Documents

Publication Publication Date Title
US20070059718A1 (en) Systems and methods for enrichment of analytes
US20100273675A1 (en) Methods for detecting fetal abnormality
US20070059774A1 (en) Kits for Prenatal Testing
US20070059719A1 (en) Business methods for prenatal Diagnosis
US20070059683A1 (en) Veterinary diagnostic system
US20070059781A1 (en) System for size based separation and analysis
US20070059680A1 (en) System for cell enrichment
EP1931800A2 (fr) Systemes et methodes d'enrichissement d'analytes
US11725180B2 (en) Microfluidic sorting using high gradient magnetic fields
US20060223178A1 (en) Devices and methods for magnetic enrichment of cells and other particles
US20070196820A1 (en) Devices and methods for enrichment and alteration of cells and other particles
US10018632B2 (en) Microfluidic devices for the capture of biological sample components
EP2409151B1 (fr) Dispositif de capture de cellules circulantes
US20110212440A1 (en) Cell sorting device
JP2009511001A (ja) 細胞及びその他の粒子を磁気濃縮するためのデバイス並びに方法
US20150118728A1 (en) Apparatus and method for separating a biological entity from a sample volume
EP2641094B1 (fr) Procédé d'échange de solutions à débit de traitement élevé pour cellules et particules en suspension
WO2013126774A2 (fr) Dispositifs microfluidiques pour la capture d'espèces cibles
WO2015095395A1 (fr) Dispositifs microfluidiques pour isoler des particules
Shin et al. Inertia-activated cell sorting of immune-specifically labeled cells in a microfluidic device
JP7486823B2 (ja) 粒子捕捉システムおよび方法
JP2014534436A (ja) 血液または他の媒質からの粒子の濾過

Legal Events

Date Code Title Description
PUAI Public reference made under article 153(3) epc to a published international application that has entered the european phase

Free format text: ORIGINAL CODE: 0009012

17P Request for examination filed

Effective date: 20080328

AK Designated contracting states

Kind code of ref document: A2

Designated state(s): AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI SK TR

AX Request for extension of the european patent

Extension state: AL BA HR MK RS

RIN1 Information on inventor provided before grant (corrected)

Inventor name: SCHMIDT, MARTIN

Inventor name: TOMPKINS, RON

Inventor name: GRISHAM, MICHAEL

Inventor name: WALSH, JOHN

Inventor name: BALIS, ULYSSES

Inventor name: GRAY, DARREN

Inventor name: CARVALHO, BRUCE

Inventor name: BARBER, TOM

Inventor name: HUANG, LOTIEN, RICHARD

Inventor name: TONER, MEHMET

Inventor name: KAPUR, RAVI

RIN1 Information on inventor provided before grant (corrected)

Inventor name: SCHMIDT, MARTIN

Inventor name: TOMPKINS, RON

Inventor name: GRISHAM, MICHAEL

Inventor name: WALSH, JOHN

Inventor name: BALIS, ULYSSES

Inventor name: GRAY, DARREN

Inventor name: CARVALHO, BRUCE

Inventor name: BARBER, TOM

Inventor name: HUANG, LOTIEN, RICHARD

Inventor name: TONER, MEHMET

Inventor name: KAPUR, RAVI

REG Reference to a national code

Ref country code: HK

Ref legal event code: DE

Ref document number: 1118869

Country of ref document: HK

A4 Supplementary search report drawn up and despatched

Effective date: 20110516

STAA Information on the status of an ep patent application or granted ep patent

Free format text: STATUS: THE APPLICATION IS DEEMED TO BE WITHDRAWN

18D Application deemed to be withdrawn

Effective date: 20111220