WO2007147018A1 - Analysis of rare cell-enriched samples - Google Patents

Analysis of rare cell-enriched samples Download PDF

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Publication number
WO2007147018A1
WO2007147018A1 PCT/US2007/071149 US2007071149W WO2007147018A1 WO 2007147018 A1 WO2007147018 A1 WO 2007147018A1 US 2007071149 W US2007071149 W US 2007071149W WO 2007147018 A1 WO2007147018 A1 WO 2007147018A1
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Prior art keywords
cells
cell
sample
cancer
rare
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PCT/US2007/071149
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French (fr)
Inventor
Martin Fuchs
Ravi Kapur
Mehmet Toner
Zihua Wang
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Cellpoint Diagnostics, Inc.
Living Microsystems, Inc.
The General Hospital Corporation
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Application filed by Cellpoint Diagnostics, Inc., Living Microsystems, Inc., The General Hospital Corporation filed Critical Cellpoint Diagnostics, Inc.
Publication of WO2007147018A1 publication Critical patent/WO2007147018A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5091—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing the pathological state of an organism
    • 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
    • G01N1/405—Concentrating samples by adsorption or absorption
    • 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
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • 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
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N2015/1006—Investigating individual particles for cytology
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N15/00—Investigating characteristics of particles; Investigating permeability, pore-volume or surface-area of porous materials
    • G01N15/10—Investigating individual particles
    • G01N2015/1029—Particle size
    • 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

Definitions

  • maternal serum alpha- fetoprotein, and levels of unconjugated estriol and human chorionic gonadotropin are used to identify a proportion of fetuses with Down's syndrome, however, these tests are not one hundred percent accurate.
  • ultrasonography is used to determine congenital defects involving neural tube defects and limb abnormalities, but is useful only after fifteen weeks' gestation
  • fetal cells in the maternal circulation and cancer cells in patients' circulation offers an opportunity to develop prenatal diagnostics that obviates the risks associated with invasive diagnostic procedure, and cancer diagnostics that allow for detecting cancer at earlier stages in the development of the disease.
  • fetal cells and cancer cells are rare as compared to the presence of other cells in the blood. Therefore, any proposed analysis of fetal cells or cancer cells to diagnose fetal abnormalities or cancers, respectively, requires enrichment of fetal cells and cancer cells. Enriching fetal cells from maternal peripheral blood and cancer cells from patient's blood is challenging, time intensive and any analysis derived there from is prone to error. The present invention addresses these challenges.
  • the methods of the present invention allow for enrichment of rare cell populations, particularly fetal cells or cancer cells, from peripheral blood samples which enrichment yields cell populations sufficient for reliable and accurate clinical diagnosis.
  • the methods of the present invention also provide analysis of said enriched rare cell populations whereby said methods allow for detection, diagnosis and prognosis of conditions or diseases, in particular fetal abnormalities or cancer.
  • the present invention relates to methods for determining a condition in a patient or a fetus by analyzing nucleic acids from cells of samples obtained from patient or maternal samples, respectively.
  • the methods include enriching the sample for cells that are normally present in vivo at a concentration of less than 1 in 100,000, obtaining the nuclei from the enriched sample cells and detecting substantially in real time one or more nucleic acids molecules.
  • the sample can be enriched for a variety of cells including fetal cells, epithelial cells, endothelial cells or progenitor cells, and the sample can be obtained from a variety of sources including 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 or genitourinary tracts fluid.
  • the sample is a blood sample.
  • samples are enriched in fetal cells, and the condition that can be determined by the methods of the invention can be a genetic or pathologic condition.
  • genetic conditions that can be determined in one or more fetal cells include trisomy 13, trisomy 18, trisomy 21, Klinefelter Syndrome, dup(17)(pl l.2pl l.2) syndrome, Down syndrome, Pelizaeus-Merzbacher disease, dup(22)(ql l.2ql l.2) syndrome, Cat eye syndrome, Cri-du-chat syndrome, Wolf-Hirschhorn syndrome, Williams-Beuren syndrome, Chare ot-Marie- Tooth disease, neuropathy with liability to pressure palsies, Smith-Magenis syndrome, neurofibromatosis, Alagille syndrome, Velocardiofacial syndrome, DiGeorge syndrome, steroid sulfatase deficiency, Kallmann syndrome, microphthalmia with linear skin defects, Adrenal hypoplasia, Gly
  • the P conditions that can be determined in one or more fetal cells include acute lymphoblastic leukemia, acute or chronic lymphocyctic or granulocytic tumor, acute myeloid leukemia, acute promyelocytic leukemia, adenocarcinoma, adenoma, adrenal cancer, basal cell carcinoma, bone cancer, brain cancer, breast cancer, bronchi cancer, cervical dysplasia, chronic myelogenous leukemia, colon cancer, epidermoid carcinoma, Ewing's sarcoma, gallbladder cancer, gallstone tumor, giant cell tumor, glioblastoma multiforma, hairy- cell tumor, head cancer, hyperplasia, hyperplastic corneal nerve tumor, in situ carcinoma, intestinal ganglioneuroma, islet cell tumor, Kaposi's sarcoma, kidney cancer, larynx cancer, leiomyomater tumor, liver cancer, lung cancer, lymphomas, malignant carcinoid, malignant hypercalcemia, malignant
  • the step of enriching a sample for a cell type includes flowing a sample or a fraction of a sample through an array of obstacles that separate the cells according to size by selectively directing cells of a predetermined size into a first outlet and directing cells of another predetermined size to a second outlet, and flowing the sample or sample fraction through one or more magnetic fields that retain paramagnetic components.
  • the method further comprises ejecting the nuclei from the cells in the sample by applying hyperbaric pressure to the sample, and flowing the sample or a sample fraction through an array of obstacles that are coated with antibodies that bind one or more cell populations in the sample.
  • the methods of the invention can be used to determine a fetal abnormality from amniotic fluid obtained from a pregnant female.
  • an amniotic fluid sample is obtained from the pregnant female and is enriched for fetal cells.
  • one or more nucleic acid molecules are obtained from the enriched cells, and are amplified on a bead. Up to 100 bases of the nucleic acid are obtained, and in some embodiments up to one million copies of the nucleic acid are amplified.
  • the amplified nucleic acids can also be sequenced.
  • the nucleic acid is genomic DNA.
  • the fetal abnormality can be determined from a sample that is obtained from a pregnant female and enriched for fetal cells by subjecting the sample to the enrichment procedure that includes separating cells according size, and flowing it through a magnetic field.
  • the size-based separation involves flowing the sample through an array of obstacles that directs cells of a size smaller than a predetermined size to a first outlet, and cells that are larger than a predetermined size to a second outlet.
  • the enriched sample is also subjected to one or more magnetic fields and hyperbaric pressure, and in some embodiments it is used for genetic analyses including SNP detection, RNA expression detection and sequence detection.
  • one or more nucleic acid fragments can be obtained from the sample that has been subjected to the hyperbaric pressure, and the nucleic acid fragments can be amplified by methods including multiple displacement amplification (MDA), degenerate oligonucleotide primed PCR (DOP), primer extension pre-amplification (PEP) or improved-PEP (I-PEP).
  • MDA multiple displacement amplification
  • DOP degenerate oligonucleotide primed PCR
  • PEP primer extension pre-amplification
  • I-PEP improved-PEP
  • the method for determining a fetal abnormality can be performed using a blood sample obtained form a pregnant female.
  • the sample can be enriched for fetal cells by flowing the sample through an array of obstacles that directs cells of a size smaller than a predetermined size to a first outlet, and cells that are larger than a predetermined size to a second outlet, and performing a genetic analysis e.g. SNP detection, RNA expression detection and sequence detection, on the enriched sample.
  • the enriched sample can comprise one or more fetal cells and one or more nonfetal cells.
  • kits providing the devices and reagents for performing one or all of the steps for determining the fetal abnormalities. These kits may include any of the devices or reagents disclosed singly or in combination.
  • the genetic analysis of SNP detection or RNA expression can be performed using microarrays. SNP detection can also be accomplished using molecular inverted probes(s), and in some embodiments, SNP detection involves highly parallel detection of at least 100,000 SNPs. RNA expression detection can also involve highly parallel interrogation of at least 10,000 transcripts.
  • sequence detection can involve determining the sequence of at least 50,000 bases per hour, and sequencing can be done in substantially real time or real time and can comprise adding a plurality of labeled nucleotides or nucleotide analogs to a sequence that is complementary to that of the enriched nucleic acid molecules, and detecting the incorporation.
  • labels can be used in the sequence detection step and include chromophores, fluorescent moieties, enzymes, antigens, heavy metal, magnetic probes, dyes, phosphorescent groups, radioactive materials, chemiluminescent moieties, scattering or fluorescent nanoparticles, Raman signal generating moieties, and electrochemical detection moieties.
  • Methods that include sequence detection can be accomplished using sequence by synthesis and they may include amplifying the nucleic acid on a bead.
  • the methods can include amplifying target nucleic acids from the enriched sample(s) by any method known in the art but preferably by multiple displacement amplification (MDA), degenerate oligonucleotide primed PCR (DOP), primer extension pre-amplification (PEP) or improved-PEP (I-PEP).
  • MDA multiple displacement amplification
  • DOP degenerate oligonucleotide primed PCR
  • PEP primer extension pre-amplification
  • I-PEP improved-PEP
  • the genetic analyses can also be performed on a control sample or reference sample, and in some instances, the control sample can be a maternal sample.
  • a method for detecting cancer in a subject includes enriching a sample from the subject (e.g., a blood sample) for rare cells through an array of obstacles coated with antibodies that specifically bind to one or more cell populations in the sample to generate a rare cell-enriched sample. The presence or absence of a rare cell nucleic acid in the rare cell-enriched sample is then detected, where the presence of the rare cell nucleic acid indicates the presence of a cancer in the subject.
  • the sample is treated with a stabilizer, a preservative, or a fixant prior to enrichment for rare cells.
  • a rare cell nucleic acid to be detected is from a circulating tumor cell, an epithelial cell, an endothelial cell, or a progenitor stem cell.
  • the expression or lack thereof of any of the genes listed in figure 5 is detected in the rare cell-enriched sample.
  • the expression level of EGFR, EGF, EpCAM , MUC-I, HER-2, or Claudin-7 is determined in the rare cell-enriched sample.
  • the presence or absence of a mutation in the gene is also determined.
  • the methods described herein can detect the presence of any one of various cancers in a subject, including, but not limited to, is acute lymphoblastic leukemia, acute or chronic lymphocyctic or granulocytic tumor, acute myeloid leukemia, acute promyelocytic leukemia, adenocarcinoma, adenoma, adrenal cancer, basal cell carcinoma, bone cancer, brain cancer, breast cancer, bronchi cancer, cervical dysplasia, chronic myelogenous leukemia, colon cancer, epidermoid carcinoma, Ewing's sarcoma, gallbladder cancer, gallstone tumor, giant cell tumor, glioblastoma multiforma, hairy-cell tumor, head cancer, hyperplasia, hyperplastic corneal nerve tumor, in situ carcinoma, intestinal ganglioneur
  • a rare-cell enriching step includes flowing a sample or a fraction thereof through one or more magnetic fields that selectively retain paramagnetic components.
  • the method includes (i) applying hyperbaric pressure to a sample from the subject or a fraction thereof prior to enriching the sample for rare cells, to selectively eject nuclei from the rare cells; or (ii) applying hyperbaric pressure to the enriched sample or a fraction thereof to selectively eject nuclei of the rare cells.
  • the antibodies coated on the array of obstacles binds to the rare cells to be enriched, so that the enriched sample is contained on the array.
  • the array can be coated with one or more antibodies against EpCAM, E-cadherin, or Muc-1, which bind to rare cells of interest.
  • the antibodies coated on the array bind to cells in the sample other than the rare cells to be enriched, so the enriched sample corresponds to the eluate from the array of antibody-coated obstacles.
  • the array can be coated with one or more antibodies against CD71, CD235a, CD36, selectin, CD45, or GPA.
  • the array is coated with two different antibodies.
  • the method is performed on a sample obtained from a subject that has undergone cancer therapy. In other embodiments, the method is performed on a sample obtained from a subject that has not undergone cancer therapy.
  • the method also includes flowing a sample or a rare cell-enriched sample through an array of obstacles that selectively directs cells larger than a predetermined size in to a first outlet and cells equal to or smaller than said predetermined size to a second outlet.
  • the predetermined size can be the size of a red blood cell, a white blood cell, a circulating tumor cell, an epithelial cell, an endothelial cell, or a progenitor stem cell. In some embodiments, the predetermined size can be about 2 to about
  • described herein is another method for detecting cancer in a subject.
  • the method includes enriching a sample from a subject for rare cells by flowing the sample through an array of obstacles that selectively directs cells larger than a predetermined size in to a first outlet and cells equal to or smaller than said predetermined size to a second outlet, wherein said sample is obtained at a time point from said subject and said rare cells in said sample are in a concentration of less than 1 in 100,000 cells, and detecting the presence or absence of a rare cell nucleic acid in the rare-cell enriched sample, where the presence of the rare cell nucleic acid indicates the presence of cancer in t subject [0017]
  • described herein is a method for determining cancer treatment efficacy in a patient.
  • the method includes (i) enriching, for epithelial cells, each of a time series of blood samples from the patient by flowing each blood sample in the set through an array of obstacles coated with one or more antibodies that specifically bind to epithelial cells to obtain a set of epithelial cell-enriched blood samples,
  • the time series of blood samples includes at least a first blood sample obtained at the beginning of the patient's cancer treatment and two more blood samples collected subsequent to the collection of the first blood sample.
  • the expression level of at least one gene expressed in epithelial cells and not expressed in other cells present in blood i.e., a rare cell-associated gene
  • a rare cell-associated gene is determined in each of the time series blood samples to obtain a temporal expression profile for the rare cell associated gene.
  • determining the expression level of the rare cell-associated gene is performed by determining an mRNA expression level for the gene.
  • the method includes detecting the expression of a gene listed in figure 5, e.g., EGFR, EGF, EpCAM, MUC-I, HER-2, or Claudin-7, or any combination thereof.
  • the method also includes detecting the presence or absence of a mutation in any of the foregoing genes. [0018] In a further aspect, described herein is a kit for detecting cancer cells in a subject.
  • the kit includes a device comprising an array of obstacles coated with antibodies that specifically bind to one or more cell populations and a set of reagents for detecting the expression of a gene identified in Figure 5, e.g., EGFR, EGF, EpCAM, MUC-I, HER-2, or Claudin-7, or any combination thereof.
  • a gene identified in Figure 5 e.g., EGFR, EGF, EpCAM, MUC-I, HER-2, or Claudin-7, or any combination thereof.
  • Figures 1A-1D illustrate embodiments of a size-based separation module.
  • FIGS 2A-2C illustrate one embodiment of an affinity separation module.
  • Figure 3 illustrate one embodiment of a magnetic separation module.
  • Figure 4 illustrates one example of a multiplex enrichment module of the present invention.
  • Figure 5 illustrates exemplary genes that can be analyzed from enriched cells, such as epithelial cells, endothelial cells, circulating tumor cells, progenitor cells, etc.
  • Figure 6 illustrates one embodiment for genotyping rare cell(s) or rare DNA using, e.g., Affymetrix DNA microarrays.
  • Figure 7 illustrates one embodiment for genotyping rare cell(s) or rare DNA using, e.g., Illumina bead arrays.
  • Figure 8 illustrates one embodiment for determining gene expression of rare cell(s) or rare DNA using, e.g., Affymetrix expression chips.
  • Figure 9 illustrates one embodiment for determining gene expression of rare cell(s) or rare DNA using, e g , Illumina bead arrays
  • Figure 10 illustrates one embodiment for high-throughput sequencing of rare cell(s) or rare DNA using, e g., single molecule sequence by synthesis methods (e.g , Helicos BioSciences Corporation)
  • Figure 11 illustrates one embodiment for high-throughput sequencing of rare cell(s) or rare DNA using, e g., amplification of nucleic acid molecules on a bead (e g., 454 Lifesciences).
  • Figure 12 illustrates one embodiment for high-throughput sequencing of rare cell(s) or rare DNA using, e g., clonal single molecule arrays technology (e g., Solexa, Inc )
  • Figure 13 illustrates one embodiment for high-throughput sequencing of rare cell(s) or rare DNA using, e.g., single base polymerization using enhanced nucleotide fluorescence (e.g , Genovoxx GmbH).
  • enhanced nucleotide fluorescence e.g , Genovoxx GmbH
  • Figures 14A-14D illustrate one embodiment of a device used to separate cells according to their size.
  • Figures 15A-15B illustrate cell smears of first and second outlet (e.g , product and waste) fractions.
  • Figures 16A-16F illustrate isolation of CD-71 positive population from a nucleated cell fraction
  • Figure 17 illustrates trisomy 21 pathology
  • Figure 18 illustrates performance of cell separation module
  • Figure 19 illustrates histograms representative of cell fractions resulting from cell separation module described herein
  • Figure 20 illustrates cytology of products from cell separation module
  • Figure 21 illustrates epithelial cells bound to obstacles and floor in a separation / enrichment module
  • Figure 22 illustrates a process for analyzing enriched epithelial cells for EGFR mutations
  • Figure 23 illustrates a method for generating sequencing templates, e.g , from EGFR mRNA
  • Figure 24 illustrates exemplary allele specific reactions showing mutations
  • Figure 25 illustrates exemplary signals from an allele-specific genotyping assay
  • Figure 26A illustrates BCKDK expressed in leukocytes and H 1650 cells
  • Figure 26B illustrates EGFR expression profile
  • the present invention provides systems, apparatus, and methods to detect the presence of or abnormalities of rare analytes or cells, such as hematopoietic bone marrow pregemtor cells, endothelial cells, fetal cells circulating m maternal peripheral blood, epithelial cells, or circulating tumor cells in a sample of a mixed analyte or cell population (e g , maternal peripheral blood samples)
  • rare analytes or cells such as hematopoietic bone marrow pregemtor cells, endothelial cells, fetal cells circulating m maternal peripheral blood, epithelial cells, or circulating tumor cells in a sample of a mixed analyte or cell population (e g , maternal peripheral blood samples)
  • Samples containing rare cells can be obtained from any animal in need of a diagnosis or prognosis or from an animal pregnant with a fetus in need of a diagnosis or prognosis
  • a sample can be obtained from animal suspected of being pregnant, pregnant, or that has been pregnant to detect the presence of a fetus or fetal abnormality
  • a sample is obtained from an animal suspected of having, having, or an animal that had a disease or condition (e g cancer)
  • a disease or condition e g cancer
  • Animal of the present invention can be a human or a domesticated animal such as a cow, chicken, pig, horse, rabbit, dogs, cat, or goat.
  • Samples derived from an animal or human can include, e.g., 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 or genitourinary tracts fluid.
  • any technique known in the art may be used, e.g. a syringe or other vacuum suction device.
  • a blood sample can be optionally pre-treated or processed prior to enrichment.
  • pre- treatment steps include the addition of a reagent such as a stabilizer, a preservative, a fixant, a lysing reagent, a diluent, an anti-apoptotic reagent, an anti-coagulation reagent, an anti-thrombotic reagent, magnetic property regulating reagent, a buffering reagent, an osmolality regulating reagent, a pH regulating reagent, and/or a cross- linking reagent.
  • a reagent such as a stabilizer, a preservative, a fixant, a lysing reagent, a diluent, an anti-apoptotic reagent, an anti-coagulation reagent, an anti-thrombotic reagent, magnetic property regulating reagent, a buffering reagent, an osmolality regulating reagent, a pH regulating reagent, and/or a cross- linking reagent.
  • a preservative such an anti-coagulation agent and/or a stabilizer is often added to the sample prior to enrichment. This allows for extended time for analysis/detection.
  • a sample such as a blood sample
  • a sample can be enriched and/or analyzed under any of the methods and systems 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 the time the sample is obtained.
  • a blood sample can be combined with an agent that selectively lyses one or more cells or components in a blood sample.
  • fetal cells can be selectively lysed releasing their nuclei when a blood sample including fetal cells is combined with deionized water. Such selective lysis allows for the subsequent enrichment of fetal nuclei using, e.g., size or affinity based separation.
  • platelets and/or enucleated red blood cells are selectively lysed to generate a sample enriched in nucleated cells, such as fetal nucleated red blood cells (friRBCs), maternal nucleated blood cells (mnBC), epithelial cells and circulating tumor cells.
  • fnRBCs can be subsequently separated from mnBCs using, e.g., antigen-i affinity or differences in hemoglobin
  • the amount can vary depending upon animal size, its gestation period, and the condition being screened. In some embodiments, up to 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 mL of a sample is obtained. In some embodiments, 1-50, 2-40, 3-30, or 4-20 mL of sample is obtained. In some embodiments, 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 sample is obtained.
  • a blood sample can be obtained from a pregnant animal or human within 36, 24, 22, 20, 18, 16, 14, 12, 10, 8, 6 or 4 weeks of gestation or even after a pregnancy has terminated.
  • a sample e.g. blood sample
  • can be enriched for rare analytes or rare cells e.g. fetal cells, epithelial cells or circulating tumor cells
  • rare cells e.g. fetal cells, epithelial cells or circulating tumor cells
  • the enrichment increases the concentration of rare cells or ratio of rare cells to non-rare cells in the sample.
  • enrichment can increase concentration of an analyte of interest such as a fetal cell or epithelial cell or CTC by a factor of at least 2, 4, 6, 8, 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 over its concentration in the original sample.
  • the initial concentration of the fetal cells may be about 1 : 50,000,000 and it may be increased to at least 1:5,000 or 1:500.
  • Enrichment can also increase concentration of rare cells in volume of rare cells / total volume of sample (removal of fluid).
  • a fluid sample e.g., a blood sample
  • 10O mL total volume comprising rare components of interest
  • Enrichment can also increase concentration of rare cells in volume of rare cells / total volume of sample (removal of fluid).
  • a fluid sample e.g., a blood sample
  • 10O mL total volume comprising rare components of interest
  • Enrichment can occur using one or more types of separation modules. Several different modules are described herein, all of which can be fluidly coupled with one another in the series for enhanced performance. [0056] In some embodiments, enrichment occurs by selective lysis as described above.
  • enrichment of rare cells occurs using one or more size-based separation modules.
  • size-based separation modules include filtration modules, sieves, matrixes, etc.
  • size-based separation modules contemplated by the present invention include those disclosed in International Publication No. WO 2004/113877.
  • Other size based separation modules are disclosed in International Publication No. WO 2004/0144651.
  • a size-based separation module comprises one or more arrays of obstacles forming a network of gaps.
  • the obstacles are configured to direct particles as they flow through the array/network of gaps into different directions or outlets based on the particle's hydrodynamic size.
  • nucleated cells or cells having a hydrodynamic size larger than a predetermined size e.g., 8 ⁇ m
  • a predetermined size e.g. 8 ⁇ m
  • the enucleated cells or cells having a hydrodynamic size smaller than a predetermined size e.g., 8 ⁇ m
  • An array can be configured to separate cells smaller or larger than a predetermined size by adjusting the size of the gaps, obstacles, and offset in the period between each successive row of obstacles.
  • obstacles or gaps between obstacles can be up to 10, 20, 50, 70, 100, 120, 150, 170, or 200 ⁇ m in length or about 2, 4, 6, 8 or 10 ⁇ m in length.
  • an array for size-based separation includes more than 100, 500, 1,000, 5,000, 10,000, 50,000 or 100,000 obstacles that are arranged into more than 10, 20, 50, 100, 200, 500, or 1000 rows.
  • obstacles in a first row of obstacles are offset from a previous (upstream) row of obstacles by up to 50% the period of the previous row of obstacles.
  • obstacles in a first row of obstacles are offset from a previous row of obstacles by up to 45, 40, 35, 30, 25, 20, 15 or 10% the period of the previous row of obstacles.
  • a separation module includes multiple discrete arrays of obstacles fluidly coupled such that they are in series with one another. Each array of obstacles has a continuous offset. But each subsequent (downstream) array of obstacles has an offset that is different from the previous
  • each subsequent array of obstacles has a smaller offset that the previous array of obstacles.
  • a plurality of arrays can be fluidly coupled in series or in parallel, (e.g., more than 2, 4, 6, 8, 10, 20, 30, 40, 50). Fluidly coupling separation modules (e.g., arrays) in parallel allows for high-throughput analysis of the sample, such that at least 1, 2, 5, 10, 20, 50, 100, 200, or 500 mL per hour flows through the enrichment modules or at least 1, 5, 10, or 50 million cells per hour are sorted or flow through the device.
  • Figure IA illustrates an example of a 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 shifted horizontally with respect to the previous row of obstacles, where the array of obstacles directs component having a hydrodynamic size smaller than a predetermined size in a first direction and component having a hydrodynamic size larger that a predetermined size in a second direction.
  • the predetermined size of an array of obstacles can be get at 6-12 ⁇ m or 6-8 ⁇ m.
  • the predetermined size of an array of obstacles can be get at between 4-10 ⁇ m or 6-8 ⁇ m.
  • the flow of sample into the array of obstacles can be aligned at a small angle (flow angle) with respect to a line-of-sight of the array.
  • the array is coupled to an infusion pump to perfuse the sample through the obstacles.
  • the flow conditions of the size-based separation module described herein are such that cells are sorted by the array with minimal damage. This allows for downstream analysis of intact cells and intact nuclei to be more efficient and reliable.
  • a size-based separation module comprises an array of obstacles configured to direct cells larger than a predetermined size to migrate along a line-of-sight within the array (e.g. towards a first outlet or bypass channel leading to a first outlet), while directing cells and analytes smaller than a predetermined size to migrate through the array of obstacles in a different direction than the larger cells (e.g. towards a second outlet).
  • an array of obstacles configured to direct cells larger than a predetermined size to migrate along a line-of-sight within the array (e.g. towards a first outlet or bypass channel leading to a first outlet), while directing cells and analytes smaller than a predetermined size to migrate through the array of obstacles in a different direction than the larger cells (e.g. towards a second outlet).
  • a variety of enrichment protocols may be utilized although gentle handling of the cells is needed to reduce any mechanical damage to the cells or their DNA. This gentle handling also preserves the small number of fetal cells in the sample. Integrity of the nucleic acid being evaluated is an important feature to permit the distinction between the genomic material from the fetal cells and other cells in the sample.
  • the enrichment and separation of the fetal cells using the arrays of obstacles produces gentle treatment which minimizes cellular damage and maximizes nucleic acid integrity permitting exceptional levels of separation and the ability to subsequently utilize various formats to very accurately analyze the genome of the cells which are present in the sample in extremely low numbers.
  • enrichment of rare cells occurs using one or more capture modules that selectively inhibit the mobility of one or more cells of interest.
  • a capture module is fluidly coupled downstream to a size-based separation module.
  • Capture modules can include a substrate having multiple obstacles that restrict the movement of cells or analytes greater than a predetermined size. Examples of capture modules that inhibit the migration of cells based on size are disclosed in U.S. Patent No. 5,837,115 and 6,692,952.
  • a capture module includes a two dimensional array of obstacles that selectively filters or captures cells or analytes having a hydrodynamic size greater than a particular gap size (predetermined size), International Publication No. WO 2004/113877. [0065] In some cases, a capture module captures analytes (e.g., cells of interest or not of interest) based on their aff ⁇ nity.
  • analytes e.g., cells of interest or not of interest
  • an affinity-based separation module that can capture cells or analytes can include an array of obstacles adapted for permitting sample flow through, but for the fact that the obstacles are covered with binding moieties that selectively bind one or more analytes (e.g., cell populations) of interest (e.g., red blood cells, fetal cells, epithelial cells or nucleated cells) or analytes not-of-interest (e.g., white blood cells).
  • Arrays of obstacles adapted for separation by capture can include obstacles having one or more shapes and can be arranged in a uniform or non-uniform order.
  • a two-dimensional array of obstacles is staggered such that each subsequent row of obstacles is offset from the previous row of obstacles to increase the number of interactions between the analytes being sorted (separated) and the obstacles.
  • a rare cell-enriched sample is generated by flowing a sample through an affinity-based separation module that includes an array of obstacles coated with binding moieties with affinity to rare cells of interest (e.g., epithelial cells, endothelial cells, or circulating tumor cells).
  • a rare cell-enriched sample generated by capture of rare cells in an, is analyzed directly (e.g., for the presence of a rare cell nucleic acid analysis), i.e., without eluting captured rare cells from the affinity-based separation module prior to analysis.
  • the rare cells can be lysed for nucleic acid extraction (e.g., for mRNA isolation or genomic DNA isolation) directly within the, and the resulting nucleic acid sample can then be analyzed for the presence, absence, or level of a rare cell nucleic acid of interest (e.g., an EGFR mRNA or mutated EGFR genomic sequence).
  • captured rare cells are eluted from an affmity- based separation module prior to analysis.
  • the binding moiety is an antibody
  • the captured cells can be released by proteolytic cleavage (e.g., by treatment with papain or trypsin).
  • antibody-rare cell interactions can be disrupted with physical-chemical perturbations that disrupt the affinity of the capture antibodies for the rare cells of interest.
  • perturbations include, e.g., alterations in pH, ionic strength, or addition of reducing agents.
  • antibodies can be bound to posts by cleavable linkers, which allow elution of captured cells along with the capture antibody by treatment with appropriate cleavage treatments (e.g., addition of a chemical cleavage agent or exposure to a photolytic cleavage treatment).
  • Binding moieties coupled to the obstacles can include e.g., proteins (e.g., ligands/receptors), nucleic acids having complementary counterparts in retained analytes, antibodies, etc.
  • an affinity-based separation module comprises a two-dimensional array of obstacles covered with one or more antibodies selected from the group consisting of: anti-CD71, anti-CD235a, anti-CD36, anti-carbohydrates, anti-selectin, anti-CD45, anti-GPA, anti-antigen-i, anti- EpCAM, anti-E-cadherin, and anti-Muc-1.
  • Figure 2A 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 analyte that does bind a post is captured by the array.
  • Figure 2B is a picture of antibody coated posts.
  • Figure 2C illustrates coupling of antibodies to a substrate (e.g., obstacles, side walls, etc.) as contemplated by the present invention. Examples of such affinity-based separation modules are described in International Publication No. WO 2004/029221.
  • a capture module utilizes a magnetic field to separate and/or enrich one or more analytes (cells) based on a magnetic property or magnetic potential in such analyte of interest or an analyte not of interest.
  • analytes cells
  • red blood cells which are slightly diamagnetic (repelled by magnetic field) in physiological conditions can be made paramagnetic (attributed by magnetic field) by deoxygenation of the hemoglobin into methemoglobin. This magnetic property can be achieved through physical or chemical treatment of the red blood cells.
  • a sample containing one or more red blood cells and one or more white blood cells can be enriched for the red blood cells by first inducing a magnetic property in the red blood cells and then separating the red blood cells from the white blood cells by flowing the sample through a magnetic field (uniform or non-uniform).
  • a maternal blood sample can flow first through a size-based separation module to remove enucleated cells and cellular components (e.g., analytes having a hydrodynamic size less than 6 ⁇ ms) based on size.
  • the enriched nucleated cells e.g., analytes having a hydrodynamic size greater than 6 ⁇ ms
  • white blood cells and nucleated red blood cells are treated with a reagent, such as CO 2 , N 2 , or NaNC> 2 , that changes the magnetic property of the red blood cells' hemoglobin.
  • a reagent such as CO 2 , N 2 , or NaNC> 2
  • the treated sample then flows through a magnetic field (e.g., a column coupled to an external magnet), such that the paramagnetic analytes (e.g., red blood cells) will be captured by the magnetic field while the white blood cells and any other non-red blood cells will flow through the device to result in a sample enriched in nucleated red blood cells (including fetal nucleated red blood cells or friRBCs).
  • a magnetic field e.g., a column coupled to an external magnet
  • enrichment involves detection and/or isolation of rare cells or rare DNA (e.g. fetal cells or fetal DNA) by selectively initiating apoptosis in the rare cells.
  • This can be accomplished, for example, by subjecting a sample that includes rare cells (e.g. a mixed sample) to hyperbaric pressure (increased levels of CO 2 ; e.g. 4% CO 2 ). This will selectively initiate condensation and/or apoptosis in the rare or fragile cells in the sample (e.g. fetal cells). Once the rare cells (e.g. fetal cells) begin apoptosis, their nuclei will condense and optionally be ejected from the rare cells.
  • rare cells or rare DNA e.g. fetal cells or fetal DNA
  • the rare cells or nuclei can be detected using any technique known in the art to detect condensed nuclei, including DNA gel electropheresis, in situ labeling fluorescence labeling, and in situ labeling of DNA nicks using terminal deoxynucleotidyl transferase (TdT)-mediated dUTP in situ nick labeling (TUNEL) (Gav ⁇ eh, Y , et al. J. Cell Biol. 119:493-501 (1992)), and ligation of DNA strand breaks having one or two-base 3' overhangs (Taq polymerase-based in situ ligation). (Didenko V., et al. J. Cell Biol. 135:1369-76 (1996)).
  • ejected nuclei can further be detected using a size based separation module adapted to selectively enrich nuclei and other analytes smaller than a predetermined size (e.g. 6 ⁇ m) and isolate them from cells and analytes having a hydrodynamic diameter larger than 6 ⁇ m.
  • a size based separation module adapted to selectively enrich nuclei and other analytes smaller than a predetermined size (e.g. 6 ⁇ m) and isolate them from cells and analytes having a hydrodynamic diameter larger than 6 ⁇ m.
  • a size based separation module adapted to selectively enrich nuclei and other analytes smaller than a predetermined size (e.g. 6 ⁇ m) and isolate them from cells and analytes having a hydrodynamic diameter larger than 6 ⁇ m.
  • Such detection and diagnosis can occur by obtaining a blood sample from the female pregnant with the fetus, enriching the sample for cells and analytes larger than 8 ⁇ m using, for example, an array of obstacles adapted for size-base separation where the predetermined size of the separation is 8 ⁇ m (e.g. the gap between obstacles is up to 8 ⁇ m). Then, the enriched product is further enriched for red blood cells (RBCs) by oxidizing the sample to make the hemaglobin paramagnetic and flowing the sample through one or more magnetic regions. This selectively captures the RBCs and removes other cells (e g. white blood cells) from the sample.
  • RBCs red blood cells
  • the fnRBCs can be enriched from mnRBC's in the second enriched product by subjecting the second enriched product to hyperbaric pressure or other stimulus that selectively causes the fetal cells to begin apoptosis and condense / eject their nuclei.
  • Such condensed nuclei are then identified/isolated using e.g. laser capture microdissection or a size based separation module that separates components smaller than 3, 4, 5 or 6 ⁇ m from a sample.
  • Such fetal nuclei can then by analyzed using any method known m the art or described herein.
  • a magnetic particle e.g., a bead
  • compound e.g , Fe 3+
  • a bead coupled to an antibody that selectively binds to an analyte of interest can be decorated with an antibody elected from the group of anti CD71 or CD75.
  • a magnetic compound, such as Fe 3+ can be couple to an antibody such as those described above.
  • Magnetic particles or magnetic antibodies herein 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)
  • Magnetic particles can also be used to decorate one or more analytes (cells of interest or not of interest) to increase the size prior to performing size-based separation.
  • Magnetic field used to separate analytes/cells in any of the embodiments herein can uniform or nonuniform as well as external or internal to the device(s) herein.
  • An external magnetic field is one whose source is outside a device herein (e.g , container, channel, obstacles).
  • An internal magnetic field is one whose source is within a device contemplated herein.
  • An example of an internal magnetic field is one where 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.
  • Analytes captured by a magnetic field can be released by demagnetizing the magnetic regions retaining the magnetic particles. For selective release of analytes from regions, 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.
  • Figure 3 illustrates an embodiment of a device configured for capture and isolation of cells expressing the transferrin receptor from a complex mixture.
  • Monoclonal antibodies to CD71 receptor are readily available off-the- shelf and can be covalently coupled to magnetic materials, such as, but not limited to any ferroparticles including but not limited to ferrous doped polystyrene and ferroparticles or ferro-colloids (e.g., from Miltenyi and Dynal).
  • the anti 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.
  • a fluid sample such as a blood sample is first flowed through one or more size-base separation module.
  • Such modules may be fluidly connected in series and/or in parallel.
  • Figure 4 illustrates one embodiment of three size-based enrichment modules that are fluidly coupled in parallel.
  • the waste e.g., cells having hydrodynamic size less than 4 ⁇ m
  • the product e.g., cells having hydrodynamic size greater than 4 ⁇ m
  • the product is subsequently enriched using the inherent magnetic property of hemoglobin.
  • the product is modified (e.g., by addition of one or more reagents) such that the hemoglobin in the red blood cells becomes paramagnetic.
  • One or more of the enrichment modules herein may be fluidly coupled in series or in parallel with one another.
  • a first outlet from a separation module can be fluidly coupled to a capture module.
  • 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.
  • the enrichment steps performed have a specificity and/or 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%
  • the retention rate of the enrichment module(s) herein is such that >50, 60, 70, 80, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 99.9 % of the analytes or cells of interest (e.g., nucleated cells or nucleated red blood cells or nucleated from red blood cells) are retained.
  • the enrichment modules are configured to remove >50, 60, 70, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 99.9 % of all unwanted analytes (e.g., red blood-platelet enriched cells) from a sample.
  • unwanted analytes e.g., red blood-platelet enriched cells
  • the analytes of interest are retained in an enriched 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 the enrichment steps increase the concentration of the analyte of interest (fetal cell), for example, by transferring them from the fluid sample to an enriched fluid sample (sometimes in a new fluid medium, such as a buffer).
  • the methods herein are used for detecting the presence or conditions of rare cells that are in a mixed sample (optionally even after enrichment) at a concentration of up to 90%, 80%, 70%, 60%, 50 %, 40%, 30%, 20%, 10%, 5% or 1% of all cells in the mixed sample, or at a concentration of less than 1:2, 1:4, 1:10, 1:50, 1:100, 1:200, 1:500, 1:1000, 1:2000, 1:5000, 1:10,000, 1:20,000, 1:50,000, 1:100,000, 1:200,000, 1:1,000,000, 1:2,000,000, 1:5,000,000, 1:10,000,000, 1:20,000,000, 1:50,000,000 or 1:100,000,000 of all cells in the sample, or at a concentration of less than 1 x 10 3 , 1 x 10 4 , I x 10 ⁇ 5 , 1 x 10 ⁇ 6 , or 1 x 10 7 cells/ ⁇ L of a fluid sample.
  • the mixed sample has a total of up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, or 100 rare cells.
  • the rare cells can be, for example, fetal cells derived from a maternal sample (e.g., blood sample), or epithelial, endothelial, CTCs or other cells derived from an animal to be diagnosed.
  • Fetal conditions that can be determined based on the methods and systems herein include the presence of a fetus and/or a condition of the fetus such as fetal aneuploidy e.g , trisomy 13, trisomy 18, trisomy 21 (Down Syndrome), Klinefelter Syndrome (XXY) and other irregular number of sex or autosomal chromosomes.
  • a condition of the fetus such as fetal aneuploidy e.g , trisomy 13, trisomy 18, trisomy 21 (Down Syndrome), Klinefelter Syndrome (XXY) and other irregular number of sex or autosomal chromosomes.
  • segmental aneuploidy such as Ip36 duplication, dup(17)(pl l.2pl l.2) syndrome, Down syndrome, Pelizaeus-Merzbacher disease, dup(22)(ql l.2ql l.2) syndrome, Cat eye syndrome.
  • the fetal abnormality to be detected is due to one or more deletions in sex or autosomal chromosomes, including C ⁇ -du-chat syndrome, Wolf-Hirschhorn syndrome, Williams-Beuren syndrome, Charcot-Ma ⁇ e-Tooth disease, Hereditary neuropathy with liability to pressure palsies, Smith-Magenis syndrome, Neurofibromatosis, Alagille syndrome, Velocardiofacial syndrome, DiGeorge syndrome, steroid sulfatase deficiency, Kallmann syndrome, Microphthalmia with linear skin defects, Adrenal hypoplasia, Glycerol kinase deficiency, Pelizaeus-Merzbacher disease, testis-determrning factor on Y, Azospermia (factor a), Azospermia (factor b), Azospermia (factor c) and Ip36 deletion.
  • the fetal abnormality is an abnormal decrease in chromosomal number, such as XO syndrome.
  • Conditions in a patient that can be detected using the systems and methods herein include, infection (e.g., bacterial, viral, or fungal infection), neoplastic or cancer conditions (e.g., acute lymphoblastic leukemia, acute or chronic lymphocyctic or granulocytic tumor, acute myeloid leukemia, acute promyelocytic leukemia, adenocarcinoma, adenoma, adrenal cancer, basal cell carcinoma, bone cancer, brain cancer, breast cancer, bronchi cancer, cervical dysplasia, chronic myelogenous leukemia, colon cancer, epidermoid carcinoma, Ewing's sarcoma, gallbladder cancer, gallstone tumor, giant cell tumor, glioblastoma multiforma, hairy-cell tumor, head cancer, hyperplasia, hyperplastic corneal nerve tumor, in situ carcinoma, intestinal ganglioneur
  • infection e
  • sample analyses involves performing one or more genetic analyses or detection steps on nucleic acids from the enriched product (e.g., enriched cells or nuclei)
  • Nucleic acids from enriched cells or enriched nuclei that can be analyzed by the methods herein include: double-stranded DNA, single-stranded DNA, single-stranded DNA hairpins, DNA/RNA hyb ⁇ ds, RNA (e.g. mRNA) and RNA hairpins.
  • Examples of genetic analyses that can be performed on enriched cells or nucleic acids include, e.g., SNP detection, STR detection, and
  • nucleic acids are obtained from the enriched sample for further genetic analysis. In some cases, about 1-5 ⁇ g, 5-10 ⁇ g, or 10-100 ⁇ g of nucleic acids are obtained from the enriched sample for further genetic analysis.
  • the nucleic acid to be analyzed is from a "rare cell-associated gene," i.e., a gene the expression of which is much higher in a particular type of rare cells (e.g., epithelial cells, circulating tumor cells, or endothelial cells) than in non-rare cells (e.g., red blood cells, white blood cells, or platelets) found in a biological sample from a patient.
  • rare cell-associated genes include, but are not limited to, the genes listed in figure 5.
  • a rare cell- associated gene is EGFR, EpCAM , MUC-I, HER-2, or Claudin-7.
  • the genetic analyses can be performed on one or more genes encoding or regulating a polypeptide listed in Figure 5.
  • a diagnosis is made by comparing results from such genetic analyses with results from similar analyses from a reference sample (one without fetal cells or CTCs, as the case may be).
  • a reference sample one without fetal cells or CTCs, as the case may be.
  • a maternal blood sample enriched for fetal cells can be analyzed to determine the presence of fetal cells and/or a condition in such cells by comparing the ratio of maternal to paternal genomic DNA (or alleles) in control and test samples.
  • target nucleic acids from a test sample are amplified and optionally results are compared with amplification of similar target nucleic acids from a non-rare cell population (reference sample).
  • Amplification of target nucleic acids can be performed by any means known in the art.
  • target nucleic acids are amplified by polymerase chain reaction (PCR).
  • PCR techniques include, but are not limited to, quantitative PCR, quantitative fluorescent PCR (QF-PCR), multiplex fluorescent PCR (MF-PCR), real time PCR (RT-PCR), single cell PCR, restriction fragment length polymorphism PCR (PCR-RFLP), PCR- RFLP/RT-PCR-RFLP, hot start PCR, nested PCR, in situ polonony PCR, in situ rolling circle amplification (RCA), bridge PCR, picotiter PCR and emulsion PCR.
  • QF-PCR quantitative fluorescent PCR
  • MF-PCR multiplex fluorescent PCR
  • RT-PCR real time PCR
  • PCR-RFLP restriction fragment length polymorphism PCR
  • PCR-RFLP PCR- RFLP/RT-PCR-RFLP
  • hot start PCR nested PCR
  • LCR ligase chain reaction
  • transcription amplification self-sustained sequence replication
  • selective amplification of target polynucleotide sequences consensus sequence primed polymerase chain reaction (CP-PCR), arbitrarily primed polymerase chain reaction (AP-PCR), degenerate oligonucleotide-primed PCR (DOP-PCR) and nucleic acid based sequence amplification (NABSA).
  • CP-PCR consensus sequence primed polymerase chain reaction
  • AP-PCR arbitrarily primed polymerase chain reaction
  • DOP-PCR degenerate oligonucleotide-primed PCR
  • NABSA nucleic acid based sequence amplification
  • Other amplification methods that can be used herein include those described in U.S. Patent Nos. 5,242,794; 5,494,810; 4,988,617; and 6,582,938.
  • amplification of target nucleic acids occurs on a bead.
  • target nucleic acids are obtained from a single cell.
  • the nucleic acid(s) of interest can be pre-amplified prior to the amplification step (e.g., PCR).
  • a nucleic acid sample may be pre-amplified to increase the overall abundance of genetic material to be analyzed (e.g., DNA).
  • Pre-amplification can therefore include whole genome amplification such as multiple displacement amplification (MDA) or amplifications with outer primers in a nested PCR approach.
  • MDA multiple displacement amplification
  • amplified nucleic acid(s) are quantified.
  • Methods for quantifying nucleic acids include, but are not limited to, gas chromatography, supercritical fluid chromatography, liquid chromatography (including partition chromatography, adsorption chromatography, ion exchange chromatography, size-exclusion chromatography, thin-layer chromatography, and affinity chromatography), electrophoresis (including capillary electrophoresis, capillary zone electrophoresis, capillary isoelectric focusing, capillary electrochromatography, micellar electrokinetic capillary chromatography, isotachophoresis, transient isotachophoresis and capillary gel electrophoresis), comparative genomic hybridization (CGH), microarrays, bead arrays, and high-throughput genotyping such as with the use of molecular inversion probe (MIP).
  • MIP molecular inversion probe
  • Quantification of amplified target nucleic acid can be used to determine gene/or allele copy number, gene or exon-level expression, methylation-state analysis, or detect a novel transcript in order to diagnose or condition, i.e. fetal abnormality or cancer.
  • analysis involves detecting one or more mutations or SNPs in DNA from e.g., enriched rare cells or enriched rare DNA.
  • detection can be performed using, for example, DNA microarrays.
  • DNA microarrays include those commercially available from Affymetrix, Inc. (Santa Clara,
  • GeneChipTM Mapping Arrays including Mapping IOOK Set, Mapping 1OK 2.0 Array, Mapping 1OK Array, Mapping 500K Array Set, and GeneChipTM Human Mitochondrial Resequencing Array 2.0.
  • the Mapping 1OK array, Mapping IOOK array set, and Mapping 500K array set interrogate more than 10,000, 100,000 and 500,000 different human SNPs, respectively. SNP detection and analysis using GeneChipTM Mapping Arrays is described in part in Kennedy, G.C., et al., Nature Biotechnology 21, 1233-1237, 2003; Liu, W.M.,
  • a microarray is used to detect at least 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000 10,000, 20,000, 50,000, 100,000, 200,000, or 500,000 different nucleic acid target(s) (e.g., SNPs, mutations or STRs) in a sample.
  • nucleic acid target(s) e.g., SNPs, mutations or STRs
  • mapping analysis using fixed content arrays preferably identify one or a few regions that show linkage or association with the phenotype of interest. Those linked regions may then be more closely analyzed to identify and genotype polymorphisms within the identified region or regions, for example, by designing a panel of MIPs targeting polymorphisms or mutations in the identified region.
  • the targeted regions may be amplified by hybridization of a target specific primer and extension of the primer by a highly processive strand displacing polymerase, such as phi29 and then analyzed, for example, by genotyping.
  • a sample comprising one or more rare cells (e.g., fetal or CTC) and non- rare cells (e.g., RBCs) is obtained from an animal such as a human.
  • rare cells or rare DNA e.g., rare nuclei
  • rare cells are enriched using one or more methods disclosed herein or known m the art.
  • rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets.
  • gDNA is obtained from both rare and non-rare cells enriched by the methods herein.
  • genomic DNA is obtained from the rare cell(s) or nuclei and optionally one or more non-rare cells remaining in the enriched mixture.
  • genomic DNA obtained from the enriched sample is digested with a restriction enzyme, such as Xbal or Hind III.
  • a restriction enzyme such as Xbal or Hind III.
  • Other DNA microarrays may be designed for use with other restriction enzymes, e.g., Sty I or Nspl.
  • all fragments resulting from the digestion are ligated on both ends with an adapter sequence that recognizes the overhangs from the restriction digest
  • the DNA fragments are diluted.
  • fragments having the adapter sequence at both ends are amplified using a generic primer that recognizes the adapter sequence.
  • the PCR conditions used for amplification preferentially amplify fragments that have a unique length, e.g., between 250 and 2,000 base pairs in length.
  • amplified DNA sequences are fragmented, labeled and hybridized with the DNA microarray (e.g., IOOK Set Array or other array). Hybridization is followed by a step 608 of washing and staining.
  • results are visualized using a scanner that enables the viewing of intensity of data collected and a software "calls" the bases present at each of the SNP positions interrogated.
  • genotyping microarrays that are used to detect SNPs can be used in combination with molecular inversion probes (MIPs) as described in Hardenbol et al., Genome Res.
  • MIP technology involves the use enzymological reactions that can score up to 10,000; 20,000, 50,000; 100,000; 200,000; 500,000; 1,000,000; 2,000,000 or 5,000,000 SNPs (target nucleic acids) m a single assay.
  • the enzymological reactions are insensitive to cross-reactivity among multiple probe molecules and there is no need for pre- amphfication p ⁇ or to hybridization of the probe with the genomic DNA.
  • the target nucleic acid(s) or SNPs are obtained from a single cell.
  • the present invention contemplate obtaining a sample enriched for fetal cells, epithelial cells or CTCs and analyzing such enriched sample using the MIP technology or oligonucleotide probes that are precircle probes i.e., probes that form a substantially complete circle when they hybridize to a SNP.
  • the precircle probes comprise a first targeting domain that hybridizes upstream to a SNP position, a second targeting domain that hybridizes downstream of a SNP position, at least a first universal priming site, and a cleavage site.
  • probes are allowed to contact genomic DNA regions of interest (comprising SNPs to be interrogated) hybridization complex forms with a precircle probe and a gap at a SNP position region.
  • ligase enzyme is used to "fill in” the gap or complete the circle.
  • the enzymatic "gap fill” process occurs in an allele-specific manner.
  • the nucleotide added to the probe to fill the gap is complementary to the nucleotide base at the SNP position.
  • the probe Once the probe is circular, it may be separated from cross-reacted or unreacted probes by a simple exonuclease reaction The circular probe is then cleaved at the cleavage site such that it becomes linear again.
  • the cleavage site can be any site in the probe other than the SNP site. Linearization of the circular probe results in the placement of universal primer region at one end of the probe.
  • the universal primer region can be coupled to a tag region.
  • the tag can be detected using amplification techniques known m the art
  • the SNP analyzed can subsequently be detected by amplifying the cleaved (linearized) probe to detect the presence of the target sequence in said sample or the presence of the tag
  • Another method contemplated by the present invention to detect SNPs involves the use of bead arrays as is commercially available by Illumina, Inc and as described in US Patent Nos. 7,040,959; 7,035,740; 7033,754; 7,025,935, 6,998,274; 6, 942,968; 6,913,884; 6,890,764; 6,890,741; 6,858,394; 6,846,460; 6,812,005; 6,770,441;
  • Figure 7 illustrates an overview of one embodiment of detecting mutations or SNPs using bead arrays.
  • a sample comprising one or more rare cells (e.g., fetal or CTC) and non-rare cells (e.g., RBCs) is obtained from an animal such as a human.
  • Rare cells or rare DNA e.g., rare nuclei
  • rare cells are enriched using one or more methods disclosed herein or known in the art.
  • rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets.
  • genomic DNA is obtained from the rare cell(s) or nuclei and, optionally, from the one or more non-rare cells remaining in the enriched mixture.
  • the assays in this embodiment require very little genomic DNA starting material, e.g., between 250 ng - 2 ⁇ g. Depending on the multiplex level, the activation step may require only 160 pg of DNA per SNP genotype call.
  • the genomic DNA is activated such that it may bind paramagnetic particles.
  • assay oligonucleotides, hybridization buffer, and paramagnetic particles are combined with the activated DNA and allowed to hybridize (hybridization step).
  • oligonucleotides are added for each SNP to be detected.
  • Two of the three oligos are specific for each of the two alleles at a SNP position and are referred to as Allele-Specific Oligos (ASOs).
  • a third oligo hybridizes several bases downstream from the SNP site and is referred to as the Locus-Specific Oligo (LSO).
  • All three oligos contain regions of genomic complementarity (Cl, C2, and C3) and universal PCR primer sites (Pl, P2 and P3).
  • the LSO also contains a unique address sequence (Address) that targets a particular bead type.
  • step 704 following the hybridization step, several wash steps are performed reducing noise by removing excess and mis-hybridized oligonucleotides.
  • Extension of the appropriate ASO and ligation of the extended product to the LSO joins information about the genotype present at the SNP site to the address sequence on the LSO.
  • step 705 the joined, full-length products provide a template for performing PCR reactions using universal PCR primers Pl, P2, and P3. Universal primers Pl and P2 are labeled with two different labels (e.g., Cy3 and Cy5).
  • step 706 the single-stranded, labeled DNAs are eluted and prepared for hybridization.
  • step 707 the single-stranded, labeled DNAs are hybridized to their complement bead type through their unique address sequence. Hybridization of the GoldenGate AssayTM products onto the Array MatrixTM of BeadchipTM allows for separation of the assay products in solution, onto a solid surface for individual SNP genotype readout.
  • step 708 the array is washed and dried.
  • a reader such as the BeadArray ReaderTM is used to analyze signals from the label.
  • the labels are dye labels such as Cy3 and Cy5
  • the reader can analyze the fluorescence signal on the Sentrix Array Matrix or BeadChip.
  • a computer program comprising a computer readable medium having a computer executable logic is used to automate genotyping clusters and callings.
  • a computer program comprising a computer readable medium having a computer executable logic is used to automate genotyping clusters and callings.
  • analysis involves detecting levels of expression of one or more genes or exons in e.g., enriched rare cells or enriched rare mRNA.
  • detection can be performed using, for example, expression microarrays.
  • the present invention contemplates a method comprising the steps of: enriching rare cells from a sample as described herein, isolating nucleic acids from the rare cells, contacting a microarray under conditions such that the nucleic acids specifically hybridize to the genetic probes on the microarray, and determining the binding specificity (and amount of binding) of the nucleic acid from the enriched sample to the probes.
  • the results from these steps can be used to obtain a binding pattern that would reflect the nucleic acid abundance and establish a gene expression profile.
  • the gene expression or copy number results from the enriched cell population is compared with gene expression or copy number of a non-rare cell population to diagnose a disease or a condition.
  • expression microarrays include those commercially available from Affymetrix, Inc. (Santa).
  • exon arrays e.g., Human Exon ST Array
  • tiling arrays e.g., Chromosome 21/22 1.0 Array Set, ENCODEOl 1.0 Array, or Human Genome Arrays +
  • 3' eukaryotic gene expression arrays e.g., Human Genome Array +, etc.
  • human genome arrays include HuGene FL Genome Array, Human Cancer Gl 10 ARray, Human Exon 1.0 ST, Human Genome Focus Array, Human Genome Ul 33 Plus 2.0, Human Genome U133 Set, Human Genome U133A 2.0, Human Promoter U95 SetX, Human Tiling 1.0R Array Set, Human Tiling 2.0R Array Set, and Human X3P Array.
  • Expression detection and analysis using microarrays is described in part in VaIk, P. J. et al. New England Journal of Medicine 350(16), 1617-28, 2004; Modlich, O. et al. Clinical Cancer Research 10(10), 3410-21, 2004; Onken, Michael D. et al. Cancer Res.
  • RNA expression e.g., using Human Genome U133A Set
  • a sample comprising one or more rare cells (e.g., fetal or CTC) and non- rare cells (e.g., RBCs) is obtained from an animal, such as a human.
  • rare cells or rare DNA e.g., rare nuclei
  • step 801 rare cells or rare DNA are enriched using one or more methods disclosed herein or known in the art.
  • rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets such that rare cells and cells larger than rare cells are directed into a first outlet and one or more cells or particles smaller than the rare cells are directed into a second outlet.
  • enriched cell(s) e.g., fetal, epithelial or CTCs
  • purification techniques known in the art. Generally, about 1 ⁇ g - 2 ⁇ g of total RNA is sufficient.
  • a first-strand complementary DNA (cDNA) is synthesized using reverse transcriptase and a single T7-oligo(dT) primer.
  • a second-strand cDNA is synthesized using DNA ligase, DNA polymerase, and RNase enzyme.
  • the double stranded cDNA (ds-cDNA) is purified.
  • the ds-cDNA serves as a template for in vitro transcription reaction.
  • the in vitro transcription reaction is carried out in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. This generates roughly ten times as many complementary RNA (cRNA) transcripts.
  • cRNA complementary RNA
  • step 809 the expression microarray (e.g., Human Genome U133 Set) is washed with the fragmented, biotin-labeled cRNAs and subsequently stained with streptavidin phycoeryth ⁇ n (SAPE). And in step 810, after final washing, the micrarray is scanned to detect hyb ⁇ dization of cRNA to probe pairs.
  • a computer program product comprising a computer executable logic analyzes images generated from the scanner to determine gene expression. Such methods are disclosed in part in US Patent No.
  • Another method contemplated by the present invention to detect and quantify gene expression involves the use of bead as is commercially available by Illumina, Inc. (San Diego) and as described in US Patent Nos. 7,035,740; 7033,754; 7,025,935, 6,998,274; 6, 942,968; 6,913,884; 6,890,764; 6,890,741; 6,858,394; 6,812,005; 6,770,441; 6,620,584; 6,544,732; 6,429,027; 6,396,995; 6,355,431 and US Publication Application Nos.
  • FIG. 9 illustrates an overview of one embodiment of detecting mutations or SNPs using bead arrays.
  • a sample comprising one or more rare cells (e g., fetal or CTC) and non-rare cells (e.g., RBCs) is obtained from an animal, such as a human.
  • rare cells or rare DNA e.g., rare nuclei
  • rare cells are enriched using one or more methods disclosed herein or known in the art.
  • rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets such that rare cells and cells larger than rare cells are directed into a first outlet and one or more cells or particles smaller than the rare cells are directed into a second outlet.
  • step 902 total RNA is extracted from enriched cells (e.g., fetal cells, CTC, or epithelial cells).
  • enriched cells e.g., fetal cells, CTC, or epithelial cells.
  • two one-quarter scale Message Amp II reactions are performed for each RNA extraction using 200 ng of total RNA.
  • MessageAmp is a procedure based on antisense RNA (aRNA) amplification, and involves a series of enzymatic reactions resulting in linear amplification of exceedingly small amounts of RNA for use in array analysis.
  • aRNA amplification maintains representation of the starting mRNA population.
  • the procedure begins with total or ⁇ oly(A) RNA that is reverse transcribed using a primer containing both ohgo(dT) and a T7 RNA polymerase promoter sequence. After first-strand synthesis, the reaction is treated with RNase H to cleave the mRNA into small fragments. These small RNA fragments serve as primers during a second-strand synthesis reaction that produces a double-stranded cDNA template for transcription. Contaminating rRNA, mRNA fragments and primers are removed and the cDNA template is then used in a large scale in vitro transcription reaction to produce linearly amplified aRNA.
  • the aRNA can be labeled with biotin rNTPS or amino allyl-UTP during transcription
  • biotin-16-UTP Perkm Elmer, Wellesley, California
  • cRNA yields are quantified using RiboGreen (Invitrogen, Carlsbad, California).
  • 1 ⁇ g of cRNA is hybridized to a bead array (e.g , Illumina Bead Array).
  • one or more washing steps is performed on the array.
  • the micrarray is scanned to detect hybridization of cRNA.
  • a computer program product comprising an executable program analyzes images generated from the scanner to determine gene expression.
  • genotyping e.g., SNP detection
  • expression analysis e.g., RNA transcript quantification
  • sequencing can be accomplished through classic Sanger sequencing methods which are well known in the art. Sequence can also be accomplished using high-throughput systems some of which allow detection of a sequenced nucleotide immediately after or upon its incorporation into a growing strand, i.e., detection of sequence in substantially real time or real time.
  • high throughput sequencing generates at least 1,000, at least 5,000, at least 10,000, at least 20,000, at least 30,000, at least 40,000, at least 50,000, at least 100,000 or at least 500,000 sequence reads per hour; with each read being at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120 or at least 150 bases per read.
  • high-throughput sequencing involves the use of technology available by Helicos BioSciences Corporation (Cambridge, Massachusetts) such as the Single Molecule Sequencing by Synthesis (SMSS) method. SMSS is unique because it allows for sequencing the entire human genome in up to 24 hours.
  • SMSS Single Molecule Sequencing by Synthesis
  • SMSS is powerful because, like the MIP technology, it does not require a preamplification step prior to hybridization. In fact, SMSS does not require any amplification. SMSS is described in part in US Publication Application Nos. 20060024711; 20060024678; 20060012793; 20060012784; and 20050100932.
  • An overview the use of SMSS for analysis of enriched cells/nucleic acids is outlined in Figure 10.
  • a sample comprising one or more rare cells (e.g., fetal or CTC) and one or more non-rare cells (e.g., RBCs) is obtained from an animal, such as a human.
  • rare cells or rare DNA e.g., rare nuclei
  • rare cells are enriched using one or more methods disclosed herein or known in the art.
  • rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets.
  • genomic DNA is obtained from the rare cell(s) or nuclei and optionally one or more non-rare cells remaining in the enriched mixture.
  • the genomic DNA is purified and optionally fragmented.
  • a universal priming sequence is generated at the end of each strand.
  • the strands are labeled with a fluorescent nucleotide. These strands will serve as templates in the sequencing reactions.
  • step 1012 universal primers are immobilized on a substrate (e.g., glass surface) inside a flow cell.
  • a substrate e.g., glass surface
  • step 1014 the labeled DNA strands are hybridized to the immobilized primers on the substrate.
  • step 1016 the hybridized DNA strands are visualized by illuminating the surface of the substrate with a laser and imaging the labeled DNA with a digital TV camera connected to a microscope. In this step, the position of all hybridization duplexes on the surface is recorded.
  • step 1018 DNA polymerase is flowed into the flow cell.
  • the polymerase catalyzes the addition of the labeled nucleotides to the correct primers.
  • step 1020 the polymerase and unincorporated nucleotides are washed away in one or more washing procedures.
  • step 1022 t e incorporate nuc eoti es are visua ize y i uminating the surface with a laser and imaging the incorporated nucleotides with a camera. In this step, recordation is made of the positions of the incorporated nucleotides.
  • step 1024 the fluorescent labels on each nucleotide are removed. [00133] Steps 1018-1024 are repeated with the next nucleotide such that the steps are repeated for A, G, T, and C. This sequence of events is repeated until the desired read length is achieved.
  • SMSS can be used, e.g., to sequence DNA from enriched CTCs to identify genetic mutations (e.g., SNPs) in DNA, or to profile gene expression of mRNA transc ⁇ ps of such cells or other cells (fetal cells). SMSS can also be used to identify genes in CTCs that are methylated ("turned off) and develop cancer diagnostics based on such methylation. Finally, enriched cells/DNA can be analyzed using SMSS to detect minute levels of DNA from pathogens such as viruses, bacteria or fungi. Such DNA analysis can further be used for serotyping to detect, e.g., drug resistance or susceptibility to disease.
  • enriched stem cells can be analyzed using SMSS to determine if various expression profiles and differentiation pathways are turned “on” or “off. This allows for a determination to be made of the enriched stem cells are prior to or post differentiation.
  • high-throughput sequencing involves the use of technology available by 454
  • step 1100 a sample comprising one or more rare cells (e.g., fetal or CTC) and one or more non-rare cells (e.g., RBC's) is obtained from an animal, such as a human.
  • rare cells or rare DNA e.g., rare nuclei
  • step 1102 rare cells or rare DNA are enriched using one or more methods disclosed herein or known in the art.
  • rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets.
  • genomic DNA is obtained from the rare cell(s) or nuclei and optionally one or more non-rare cells remaining m the enriched mixture.
  • the enriched genomic DNA is fragmented to generate a library of hundreds of DNA fragments for sequencing runs. Genomic DNA (gDNA) is fractionated into smaller fragments (300-500 base pairs) that are subsequently polished (blunted).
  • short adaptors e g., A and B
  • These adaptors provide priming sequences for both amplification and sequencing of the sample-library fragments.
  • One of the adaptors (e.g , Adaptor B) contains a 5'-biotin tag or other tag that enables immobilization of the library onto beads (e g., streptavidin coated beads).
  • beads e.g., streptavidin coated beads.
  • Adaptor A and B are selected using avidin-blottmg purification.
  • the sstDNA library is assessed for its quality and the optimal amount (DNA copies per bead) needed for subsequent amplification is determined by titration.
  • the sstDNA library is annealed and immobilized onto an excess of capture beads (e.g., streptavidin coated beads). The latter occurs under conditions that favor each bead to carry only a single sstDNA molecule.
  • each bead is captured in its own microreactor, such as a well, which may optionally be addressable, or a picohtre-sized well.
  • the bead-bound library is amplified using, e.g , emPCR. This can be accomplished by capturing each bead within a droplet of a PCR- reaction-mixture-m-oil-emulsion.
  • the bead- bound library can be emulsified with the amplification reagents in a water-in-oil mixture.
  • EmPCR enables the amplification of a DNA fragment immobilized on a bead from a single fragment to 10 million identical copies.
  • This amplification step generates sufficient identical DNA fragments to obtain a strong signal in the subsequent sequencing step.
  • the amplification step results m bead-immobilized, clonally amplified DNA fragments.
  • the amplification on the bead results can result in each bead carrying at least one million, at least 5 million, or at least 10 million copies of the unique target nucleic acid.
  • the emulsion droplets can then be broken, genomic material on each bead may be denatured, and single- stranded nucleic acids clones can be deposited into wells, such as picolitre-sized wells, for further analysis including, but are not limited to quantifying said amplified nucleic acid, gene and exon-level expression analysis, methylation-state analysis, novel transcript discovery, sequencing, genotyping or resequencing.
  • the sstDNA library beads are added to a DNA bead incubation mix (containing DNA polymerase) and are layered with enzyme beads (containing sulfurylase and luciferase as is described in US Patent Nos.
  • each well contains a single amplified library bead.
  • step 1119 the loaded fiber optic plate (e g., PicoTiterPlate device) is then placed into a sequencing apparatus (e.g., the Genome Sequencer 20 Instrument). Fluidics subsystems flow sequencing reagents (containing buffers and nucleotides) across the wells of the plate. Nucleotides are flowed sequentially in a fixed order across the fiber optic plate during a sequencing run. In step 1120, each of the hundreds of thousands of beads with millions of copies of DNA is sequenced in parallel during the nucleotide flow.
  • a sequencing apparatus e.g., the Genome Sequencer 20 Instrument
  • the polymerase extends the existing DNA strand by addmg nucleotide(s) which transmits a chemilluminescent signal.
  • the addition of one (or more) nucleotide(s) results in a reaction that generates a chemilluminescent signal that is recorded by a digital camera or CCD camera in the instrument The signal strength of the chemilluminescent signal is proportional to the number of nucleotides added.
  • a computer program product comprising an executable logic processes the chemilluminescent signal produced by the sequencing reaction. Such logic enables whole genome sequencing for de novo or resequencing projects.
  • high-throughput sequencing is performed using Clonal Single Molecule Array (Solexa, Inc.) or sequencmg-by-synthesis (SBS) utilizing reversible terminator chemistry.
  • Solexa, Inc. Clonal Single Molecule Array
  • SBS sequencmg-by-synthesis
  • a sample comprising one or more rare cells (e.g , fetal or CTC) and one or more non-rare cells (e g., RBCs) is obtained from an animal, such as a human.
  • rare cells, rare DNA (e.g., rare nuclei), or rare mRNA is enriched using one or more methods disclosed herein or known in the art.
  • rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets.
  • step 1204 enriched genetic material e g., gDNA is obtained using methods known in the art or disclosed herein
  • the genetic material e g., gDNA is randomly fragmented.
  • the randomly fragmented gDNA is ligated with adapters on both ends.
  • the genetic material, e.g., ssDNA are bound randomly to inside surface of a flow cell channels.
  • unlabeled nucleotides and enzymes are added to initiate solid phase bridge amplification. The above step results in genetic material fragments becoming double stranded and bound at either end to the substrate.
  • step 1225 the double stranded bridge is denatured to create to immobilized smgle stranded genomic DNA (e.g., ssDNA) sequencing complementary to one another.
  • the above b ⁇ dge amplification and denaturation steps are repeated multiple times (e.g., at least 10, 50, 100, 500, 1,000, 5,000, 10,000, 50,000, 100,000, 500,000, 1,000,000, 5,000,000 times) such that several million dense clusters of dsDNA (or immobilized ssDNA pairs complementary to one another) are generated in each channel of the flow cell.
  • the first sequencing cycle is initiated by adding all four labeled reversible terminators, primers, and DNA polymerase enzyme to the flow cell.
  • This sequencing-by-synthesis (SBS) method utilizes four fluorescently labeled modified nucleotides that are especially created to posses a reversible termination property, which allow each cycle of the sequencing reaction to occur simultaneously in the presence of all four nucleotides (A, C, T, G).
  • the polymerase is able to select the correct base to incorporate, with the natural competition between all four alternatives leading to higher accuracy than methods where only one nucleotide is present m the reaction mix at a time which require the enzyme to reject an incorrect nucleotide.
  • step 1227 all unincorporated labeled terminators are then washed off.
  • laser is applied to the flow cell.
  • Laser excitation captures an image of emitted fluorescence from each cluster on the flow cell.
  • a computer program product comprising a computer executable logic records the identity of the first base for each cluster.
  • the 3' terminus and the fluorescence from each incorporated base are removed.
  • a second sequencing cycle is initiated, just as the first was by adding all four labeled reversible terminators, primers, and DNA polymerase enzyme to the flow cell.
  • a second sequencing read occurs by applying a laser to the flow cell to capture emitted fluorescence from each cluster on the flow cell which is read and analyzed by a computer program product that comprises a computer executable logic to identify the first base for each cluster.
  • anyDot.chips Genevoxx, Germany
  • SNP detection mRNA expression or allele variability
  • the AnyDot chips allow for 10x — 50x enhancement of nucleotide fluorescence signal detection. AnyDot.chips and methods for using them are described in part in International Publication Application Nos.
  • a sample comprising one or more rare cells (e.g., fetal or CTC) and one or more non-rare cells (e g., RBCs) is obtained from an animal, such as a human.
  • rare cells e.g., fetal or CTC
  • non-rare cells e.g., RBCs
  • step 1304 genetic material is obtained from the enriched sample.
  • the genetic material e.g , gDNA
  • the genetic material is fragmented mto millions of individual nucleic acid molecules and in step 1308, a universal primer binding site is added to each fragment (nucleic acid molecule).
  • the fragments are randomly distributed, fixed and primed on a surface of a substrate, such as an AnyDot.chip. Distance between neighboring molecules averages 0.1-10 ⁇ m or about 1 ⁇ m.
  • a sample is applied by simple liquid exchange within a microfluidic system. Each mm 2 contains 1 million single DNA molecules ready for sequencing.
  • step 1334 unbound DNA fragments are removed from the substrate; and in step 1336, a solution containing polymerase and labeled nucleotide analogs having a reversible terminator that limits extension to a single base, such as AnyBase. nucleotides are applied to the substrate.
  • a solution containing polymerase and labeled nucleotide analogs having a reversible terminator that limits extension to a single base such as AnyBase. nucleotides are applied to the substrate.
  • nucleotide analogs When incorporated into the primer-DNA hybrid, such nucleotide analogs cause a reversible stop of the primer-extension (terminating property of nucleotides).
  • This step represents a single-base extension. During the stop, incorporated bases, which include a fluorescence label, can be detected on the surface of the substrate.
  • step 1338 fluorescent dots are detected by a single-molecule fluorescence detection system (e.g., fluorescent microscope).
  • a single fluorescence signal 300 nm in diameter
  • the terminating property and fluorescent label of the incorporated nucleotide analogs are removed.
  • the nucleotides are now extendable similarly to native nucleotides.
  • steps 1336-1340 are thus repeated, e.g., at least 2, 10, 20, 100, 200, 1,000, 2,000 times.
  • Sequence can then be deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions.
  • a polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site.
  • a plurality of labeled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence.
  • the growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site.
  • the nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified.
  • the steps of providing labeled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.
  • Analyzing the rare cells to determine the existence of condition or disease may also include detecting mitochondrial DNA, telomerase, or a nuclear matrix protein in the enriched rare cell sample; detecting the presence or absence of perinuclear compartments in a cell of the enriched sample; or performing gene expression analysis, determining nucleic acid copy number, in-cell PCR, or fluorescence in-situ hybridization of the enriched sample.
  • PCR-amplified single-strand nucleic acid is hybridized to a primer and incubated with a polymerase, ATP sulfurylase, Iuciferase, apyrase, and the substrates luciferin and adenosine 5' phosphosulfate.
  • deoxynucleotide triphosphates corresponding to the bases A, C, G, and T (U) are added sequentially.
  • Each base incorporation is accompanied by release of pyrophosphate, converted to ATP by sulfurylase, which drives synthesis of oxyluciferin and the release of visible light. Since pyrophosphate release is equimolar with the number of incorporated bases, the light given off is proportional to the number of nucleotides adding in any one step. The process repeats until the entire sequence is determined.
  • pyrosequencing analyzes DNA methylations, mutation and SNPs.
  • pyrosequencing also maps surrounding sequences as an internal quality control. Pyrosequencing analysis methods are known in the art.
  • sequence analysis of the rare cell's genetic material may include a four-color sequencing by ligation scheme (degenerate ligation), which involves hybridizing an anchor primer to one of four positions. Then an enzymatic ligation reaction of the anchor primer to a population of degenerate nonamers that are labeled with fluorescent dyes is performed. At any given cycle, the population of nonamers that is used is structure such that the identity of one of its positions is correlated with the identity of the fluorophore attached to that nonamer. To the extent that the ligase discriminates for complementarily at that queried position, the fluorescent signal allows the inference of the identity of the base.
  • degenerate ligation involves hybridizing an anchor primer to one of four positions. Then an enzymatic ligation reaction of the anchor primer to a population of degenerate nonamers that are labeled with fluorescent dyes is performed. At any given cycle, the population of nonamers that is used is structure such that the identity of one of its positions is correlated with the
  • the efficacy of a cancer treatment in a cancer patient is determined by measuring the expression level of a rare-cell associated gene over time (a temporal gene expression profile) in rare cell-enriched samples obtained from patient samples collected at a series of timepoints, including during and/or after cancer treatment.
  • a temporal gene expression profile starting from the beginning of treatment and showing decreasing expression levels of the rare cell-associated gene over time indicates that the cancer treatment is efficacious in the patient.
  • determining the temporal expression profile includes determining the expression level of the rare-cell associated gene prior to the beginning of the cancer treatment. In some embodiments, determining the temporal expression profile includes determining the expression level of the rare cell-associated gene at the end of the cancer treatment period, after the end of the cancer treatment period, or both.
  • kits for performing some or all of the steps of the invention may include devices and reagents in any combination to perform any or all of the steps.
  • the kits may include the arrays for the size-based separation or enrichment, the device and reagents for magnetic separation and the reagents needed for the genetic analysis, e.g., reagents to determine an expression level of a rare cell-associated gene, e.g., EGFR.
  • Figures 14A-14D shows a schematic of the device used to separate nucleated cells from fetal cord blood. [00157] Dimensions: 100 mm x 28 mm x lmm
  • Device fabrication The arrays 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.
  • Device operation 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).
  • BSA Bovine Serum Albumin
  • 2 mM EDTA 15575-020, Invitrogen, Carlsbad, CA.
  • Example 2 Isolation of Fetal Cells from Maternal blood [00165] 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. [00168] Performance: Isolation of fetal cells was confirmed by the reliable presence of male cells in the CD71- positive population prepared from the nucleated cell fractions ( Figure 16). In the single abnormal case tested, the trisomy 21 pathology was also identified ( Figure 17).
  • FISH fluorescence in situ hybridization
  • Fetal cells or nuclei can be isolated as describe in the enrichment section or as described in example 1 and 2.
  • DNA from the fetal cells or isolated nuclei from fetal cells can be obtained using any methods known in the art.
  • STR loci can be chosen on the suspected trisomic chromosomes (X, 13, 18, or 21) and on other control chromosomes. These would be selected for high heterozygosity (variety of alleles) so that the paternal allele of the fetal cells is more likely to be distinct in length from the maternal alleles, with resulting improved power to detect.
  • Di-, tri-, or terra- nucleotide repeat loci can be used.
  • the STR loci can then be amplified according the methods described in the amplification section.
  • the genomic DNA from the enriched fetal cells and a maternal control sample can be fragmented, and separated into single strands.
  • the single strands of the target nucleic acids would be bound to beads under conditions that favor each single strand molecule of DNA to bind a different bead.
  • Each bead would then be captured within a droplet of a PCR- reaction-mixture-in-oil-emulsion and PCR amplification occurs within each droplet.
  • the amplification on the bead could results in each bead carrying at least one 10 million copies of the unique single stranded target nucleic acid.
  • the emulsion would be broken, the DNA is denatured and the beads carrying single-stranded nucleic acids clones would be deposited into a picolitre-sized well for further analysis.
  • the beads can then be placed into a highly parallel sequencing by synthesis machine which can generate over 400,000 reads ( ⁇ 100bp per read) in a single 4 hour run. Sequence by synthesis involves inferring the sequence of the template by synthesizing a strand complementary to the target nucleic acid sequence. The identity of each nucleotide would be detected after the incorporation of a labeled nucleotide or nucleotide analog into a growing strand of a complementary nucleic acid sequence in a polymerase reaction.
  • a signal After the successful incorporation of a label nucleotide, a signal would be measured and then nulled and the incorporation process would be repeated until the sequence of the target nucleic acid is identified.
  • the allele abundances for each of the STRs loci can then be determined.
  • the presence of trisomy would be determined by comparing abundance for each of the STR loci in the fetal cells with the abundance for each of the SRTs loci in a maternal control sample.
  • the enrichment, amplification and sequencing methods described in this example allow for the analysis of rare alleles from fetal cells, even in circumstances where fetal cells are in a mixed sample comprising other maternal cells, and even in circumstances where other maternal cells dominate the mixture.
  • Fetal cells or nuclei can be isolated as describe in the Enrichment section or as described in example 1 and 2.
  • DNA from the fetal cells or isolated nuclei from fetal cells can be obtained using any methods known in the art. The presence of mutations of DNA or RNA from the genes listed in Figure 4 can then be analyzed. DNA or RNA of any of the genes listed in table 2 can then be amplified according the methods described in the amplification section.
  • the genomic DNA from the enriched fetal cells and a maternal control sample can be fragmented, and separated into single strands.
  • the single strands of the target nucleic acids would be bound to beads under conditions that favor each single strand molecule of DNA to bind a different bead. Each bead would then be captured within a droplet of a PCR- reaction-mixture-in-oil-emulsion and PCR amplification occurs within each droplet. The amplification on the bead could results in each bead carrying at least one 10 million copies of the unique single stranded target nucleic acid. The emulsion would be broken, the DNA would be denatured and the beads carrying single-stranded nucleic acids clones would be deposited into a picolitre-sized well for further analysis.
  • the beads can then be placed into a highly parallel sequencing by synthesis machine which can generate over 400,000 reads (—lOObp per read) in a single 4 hour run.
  • Sequence by synthesis involves inferring the sequence of the template by synthesizing a strand complementary to the target nucleic acid sequence. The identity of each nucleotide would be detected after the incorporation of a labeled nucleotide or nucleotide analog into a growing strand of a complementary nucleic acid sequence in a polymerase reaction. After the successful incorporation of a label nucleotide, a signal would be measured and then nulled and the incorporation process would be repeated until the sequence of the target nucleic acid is identified.
  • Fetal cells or nuclei can be isolated as desc ⁇ bed in the enrichment section or as described in example 1 and 2. Quantitative genotyping can then be used to detect chromosome copy number changes. The output of the enrichment procedure would be divided into separate wells of a microtiter plate with the number of wells chosen so no more than one cell or genome copy is located per well, and where some wells may have no cell or genome copy at all.
  • PCR primer pairs for multiple (40 - 100) highly polymorphic SNPs can then be added to each well m the microtiter plate
  • SNPs primers can be designed along chromosomes 13, 18, 21 and X to detect the most frequent aneuploidies, and along control regions of the genome where aneuploidy is not expected.
  • Multiple ( ⁇ 10) SNPs would be designed for each chromosome of interest to allow for non-informative genotypes and to ensure accurate results.
  • PCR primers would be chosen to be multiplexible with other pairs (fairly uniform melting temperature, absence of cross-priming on the human genome, and absence of primer-primer interaction based on sequence analysis).
  • the primers would be designed to generate amplicons 70 - 100 bp in size to mcrease the performance of the multiplex PCR.
  • the p ⁇ mers would contam a 22 bp tag on the 5' which is used in the genotyping analysis.
  • a second of round of PCR using nested primers may be performed to ensure optimal performance of the multiplex amplification.
  • the Molecular Inversion Probe (MIP) technology developed by Affymetrix (Santa Clara, CA) can genotype 20,000 SNPs or more in a single reaction. In the typical MIP assay, each SNP would be assigned a 22bp DNA tag which allows the SNP to be uniquely identified during the highly parallel genotyping assay.
  • the DNA tags serve two roles: 1) determine the identity of the different SNPs and 2) determine the identity of the well from which the genotype was derived.
  • the tagged MIP probes would be combined with the amplicons from the initial multiplex single-cell PCR and the genotyping reactions would be performed.
  • the probe/template mix would be divided into 4 tubes each containing a different nucleotide (e.g. G, A, T or C). Following an extension and ligation step, the mixture would be treated with exonuclease to remove all linear molecules and the tags of the surviving circular molecules would be amplified using PCR.
  • the amplified tags form all of the bins would then be pooled and hybridized to a single DNA microarray contaimng the complementary sequences to each of the 20,000 tags.
  • Identify bins with non-maternal alleles e g. fetal cells '
  • the first step m the data analysis procedure would be to use the 22bp tags to sort the 20,000 genotypes into bins which correspond to the individual wells of the original microtiter plates.
  • the second step would be to identify bins contain non-maternal alleles which correspond to wells that contained fetal cells.
  • Determining the number bms with non-maternal alleles relative to the total number of bins would provide an accurate estimate of the number of fnRBCs that were present in the original enriched cell population.
  • the non-maternal alleles would be detected by 40 independent SNPs which provide an extremely high level of confidence in the result.
  • Detect ploidv for chromosomes 13. 18, and 21 After identifying approximately 10 bins that contain fetal cells, the next step would be to determine the ploidy of chromosomes 13, 18, 21 and X by comparing ratio of maternal to paternal alleles for each of the 10 SNPs on each chromosome.
  • the ratios for the multiple SNPs on each chromosome can be combined (averaged) to increase the confidence of the aneuploidy call for that chromosome.
  • the information from the approximate 10 independent bins containing fetal cells can also be combined to further increase the confidence of the call.
  • Fetal cells or nuclei can be isolated as described m the enrichment section or as described in example 1 and 2 Comparative genomic hybridization (CGH) can be used to determine copy numbers of genes and chromosomes DNA extracted from the enriched fetal cells would be hybridized to immobilized reference genomic DNA which can be in the form of bacte ⁇ al artificial chromosome (BAC) clones, or PCR products, or synthesized DNA oligos representing specific genomic sequence tags Comparing the strength of hybridization fetal cells and maternal control cells to the immobilized DNA segments gives a copy number ratio between the two samples.
  • CGH Comparative genomic hybridization
  • the DNA from the enriched fetal cells can be amplified according to the methods described in the amplification section [00182] A ratio-preserving amplification of the DNA would be done to minimize these errors, i e.
  • this amplification method would be chosen to produce as close as possible the same amplification factor for all target regions of the genome
  • Approp ⁇ ate methods would include multiple displacement amplification, the two-stage PCR, and linear amplification methods such as in vitro transcription [00183]
  • amplification errors are random their effect can be reduced by averaging the copy number or copy number ratios determined at different loci over a genomic region in which aneuploidy is suspected
  • a microarray with 1000 ohgo probes per chromosome could provide a chromosome copy number with error bars ⁇ sqrt(1000) times smaller than those from the determination based on a single probe
  • It is also important to perform the probe averaging over the specific genomic region(s) suspected for aneuploidy For example, a common known segmental aneuploidy would be tested for by averaging the probe data only over that known chromosome region rather than the entire chromosome Random errors could be reduced by a very large factor using DNA microarrays such as
  • Microfluidic devices of the invention were designed by computer-aided design (CAD) and microfab ⁇ cated by photolithography. A two-step process was developed in which a blood sample is first debulked to remove the large population of small cells, and then the rare target epithelial cells target cells are recovered by immunoaffmity capture. The devices were defined by photolithography and etched into a silicon substrate based on the CAD- generated design.
  • the cell enrichment module which is approximately the size of a standard microscope slide, contains 14 parallel sample processing sections and associated sample handling channels that connect to common sample and buffer inlets and product and waste outlets. Each section contains an array of microfabricated obstacles that is optimized to enrich the target cell type by hydrodynamic size via displacement of the larger cells into the product stream.
  • the microchip was designed to separate red blood cells (RBCs) and platelets from the larger leukocytes and CTCs. Enriched populations of target cells were recovered from whole blood passed through the device. Performance of the cell enrichment microchip was evaluated by separating RBCs and platelets from white blood cells (WBCs) in normal whole blood (Figure 18). In cancer patients, CTCs are found in the larger WBC fraction. Blood was minimally diluted (30%), and a 6 ml sample was processed at a flow rate of up to 6 ml/hr. The product and waste stream were evaluated in a Coulter Model "A c -T diff ' clinical blood analyzer, which automatically distinguishes, sizes, and counts different blood cell populations.
  • RBCs red blood cells
  • WBCs white blood cells
  • the enrichment chip achieved separation of RBCs from WBCs, in which the WBC fraction had >99% retention of nucleated cells, >99% depletion of RBCs, and >97% depletion of platelets. Representative histograms of these cell fractions are shown in Figure 19. Routine cytology confirmed the high degree of enrichment of the WBC and RBC fractions ( Figure 20). [00188] Next, epithelial cells were recovered by affinity capture in a microfluidic module that is functionalized with immobilized antibody. A capture module with a single chamber containing a regular array of antibody-coated microfabricated obstacles was designed.
  • the capture modules may be operated under conditions of relatively high flow rate but low shear to protect cells against damage.
  • the surface of the capture module was functionalized by sequential treatment with 10% silane, 0.5% gluteraldehyde, and avidin, followed by biotinylated anti-EpCAM. Active sites were blocked with 3% bovine serum albumin in PBS, quenched with dilute Tris HCl, and stabilized with dilute L-histidine. Modules were washed in PBS after each stage and finally dried and stored at room temperature.
  • Capture performance was measured with the human advanced lung cancer cell line NCI-H1650 (ATCC Number CRL-5883). This cell line has a heterozygous 15 bp in-frame deletion in exon 19 of EGFR that renders it susceptible to gef ⁇ tinib.
  • Cells from confluent cultures were harvested with trypsin, stained with the vital dye Cell Tracker Orange (CMRA reagent, Molecular Probes, Eugene, OR), resuspended in fresh whole blood, and fractionated in the microfluidic chip at various flow rates.
  • CMRA reagent Cell Tracker Orange
  • NCI-H 1650 cells that were spiked into whole blood and recovered by size fractionation and affinity capture as described above were successfully analyzed in situ.
  • a trial run to distinguish epithelial cells from leukocytes 0.5 ml of a stock solution of fluorescein-labeled CD45 pan-leukocyte monoclonal antibody were passed into the capture module and incubated at room temperature for 30 minutes. The module was washed with buffer to remove unbound antibody, and the cells were fixed on the chip with 1% paraformaldehyde and observed by fluorescence microscopy. As shown in Figure 21 the epithelial cells were bound to the obstacles and floor of the capture module. Background staining of the flow passages with CD45 pan-leukocyte antibody is visible, as are several stained leukocytes, apparently because of a low level of non-specific capture.
  • a blood sample from a cancer patient is processed and analyzed using the devices and methods of the invention, e.g., those of Example 6, resulting in an enriched sample of epithelial cells containing CTCs. This sample is then analyzed to identify potential EGFR mutations.
  • the method permits both identification of known, clinically relevant EGFR mutations as well as discovery of novel mutations. An overview of this process is shown in Figure 22. (00191] Below is an outline of the strategy for detection and confirmation of EGFR mutations:
  • Sequence CTC EGFR mRNA a) Purify CTCs from blood sample; b) Purify total RNA from CTCs; c) Convert RNA to cDNA using reverse transcriptase; d) Use resultant cDNA to perform first and second PCR reactions for generating sequencing templates; and e) Purify the nested PCR amplicon and use as a sequencing template to sequence EGFR exons 18-21.
  • Total RNA is then purified from isolated CTC populations using, e.g., the Qiagen Micro RNeasy kit, or a similar total RNA purification protocol from another manufacturer; alternatively, standard RNA purification protocols such as guanidium isothiocyanate homogenization followed by phenol/chloroform extraction and ethanol precipitation may be used.
  • RNA purification protocols such as guanidium isothiocyanate homogenization followed by phenol/chloroform extraction and ethanol precipitation may be used.
  • c) Convert RNA to cDNA using reverse transcriptase. cDNA reactions are carried out based on the protocols of the supplier of reverse transcriptase. Typically, the amount of input RNA into the cDNA reactions is in the range of 10 picograms (pg) to 2 micrograms ( ⁇ g) total RNA.
  • First-strand DNA synthesis is carried out by hybridizing random 7mer DNA primers, or oligo-dT primers, or gene-specific primers, to RNA templates at 65°C followed by snap-chilling on ice.
  • cDNA synthesis is initiated by the addition of iScript Reverse Transcriptase (BioRad) or Superscript Reverse Transcriptase (Invitrogen) or a reverse transcriptase from another commercial vendor along with the appropriate enzyme reaction buffer.
  • iScript reverse transcriptase reactions are carried out at 42°C for 30-45 minutes, followed by enzyme inactivation for 5 minutes at 85°C.
  • cDNA is stored at -20 0 C until use or used immediately in PCR reactions.
  • cDNA reactions are carried out in a final volume of 20 ⁇ l, and 10% (2 ⁇ l) of the resultant cDNA is used in subsequent PCR reactions.
  • d) Use resultant cDNA to perform first and second PCR reactions for generating sequencing templates.
  • cDNA from the reverse transcriptase reactions is mixed with DNA primers specific for the region of interest ( Figure 23). See Table 2 for sets of primers that may be used for amplification of exons 18-21.
  • primer set M13(+)/M12(-) is internal to primer set Ml l(+)/M14(-).
  • primers M13(+) and M12(-) may be used in the nested round of amplification, if primers Ml 1(+) and M14(-) were used in the first round of expansion.
  • primer set Ml l(+)/M14(-) is internal to primer set M15(+)/M16(-)
  • primer set M23(+)/M24(-) is internal to primer set M21(+)/M22(-).
  • Hot Start PCR reactions are performed using Qiagen Hot-Star Taq Polymerase kit, or Applied Biosystems HotStart TaqMan polymerase, or other Hot Start thermostable polymerase, or without a hot start using Promega GoTaq Green Taq Polymerase master mix, TaqMan DNA polymerase, or other thermostable DNA polymerase.
  • reaction volumes are 50 ⁇ l
  • nucleotide triphosphates are present at a final concentration of 200 ⁇ M for each nucleotide
  • MgCl 2 is present at a final concentration of 1-4 mM
  • oligo primers are at a final concentration of 0.5 ⁇ M.
  • Hot start protocols begin with a 10-15 minute incubation at 95°C, followed by 40 cycles of 94°C for one minute (denaturation), 52°C for one minute (annealing), and 72°C for one minute (extension). A lO minute terminal extension at 72°C is performed before samples are stored at 4°C until they are either used as template in the second (nested) round of PCRs, or purified using QiaQuick Spin Columns (Qiagen) prior to sequencing. If a hot-start protocol is not used, the initial incubation at 95°C is omitted. If a PCR product is to be used in a second round of PCRs, 2 ⁇ l (4%) of the initial PCR product is used as template in the second round reactions, and the identical reagent concentrations and cycling parameters are used.
  • PCR products are purified using Qiagen QuickSpm columns, the Agencourt AMPure PCR Purification System, or PCR product purification kits obtained from other vendors After PCR products are purified, the nucleotide concentration and purity is determined with a Nanodrop 7000 spectrophotometer, and the PCR product concentration is brought to a concentration of 25 ng/ ⁇ l As a quality control measure, only PCR products that have a UV-light absorbance ratio (A 26 c/A 28 o) greater than 1 8 are used for sequencing Sequencing primers are brought to a concentration of 3 2 pmol/ ⁇ l
  • CTCs are isolated using any of the size-based enrichment and/or affinity purification devices of the invention
  • gDNA Purify genomic DNA (gDNA) from CTCs
  • Genomic DNA is purified using the Qiagen DNeasy Mini kit, the Invitrogen ChargeSwitch gDNA kit, or another commercial kit, or via the following protocol:
  • Cell pellets are either lysed fresh or stored at -80°C and are thawed immediately before lysis.
  • a unique probe is designed for each wild type allele and mutant allele sequence. Wild-type sequences are marked with the fluorescent dye VIC at the 5' end, and mutant sequences with the fluorophore FAM A fluorescence quencher and Minor Groove Binding moiety are attached to the 3' ends of the probes ROX is used as a passive reference dye for normalization purposes.
  • Example 7 The protocol of Example 7 would be most useful if EGFR were expressed in target cancer cells but not in background leukocytes.
  • EGFR mRNA was present in leukocytes.
  • Table 5 Four sets of primers, shown in Table 5, were designed to amplify four corresponding genes:
  • BCKDK branched-chain a-ketoacid dehydrogenase complex kinase
  • RNAs of approximately 9xlO 6 leukocytes isolated using a cell enrichment device of the invention (cutoff size 4 ⁇ m) and 5x10 6 H 1650 cells were isolated by using RNeasy mini kit (Qiagen). Two micrograms of total RNAs from leukocytes and H1650 cells were reverse transcribed to obtain first strand cDNAs using 100 pmol random hexamer (Roche) and 200 U Superscript II (Invitrogen) in a 20 ⁇ l reaction. The subsequent PCR was carried out using 0.5 ⁇ l of the first strand cDNA reaction and 10 pmol of forward and reverse primers in total 25 ⁇ l of mixture.
  • the PCR was ran for 40 cycles of 95 0 C for 20 seconds, 56°C for 20 seconds, and 70 0 C for 30 seconds.
  • the amplified products were separated on a 1% agarose gel.
  • BCKDK was found to be expressed in both leukocytes and Hl 650 cells; CD45 was expressed only in leukocytes; and both EpCAM and EGFR were expressed only in H1650 cells.

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Abstract

The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g., epithelial cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject by analyzing a cellular sample from the subject.

Description

ANALYSIS OF RARE CELL-ENRICHED SAMPLES
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority, under 35 U.S.C. §119, to U.S. provisional patent application
Nos. 60/804,819 and 60/804,817 both filed on June 14, 2006 and incorporated herein by reference in their entirety.
BACKGROUND OF THE INVENTION
[0002] Analysis of specific cells can give insight into a variety of diseases. These analyses can provide noninvasive 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. Because of the inherent risks posed by amniocentesis and CVS, these procedures are offered primarily to older women, i.e., those over 35 years of age, who have a statistically greater probability of bearing children with congenital defects. As a result, a pregnant woman at the age of 35 has to balance an average risk of 0.5-1% to induce an abortion by amniocentesis against an age related probability for trisomy 21 of less than 0.3%. To eliminate the risks associated with invasive prenatal screening procedures, non- invasive tests for detection, diagnosis and prognosis of diseases, have been utilized. For example, maternal serum alpha- fetoprotein, and levels of unconjugated estriol and human chorionic gonadotropin are used to identify a proportion of fetuses with Down's syndrome, however, these tests are 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
[0003] Moreover, despite decades of advances in cancer diagnosis and therapy, many cancers continue to go undetected until late in their development. As one example, most early-stage lung cancers are asymptomatic and are not detected in time for curative treatment, resulting in an overall five-year survival rate for patients with lung cancer of less than 15%. However, in those instances in which lung cancer is detected and treated at an early stage, the prognosis is much more favorable.
[0004] The presence of fetal cells in the maternal circulation and cancer cells in patients' circulation offers an opportunity to develop prenatal diagnostics that obviates the risks associated with invasive diagnostic procedure, and cancer diagnostics that allow for detecting cancer at earlier stages in the development of the disease. However, fetal cells and cancer cells are rare as compared to the presence of other cells in the blood. Therefore, any proposed analysis of fetal cells or cancer cells to diagnose fetal abnormalities or cancers, respectively, requires enrichment of fetal cells and cancer cells. Enriching fetal cells from maternal peripheral blood and cancer cells from patient's blood is challenging, time intensive and any analysis derived there from is prone to error. The present invention addresses these challenges. [0005] The methods of the present invention allow for enrichment of rare cell populations, particularly fetal cells or cancer cells, from peripheral blood samples which enrichment yields cell populations sufficient for reliable and accurate clinical diagnosis. The methods of the present invention also provide analysis of said enriched rare cell populations whereby said methods allow for detection, diagnosis and prognosis of conditions or diseases, in particular fetal abnormalities or cancer. SUMMARY OF THE INVENTION
[0006] The present invention relates to methods for determining a condition in a patient or a fetus by analyzing nucleic acids from cells of samples obtained from patient or maternal samples, respectively. The methods include enriching the sample for cells that are normally present in vivo at a concentration of less than 1 in 100,000, obtaining the nuclei from the enriched sample cells and detecting substantially in real time one or more nucleic acids molecules. The sample can be enriched for a variety of cells including fetal cells, epithelial cells, endothelial cells or progenitor cells, and the sample can be obtained from a variety of sources including 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 or genitourinary tracts fluid. Preferably, the sample is a blood sample.
[0007] In some embodiments, samples are enriched in fetal cells, and the condition that can be determined by the methods of the invention can be a genetic or pathologic condition. In some embodiments, genetic conditions that can be determined in one or more fetal cells include trisomy 13, trisomy 18, trisomy 21, Klinefelter Syndrome, dup(17)(pl l.2pl l.2) syndrome, Down syndrome, Pelizaeus-Merzbacher disease, dup(22)(ql l.2ql l.2) syndrome, Cat eye syndrome, Cri-du-chat syndrome, Wolf-Hirschhorn syndrome, Williams-Beuren syndrome, Chare ot-Marie- Tooth disease, neuropathy with liability to pressure palsies, Smith-Magenis syndrome, neurofibromatosis, Alagille syndrome, Velocardiofacial syndrome, DiGeorge syndrome, steroid sulfatase deficiency, Kallmann syndrome, microphthalmia with linear skin defects, Adrenal hypoplasia, Glycerol kinase deficiency, Pelizaeus-Merzbacher disease, testis-determining factor on Y, Azospermia (factor a), Azospermia (factor b), Azospermia (factor c), or Ip36 deletion. In other embodiments, the P conditions that can be determined in one or more fetal cells include acute lymphoblastic leukemia, acute or chronic lymphocyctic or granulocytic tumor, acute myeloid leukemia, acute promyelocytic leukemia, adenocarcinoma, adenoma, adrenal cancer, basal cell carcinoma, bone cancer, brain cancer, breast cancer, bronchi cancer, cervical dysplasia, chronic myelogenous leukemia, colon cancer, epidermoid carcinoma, Ewing's sarcoma, gallbladder cancer, gallstone tumor, giant cell tumor, glioblastoma multiforma, hairy- cell tumor, head cancer, hyperplasia, hyperplastic corneal nerve tumor, in situ carcinoma, intestinal ganglioneuroma, islet cell tumor, Kaposi's sarcoma, kidney cancer, larynx cancer, leiomyomater tumor, liver cancer, lung cancer, lymphomas, malignant carcinoid, malignant hypercalcemia, malignant melanomas, marfanoid habitus tumor, medullary carcinoma, metastatic skin carcinoma, mucosal neuromas, mycosis fungoide, myelodysplastic syndrome, myeloma, neck cancer, neural tissue cancer, neuroblastoma, osteogenic sarcoma, osteosarcoma, ovarian tumor, pancreas cancer, parathyroid cancer, pheochromocytoma, polycythemia vera, primary brain tumor, prostate cancer, rectum cancer, renal cell tumor, retinoblastoma, rhabdomyosarcoma, seminoma, skin cancer, small-cell lung tumor, soft tissue sarcoma, squamous cell carcinoma, stomach cancer, thyroid cancer, topical skin lesion, veticulum cell sarcoma, or Wilm's tumor. [0008] In some embodiments, the step of enriching a sample for a cell type includes flowing a sample or a fraction of a sample through an array of obstacles that separate the cells according to size by selectively directing cells of a predetermined size into a first outlet and directing cells of another predetermined size to a second outlet, and flowing the sample or sample fraction through one or more magnetic fields that retain paramagnetic components. The method further comprises ejecting the nuclei from the cells in the sample by applying hyperbaric pressure to the sample, and flowing the sample or a sample fraction through an array of obstacles that are coated with antibodies that bind one or more cell populations in the sample.
[0009] In some embodiments, the methods of the invention can be used to determine a fetal abnormality from amniotic fluid obtained from a pregnant female. In these embodiments, an amniotic fluid sample is obtained from the pregnant female and is enriched for fetal cells. Subsequently, one or more nucleic acid molecules are obtained from the enriched cells, and are amplified on a bead. Up to 100 bases of the nucleic acid are obtained, and in some embodiments up to one million copies of the nucleic acid are amplified. The amplified nucleic acids can also be sequenced. Preferably, the nucleic acid is genomic DNA. [0010] In some embodiments, the fetal abnormality can be determined from a sample that is obtained from a pregnant female and enriched for fetal cells by subjecting the sample to the enrichment procedure that includes separating cells according size, and flowing it through a magnetic field. The size-based separation involves flowing the sample through an array of obstacles that directs cells of a size smaller than a predetermined size to a first outlet, and cells that are larger than a predetermined size to a second outlet. The enriched sample is also subjected to one or more magnetic fields and hyperbaric pressure, and in some embodiments it is used for genetic analyses including SNP detection, RNA expression detection and sequence detection. In some embodiments, one or more nucleic acid fragments can be obtained from the sample that has been subjected to the hyperbaric pressure, and the nucleic acid fragments can be amplified by methods including multiple displacement amplification (MDA), degenerate oligonucleotide primed PCR (DOP), primer extension pre-amplification (PEP) or improved-PEP (I-PEP). [0011] In some embodiments, the method for determining a fetal abnormality can be performed using a blood sample obtained form a pregnant female. The sample can be enriched for fetal cells by flowing the sample through an array of obstacles that directs cells of a size smaller than a predetermined size to a first outlet, and cells that are larger than a predetermined size to a second outlet, and performing a genetic analysis e.g. SNP detection, RNA expression detection and sequence detection, on the enriched sample. The enriched sample can comprise one or more fetal cells and one or more nonfetal cells.
[0012] In some embodiments the invention includes kits providing the devices and reagents for performing one or all of the steps for determining the fetal abnormalities. These kits may include any of the devices or reagents disclosed singly or in combination. [0013] In some embodiments, the genetic analysis of SNP detection or RNA expression can be performed using microarrays. SNP detection can also be accomplished using molecular inverted probes(s), and in some embodiments, SNP detection involves highly parallel detection of at least 100,000 SNPs. RNA expression detection can also involve highly parallel interrogation of at least 10,000 transcripts. In some embodiments, sequence detection can involve determining the sequence of at least 50,000 bases per hour, and sequencing can be done in substantially real time or real time and can comprise adding a plurality of labeled nucleotides or nucleotide analogs to a sequence that is complementary to that of the enriched nucleic acid molecules, and detecting the incorporation. A variety of labels can be used in the sequence detection step and include chromophores, fluorescent moieties, enzymes, antigens, heavy metal, magnetic probes, dyes, phosphorescent groups, radioactive materials, chemiluminescent moieties, scattering or fluorescent nanoparticles, Raman signal generating moieties, and electrochemical detection moieties. Methods that include sequence detection can be accomplished using sequence by synthesis and they may include amplifying the nucleic acid on a bead. In some embodiments, the methods can include amplifying target nucleic acids from the enriched sample(s) by any method known in the art but preferably by multiple displacement amplification (MDA), degenerate oligonucleotide primed PCR (DOP), primer extension pre-amplification (PEP) or improved-PEP (I-PEP). [0014] The genetic analyses can be performed on DNA of chromosomes X, Y, 13, 18 or 21 or on the RNA transcribed therefrom. In some embodiments, the genetic analyses can also be performed on a control sample or reference sample, and in some instances, the control sample can be a maternal sample. [0015] In one aspect, described herein is a method for detecting cancer in a subject. The method includes enriching a sample from the subject (e.g., a blood sample) for rare cells through an array of obstacles coated with antibodies that specifically bind to one or more cell populations in the sample to generate a rare cell-enriched sample. The presence or absence of a rare cell nucleic acid in the rare cell-enriched sample is then detected, where the presence of the rare cell nucleic acid indicates the presence of a cancer in the subject. In some embodiments, the sample is treated with a stabilizer, a preservative, or a fixant prior to enrichment for rare cells. In some embodiments, a rare cell nucleic acid to be detected is from a circulating tumor cell, an epithelial cell, an endothelial cell, or a progenitor stem cell. In other embodiments, the expression or lack thereof of any of the genes listed in figure 5 is detected in the rare cell-enriched sample. In another embodiment, the expression level of EGFR, EGF, EpCAM , MUC-I, HER-2, or Claudin-7 is determined in the rare cell-enriched sample. In some embodiments, in addition to detecting an expression level of one of the above-mentioned genes, the presence or absence of a mutation in the gene (e.g., an EGFR gene mutation) is also determined. The methods described herein can detect the presence of any one of various cancers in a subject, including, but not limited to, is acute lymphoblastic leukemia, acute or chronic lymphocyctic or granulocytic tumor, acute myeloid leukemia, acute promyelocytic leukemia, adenocarcinoma, adenoma, adrenal cancer, basal cell carcinoma, bone cancer, brain cancer, breast cancer, bronchi cancer, cervical dysplasia, chronic myelogenous leukemia, colon cancer, epidermoid carcinoma, Ewing's sarcoma, gallbladder cancer, gallstone tumor, giant cell tumor, glioblastoma multiforma, hairy-cell tumor, head cancer, hyperplasia, hyperplastic corneal nerve tumor, in situ carcinoma, intestinal ganglioneuroma, islet cell tumor, Kaposi's sarcoma, kidney cancer, larynx cancer, leiomyomater tumor, liver cancer, lung cancer, lymphomas, malignant carcinoid, malignant hypercalcemia, malignant melanomas, marfanoid habitus tumor, medullary carcinoma, metastatic skin carcinoma, mucosal neuromas, mycosis fungoide, myelodysplastic syndrome, myeloma, neck cancer, neural tissue cancer, neuroblastoma, osteogenic sarcoma, osteosarcoma, ovarian tumor, pancreas cancer, parathyroid cancer, pheochromocytoma, polycythemia vera, primary brain tumor, prostate cancer, rectum cancer, renal cell tumor, retinoblastoma, rhabdomyosarcoma, seminoma, skin cancer, small-cell lung tumor, soft tissue sarcoma, squamous cell carcinoma, stomach cancer, thyroid cancer, topical skin lesion, veticulum cell sarcoma, or Wilm's tumor. In some embodiments, a rare-cell enriching step includes flowing a sample or a fraction thereof through one or more magnetic fields that selectively retain paramagnetic components. In other embodiments, the method includes (i) applying hyperbaric pressure to a sample from the subject or a fraction thereof prior to enriching the sample for rare cells, to selectively eject nuclei from the rare cells; or (ii) applying hyperbaric pressure to the enriched sample or a fraction thereof to selectively eject nuclei of the rare cells. In some embodiments, the antibodies coated on the array of obstacles binds to the rare cells to be enriched, so that the enriched sample is contained on the array. For example, the array can be coated with one or more antibodies against EpCAM, E-cadherin, or Muc-1, which bind to rare cells of interest. In other embodiments, the antibodies coated on the array bind to cells in the sample other than the rare cells to be enriched, so the enriched sample corresponds to the eluate from the array of antibody-coated obstacles. For example, the array can be coated with one or more antibodies against CD71, CD235a, CD36, selectin, CD45, or GPA. In some embodiments, the array is coated with two different antibodies. In some embodiments, the method is performed on a sample obtained from a subject that has undergone cancer therapy. In other embodiments, the method is performed on a sample obtained from a subject that has not undergone cancer therapy. In some embodiments, the method also includes flowing a sample or a rare cell-enriched sample through an array of obstacles that selectively directs cells larger than a predetermined size in to a first outlet and cells equal to or smaller than said predetermined size to a second outlet. For example, the predetermined size can be the size of a red blood cell, a white blood cell, a circulating tumor cell, an epithelial cell, an endothelial cell, or a progenitor stem cell. In some embodiments, the predetermined size can be about 2 to about
10 μm or any other range between 2 to about 10 μm
[00161 In a related aspect, described herein is another method for detecting cancer in a subject. The method includes enriching a sample from a subject for rare cells by flowing the sample through an array of obstacles that selectively directs cells larger than a predetermined size in to a first outlet and cells equal to or smaller than said predetermined size to a second outlet, wherein said sample is obtained at a time point from said subject and said rare cells in said sample are in a concentration of less than 1 in 100,000 cells, and detecting the presence or absence of a rare cell nucleic acid in the rare-cell enriched sample, where the presence of the rare cell nucleic acid indicates the presence of cancer in t subject [0017] In another aspect, described herein is a method for determining cancer treatment efficacy in a patient. The method includes (i) enriching, for epithelial cells, each of a time series of blood samples from the patient by flowing each blood sample in the set through an array of obstacles coated with one or more antibodies that specifically bind to epithelial cells to obtain a set of epithelial cell-enriched blood samples, The time series of blood samples includes at least a first blood sample obtained at the beginning of the patient's cancer treatment and two more blood samples collected subsequent to the collection of the first blood sample. After obtaining rare-cell enriched blood samples, the expression level of at least one gene expressed in epithelial cells and not expressed in other cells present in blood (i.e., a rare cell-associated gene) is determined in each of the time series blood samples to obtain a temporal expression profile for the rare cell associated gene. The cancer treatment is deemed efficacious if said temporal expression profile indicates a decreasing trend of expression levels for the rare cell-associated gene in the time series or rare cell-enriched blood samples. In some embodiments, determining the expression level of the rare cell- associated gene is performed by determining an mRNA expression level for the gene. In some embodiments, the method includes detecting the expression of a gene listed in figure 5, e.g., EGFR, EGF, EpCAM, MUC-I, HER-2, or Claudin-7, or any combination thereof. In some embodiments, the method also includes detecting the presence or absence of a mutation in any of the foregoing genes. [0018] In a further aspect, described herein is a kit for detecting cancer cells in a subject. The kit includes a device comprising an array of obstacles coated with antibodies that specifically bind to one or more cell populations and a set of reagents for detecting the expression of a gene identified in Figure 5, e.g., EGFR, EGF, EpCAM, MUC-I, HER-2, or Claudin-7, or any combination thereof.
SUMMARY OF THE DRAWINGS [0019] Figures 1A-1D illustrate embodiments of a size-based separation module.
[0020] Figures 2A-2C illustrate one embodiment of an affinity separation module.
[0021] Figure 3 illustrate one embodiment of a magnetic separation module.
[0022] Figure 4 illustrates one example of a multiplex enrichment module of the present invention.
[0023] Figure 5 illustrates exemplary genes that can be analyzed from enriched cells, such as epithelial cells, endothelial cells, circulating tumor cells, progenitor cells, etc.
[0024] Figure 6 illustrates one embodiment for genotyping rare cell(s) or rare DNA using, e.g., Affymetrix DNA microarrays.
[0025] Figure 7 illustrates one embodiment for genotyping rare cell(s) or rare DNA using, e.g., Illumina bead arrays. [0026] Figure 8 illustrates one embodiment for determining gene expression of rare cell(s) or rare DNA using, e.g., Affymetrix expression chips. [0027] Figure 9 illustrates one embodiment for determining gene expression of rare cell(s) or rare DNA using, e g , Illumina bead arrays
[0028] Figure 10 illustrates one embodiment for high-throughput sequencing of rare cell(s) or rare DNA using, e g., single molecule sequence by synthesis methods (e.g , Helicos BioSciences Corporation) [0029] Figure 11 illustrates one embodiment for high-throughput sequencing of rare cell(s) or rare DNA using, e g., amplification of nucleic acid molecules on a bead (e g., 454 Lifesciences).
[0030] Figure 12 illustrates one embodiment for high-throughput sequencing of rare cell(s) or rare DNA using, e g., clonal single molecule arrays technology (e g., Solexa, Inc )
[0031] Figure 13 illustrates one embodiment for high-throughput sequencing of rare cell(s) or rare DNA using, e.g., single base polymerization using enhanced nucleotide fluorescence (e.g , Genovoxx GmbH).
[0032] Figures 14A-14D illustrate one embodiment of a device used to separate cells according to their size.
[0033] Figures 15A-15B illustrate cell smears of first and second outlet (e.g , product and waste) fractions.
[0034] Figures 16A-16F illustrate isolation of CD-71 positive population from a nucleated cell fraction
[0035] Figure 17 illustrates trisomy 21 pathology [0036] Figure 18 illustrates performance of cell separation module
[0037] Figure 19 illustrates histograms representative of cell fractions resulting from cell separation module described herein
[0038] Figure 20 illustrates cytology of products from cell separation module
[0039] Figure 21 illustrates epithelial cells bound to obstacles and floor in a separation / enrichment module [0040] Figure 22 illustrates a process for analyzing enriched epithelial cells for EGFR mutations
[0041] Figure 23 illustrates a method for generating sequencing templates, e.g , from EGFR mRNA
[0042] Figure 24 illustrates exemplary allele specific reactions showing mutations
[0043] Figure 25 illustrates exemplary signals from an allele-specific genotyping assay
[0044] Figure 26A illustrates BCKDK expressed in leukocytes and H 1650 cells [0045] Figure 26B illustrates EGFR expression profile
INCORPORATION BY REFERENCE
[0046] All publications and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference
DETAILED DESCRIPTION OF THE INVENTION
[0047] The present invention provides systems, apparatus, and methods to detect the presence of or abnormalities of rare analytes or cells, such as hematopoietic bone marrow pregemtor cells, endothelial cells, fetal cells circulating m maternal peripheral blood, epithelial cells, or circulating tumor cells in a sample of a mixed analyte or cell population (e g , maternal peripheral blood samples) I Sample Collection/Preparation
[0048] Samples containing rare cells can be obtained from any animal in need of a diagnosis or prognosis or from an animal pregnant with a fetus in need of a diagnosis or prognosis In one example, a sample can be obtained from animal suspected of being pregnant, pregnant, or that has been pregnant to detect the presence of a fetus or fetal abnormality In another example, a sample is obtained from an animal suspected of having, having, or an animal that had a disease or condition (e g cancer) Such condition can be diagnosed, prognosed, monitored and therapy can be determined based on the methods and systems herein Animal of the present invention can be a human or a domesticated animal such as a cow, chicken, pig, horse, rabbit, dogs, cat, or goat. Samples derived from an animal or human can include, e.g., 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 or genitourinary tracts fluid. [0049] To obtain a blood sample, any technique known in the art may be used, e.g. a syringe or other vacuum suction device. A blood sample can be optionally pre-treated or processed prior to enrichment. Examples of pre- treatment steps include the addition of a reagent such as a stabilizer, a preservative, a fixant, a lysing reagent, a diluent, an anti-apoptotic reagent, an anti-coagulation reagent, an anti-thrombotic reagent, magnetic property regulating reagent, a buffering reagent, an osmolality regulating reagent, a pH regulating reagent, and/or a cross- linking reagent.
[0050] When a blood sample is obtained, a preservative such an anti-coagulation agent and/or a stabilizer is often added to the sample prior to enrichment. This allows for extended time for analysis/detection. Thus, a sample, such as a blood sample, can be enriched and/or analyzed under any of the methods and systems 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 the time the sample is obtained. [0051] In some embodiments, a blood sample can be combined with an agent that selectively lyses one or more cells or components in a blood sample. For example, fetal cells can be selectively lysed releasing their nuclei when a blood sample including fetal cells is combined with deionized water. Such selective lysis allows for the subsequent enrichment of fetal nuclei using, e.g., size or affinity based separation. In another example platelets and/or enucleated red blood cells are selectively lysed to generate a sample enriched in nucleated cells, such as fetal nucleated red blood cells (friRBCs), maternal nucleated blood cells (mnBC), epithelial cells and circulating tumor cells. fnRBCs can be subsequently separated from mnBCs using, e.g., antigen-i affinity or differences in hemoglobin
[0052] When obtaining a sample from an animal (e.g., blood sample), the amount can vary depending upon animal size, its gestation period, and the condition being screened. In some embodiments, up to 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 mL of a sample is obtained. In some embodiments, 1-50, 2-40, 3-30, or 4-20 mL of sample is obtained. In some embodiments, 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 sample is obtained.
[0053] To detect fetal abnormality, a blood sample can be obtained from a pregnant animal or human within 36, 24, 22, 20, 18, 16, 14, 12, 10, 8, 6 or 4 weeks of gestation or even after a pregnancy has terminated. II. Enrichment
[0054] A sample (e.g. blood sample) can be enriched for rare analytes or rare cells (e.g. fetal cells, epithelial cells or circulating tumor cells) using one or more any methods known in the art (e.g. Guetta, EM et al. Stem Cells Dev, 13(l):93-9 (2004)) or described herein. The enrichment increases the concentration of rare cells or ratio of rare cells to non-rare cells in the sample. For example, enrichment can increase concentration of an analyte of interest such as a fetal cell or epithelial cell or CTC by a factor of at least 2, 4, 6, 8, 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 over its concentration in the original sample. In particular, when enriching fetal cells from a maternal peripheral venous blood sample, the initial concentration of the fetal cells may be about 1 : 50,000,000 and it may be increased to at least 1:5,000 or 1:500. Enrichment can also increase concentration of rare cells in volume of rare cells / total volume of sample (removal of fluid). A fluid sample (e.g., a blood sample) of greater than 10, 15, 20, 50, or 10O mL total volume comprising rare components of interest, and it can be concentrated such that the rare component of interest into a concentrated solution of less than 0.5, 1, 2, 3, 5, or 10 mL total volume.
[0055] Enrichment can occur using one or more types of separation modules. Several different modules are described herein, all of which can be fluidly coupled with one another in the series for enhanced performance. [0056] In some embodiments, enrichment occurs by selective lysis as described above.
[0057] In one embodiment, enrichment of rare cells occurs using one or more size-based separation modules. Examples of size-based separation modules include filtration modules, sieves, matrixes, etc. Examples of size-based separation modules contemplated by the present invention include those disclosed in International Publication No. WO 2004/113877. Other size based separation modules are disclosed in International Publication No. WO 2004/0144651.
[0058] In some embodiments, a size-based separation module comprises one or more arrays of obstacles forming a network of gaps. The obstacles are configured to direct particles as they flow through the array/network of gaps into different directions or outlets based on the particle's hydrodynamic size. For example, as a blood sample flows through an array of obstacles, nucleated cells or cells having a hydrodynamic size larger than a predetermined size, e.g., 8 μm, are directed to a first outlet located on the opposite side of the array of obstacles from the fluid flow inlet, while the enucleated cells or cells having a hydrodynamic size smaller than a predetermined size, e.g., 8 μm, are directed to a second outlet also located on the opposite side of the array of obstacles from the fluid flow inlet. [0059] An array can be configured to separate cells smaller or larger than a predetermined size by adjusting the size of the gaps, obstacles, and offset in the period between each successive row of obstacles. For example, in some embodiments, obstacles or gaps between obstacles can be up to 10, 20, 50, 70, 100, 120, 150, 170, or 200 μm in length or about 2, 4, 6, 8 or 10 μm in length. In some embodiments, an array for size-based separation includes more than 100, 500, 1,000, 5,000, 10,000, 50,000 or 100,000 obstacles that are arranged into more than 10, 20, 50, 100, 200, 500, or 1000 rows. Preferably, obstacles in a first row of obstacles are offset from a previous (upstream) row of obstacles by up to 50% the period of the previous row of obstacles. In some embodiments, obstacles in a first row of obstacles are offset from a previous row of obstacles by up to 45, 40, 35, 30, 25, 20, 15 or 10% the period of the previous row of obstacles. Furthermore, the distance between a first row of obstacles and a second row of obstacles can be up to 10, 20, 50, 70, 100, 120, 150, 170 or 200 μm. A particular offset can be continuous (repeating for multiple rows) or non-continuous. In some embodiments, a separation module includes multiple discrete arrays of obstacles fluidly coupled such that they are in series with one another. Each array of obstacles has a continuous offset. But each subsequent (downstream) array of obstacles has an offset that is different from the previous
(upstream) offset. Preferably, each subsequent array of obstacles has a smaller offset that the previous array of obstacles. This allows for a refinement in the separation process as cells migrate through the array of obstacles. Thus, a plurality of arrays can be fluidly coupled in series or in parallel, (e.g., more than 2, 4, 6, 8, 10, 20, 30, 40, 50). Fluidly coupling separation modules (e.g., arrays) in parallel allows for high-throughput analysis of the sample, such that at least 1, 2, 5, 10, 20, 50, 100, 200, or 500 mL per hour flows through the enrichment modules or at least 1, 5, 10, or 50 million cells per hour are sorted or flow through the device.
[0060] Figure IA illustrates an example of a 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 shifted horizontally with respect to the previous row of obstacles, where the array of obstacles directs component having a hydrodynamic size smaller than a predetermined size in a first direction and component having a hydrodynamic size larger that a predetermined size in a second direction. For enriching epithelial or circulating tumor cells from enucleated, the predetermined size of an array of obstacles can be get at 6-12 μm or 6-8 μm. For enriching fetal cells from a mixed sample (e.g. maternal blood sample) the predetermined size of an array of obstacles can be get at between 4-10 μm or 6-8 μm. The flow of sample into the array of obstacles can be aligned at a small angle (flow angle) with respect to a line-of-sight of the array. Optionally, the array is coupled to an infusion pump to perfuse the sample through the obstacles. The flow conditions of the size-based separation module described herein are such that cells are sorted by the array with minimal damage. This allows for downstream analysis of intact cells and intact nuclei to be more efficient and reliable.
[0061] In some embodiments, a size-based separation module comprises an array of obstacles configured to direct cells larger than a predetermined size to migrate along a line-of-sight within the array (e.g. towards a first outlet or bypass channel leading to a first outlet), while directing cells and analytes smaller than a predetermined size to migrate through the array of obstacles in a different direction than the larger cells (e.g. towards a second outlet). Such embodiments are illustrated in part in Figures IB-ID.
[0062] A variety of enrichment protocols may be utilized although gentle handling of the cells is needed to reduce any mechanical damage to the cells or their DNA. This gentle handling also preserves the small number of fetal cells in the sample. Integrity of the nucleic acid being evaluated is an important feature to permit the distinction between the genomic material from the fetal cells and other cells in the sample. In particular, the enrichment and separation of the fetal cells using the arrays of obstacles produces gentle treatment which minimizes cellular damage and maximizes nucleic acid integrity permitting exceptional levels of separation and the ability to subsequently utilize various formats to very accurately analyze the genome of the cells which are present in the sample in extremely low numbers.
[0063] In some embodiments, enrichment of rare cells (e.g., fetal cells, epithelial cells, or circulating tumor cells) occurs using one or more capture modules that selectively inhibit the mobility of one or more cells of interest. Preferably, a capture module is fluidly coupled downstream to a size-based separation module. Capture modules can include a substrate having multiple obstacles that restrict the movement of cells or analytes greater than a predetermined size. Examples of capture modules that inhibit the migration of cells based on size are disclosed in U.S. Patent No. 5,837,115 and 6,692,952.
[0064] In some embodiments, a capture module includes a two dimensional array of obstacles that selectively filters or captures cells or analytes having a hydrodynamic size greater than a particular gap size (predetermined size), International Publication No. WO 2004/113877. [0065] In some cases, a capture module captures analytes (e.g., cells of interest or not of interest) based on their affϊnity. For example, an affinity-based separation module that can capture cells or analytes can include an array of obstacles adapted for permitting sample flow through, but for the fact that the obstacles are covered with binding moieties that selectively bind one or more analytes (e.g., cell populations) of interest (e.g., red blood cells, fetal cells, epithelial cells or nucleated cells) or analytes not-of-interest (e.g., white blood cells). Arrays of obstacles adapted for separation by capture can include obstacles having one or more shapes and can be arranged in a uniform or non-uniform order. In some embodiments, a two-dimensional array of obstacles is staggered such that each subsequent row of obstacles is offset from the previous row of obstacles to increase the number of interactions between the analytes being sorted (separated) and the obstacles. . In some embodiments, a rare cell-enriched sample is generated by flowing a sample through an affinity-based separation module that includes an array of obstacles coated with binding moieties with affinity to rare cells of interest (e.g., epithelial cells, endothelial cells, or circulating tumor cells). In some embodiments, a rare cell-enriched sample, generated by capture of rare cells in an, is analyzed directly (e.g., for the presence of a rare cell nucleic acid analysis), i.e., without eluting captured rare cells from the affinity-based separation module prior to analysis. For example, the rare cells can be lysed for nucleic acid extraction (e.g., for mRNA isolation or genomic DNA isolation) directly within the, and the resulting nucleic acid sample can then be analyzed for the presence, absence, or level of a rare cell nucleic acid of interest (e.g., an EGFR mRNA or mutated EGFR genomic sequence). In other embodiments, captured rare cells are eluted from an affmity- based separation module prior to analysis. For example, where the binding moiety is an antibody the captured cells can be released by proteolytic cleavage (e.g., by treatment with papain or trypsin). Alternatively, antibody-rare cell interactions can be disrupted with physical-chemical perturbations that disrupt the affinity of the capture antibodies for the rare cells of interest. Such perturbations include, e.g., alterations in pH, ionic strength, or addition of reducing agents. In other embodiments, antibodies can be bound to posts by cleavable linkers, which allow elution of captured cells along with the capture antibody by treatment with appropriate cleavage treatments (e.g., addition of a chemical cleavage agent or exposure to a photolytic cleavage treatment).
[0066] Binding moieties coupled to the obstacles can include e.g., proteins (e.g., ligands/receptors), nucleic acids having complementary counterparts in retained analytes, antibodies, etc. In some embodiments, an affinity-based separation module comprises a two-dimensional array of obstacles covered with one or more antibodies selected from the group consisting of: anti-CD71, anti-CD235a, anti-CD36, anti-carbohydrates, anti-selectin, anti-CD45, anti-GPA, anti-antigen-i, anti- EpCAM, anti-E-cadherin, and anti-Muc-1.
[0067J Figure 2A 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 analyte that does bind a post is captured by the array. Figure 2B is a picture of antibody coated posts. Figure 2C illustrates coupling of antibodies to a substrate (e.g., obstacles, side walls, etc.) as contemplated by the present invention. Examples of such affinity-based separation modules are described in International Publication No. WO 2004/029221.
[0068] In some embodiments, a capture module utilizes a magnetic field to separate and/or enrich one or more analytes (cells) based on a magnetic property or magnetic potential in such analyte of interest or an analyte not of interest. For example, red blood cells which are slightly diamagnetic (repelled by magnetic field) in physiological conditions can be made paramagnetic (attributed by magnetic field) by deoxygenation of the hemoglobin into methemoglobin. This magnetic property can be achieved through physical or chemical treatment of the red blood cells. Thus, a sample containing one or more red blood cells and one or more white blood cells can be enriched for the red blood cells by first inducing a magnetic property in the red blood cells and then separating the red blood cells from the white blood cells by flowing the sample through a magnetic field (uniform or non-uniform). [0069] For example, a maternal blood sample can flow first through a size-based separation module to remove enucleated cells and cellular components (e.g., analytes having a hydrodynamic size less than 6 μms) based on size. Subsequently, the enriched nucleated cells (e.g., analytes having a hydrodynamic size greater than 6 μms) white blood cells and nucleated red blood cells are treated with a reagent, such as CO2, N2, or NaNC>2, that changes the magnetic property of the red blood cells' hemoglobin. The treated sample then flows through a magnetic field (e.g., a column coupled to an external magnet), such that the paramagnetic analytes (e.g., red blood cells) will be captured by the magnetic field while the white blood cells and any other non-red blood cells will flow through the device to result in a sample enriched in nucleated red blood cells (including fetal nucleated red blood cells or friRBCs). Additional examples of magnetic separation modules are described in US Application Serial No. 11/323,971, filed December 29, 2005 entitled "Devices and Methods for Magnetic Enrichment of Cells and Other Particles" and US Application Serial No. 11/227,904, filed September 15, 2005, entitled "Devices and Methods for Enrichment and Alteration of Cells and Other Particles". [0070] Subsequent enrichment steps can be used to separate the rare cells (e.g fnRBCs) from the non-rare cells maternal nucleated red blood cells. In some embodiments, a sample enriched by size-based separation followed by affinity/magnetic separation is further enriched for rare cells using fluorescence activated cell sorting (FACS) or selective lysis of a subset of the cells. [0071] In some embodiments, enrichment involves detection and/or isolation of rare cells or rare DNA (e.g. fetal cells or fetal DNA) by selectively initiating apoptosis in the rare cells. This can be accomplished, for example, by subjecting a sample that includes rare cells (e.g. a mixed sample) to hyperbaric pressure (increased levels of CO2; e.g. 4% CO2). This will selectively initiate condensation and/or apoptosis in the rare or fragile cells in the sample (e.g. fetal cells). Once the rare cells (e.g. fetal cells) begin apoptosis, their nuclei will condense and optionally be ejected from the rare cells. At that point, the rare cells or nuclei can be detected using any technique known in the art to detect condensed nuclei, including DNA gel electropheresis, in situ labeling fluorescence labeling, and in situ labeling of DNA nicks using terminal deoxynucleotidyl transferase (TdT)-mediated dUTP in situ nick labeling (TUNEL) (Gavπeh, Y , et al. J. Cell Biol. 119:493-501 (1992)), and ligation of DNA strand breaks having one or two-base 3' overhangs (Taq polymerase-based in situ ligation). (Didenko V., et al. J. Cell Biol. 135:1369-76 (1996)).
[0072] In some embodiments ejected nuclei can further be detected using a size based separation module adapted to selectively enrich nuclei and other analytes smaller than a predetermined size (e.g. 6 μm) and isolate them from cells and analytes having a hydrodynamic diameter larger than 6 μm. Thus, in one embodiment, the present invention contemplated detecting fetal cells/fetal DNA and optionally using such fetal DNA to diagnose or prognose a condition in a fetus. Such detection and diagnosis can occur by obtaining a blood sample from the female pregnant with the fetus, enriching the sample for cells and analytes larger than 8 μm using, for example, an array of obstacles adapted for size-base separation where the predetermined size of the separation is 8 μm (e.g. the gap between obstacles is up to 8 μm). Then, the enriched product is further enriched for red blood cells (RBCs) by oxidizing the sample to make the hemaglobin paramagnetic and flowing the sample through one or more magnetic regions. This selectively captures the RBCs and removes other cells (e g. white blood cells) from the sample.
Subsequently, the fnRBCs can be enriched from mnRBC's in the second enriched product by subjecting the second enriched product to hyperbaric pressure or other stimulus that selectively causes the fetal cells to begin apoptosis and condense / eject their nuclei. Such condensed nuclei are then identified/isolated using e.g. laser capture microdissection or a size based separation module that separates components smaller than 3, 4, 5 or 6 μm from a sample. Such fetal nuclei can then by analyzed using any method known m the art or described herein.
[0073] In some embodiments, when the analyte desired to be separated (e.g , red blood cells or white blood cells) is not ferromagnetic or does not have a potential magnetic property, a magnetic particle (e.g., a bead) or compound (e.g , Fe3+) can be coupled to the analyte to give it a magnetic property. In some embodiments, a bead coupled to an antibody that selectively binds to an analyte of interest can be decorated with an antibody elected from the group of anti CD71 or CD75. In some embodiments a magnetic compound, such as Fe3+, can be couple to an antibody such as those described above. The magnetic particles or magnetic antibodies herein 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) Magnetic particles can also be used to decorate one or more analytes (cells of interest or not of interest) to increase the size prior to performing size-based separation. [0074] Magnetic field used to separate analytes/cells in any of the embodiments herein can uniform or nonuniform as well as external or internal to the device(s) herein. An external magnetic field is one whose source is outside a device herein (e.g , container, channel, obstacles). An internal magnetic field is one whose source is within a device contemplated herein. An example of an internal magnetic field is one where 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. Analytes captured by a magnetic field can be released by demagnetizing the magnetic regions retaining the magnetic particles. For selective release of analytes from regions, the demagnetization can be limited to selected obstacles or regions. For example, 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.
[0075] Figure 3 illustrates an embodiment of a device configured for capture and isolation of cells expressing the transferrin receptor from a complex mixture. Monoclonal antibodies to CD71 receptor are readily available off-the- shelf and can be covalently coupled to magnetic materials, such as, but not limited to any ferroparticles including but not limited to ferrous doped polystyrene and ferroparticles or ferro-colloids (e.g., from Miltenyi and Dynal). The anti 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.
[0076] In some cases, a fluid sample such as a blood sample is first flowed through one or more size-base separation module. Such modules may be fluidly connected in series and/or in parallel. Figure 4 illustrates one embodiment of three size-based enrichment modules that are fluidly coupled in parallel. The waste (e.g., cells having hydrodynamic size less than 4 μm) are directed into a first outlet and the product (e.g., cells having hydrodynamic size greater than 4 μm) are directed to a second outlet. The product is subsequently enriched using the inherent magnetic property of hemoglobin. The product is modified (e.g., by addition of one or more reagents) such that the hemoglobin in the red blood cells becomes paramagnetic. Subsequently, the product is flowed through one or more magnetic fields. The cells that are trapped by the magnetic field are subsequently analyzed using the one or more methods herein. [0077] One or more of the enrichment modules herein (e.g., size-based separation module(s) and capture module(s)) may be fluidly coupled in series or in parallel with one another. For example a first outlet from a separation module can be fluidly coupled to a capture module. In some embodiments, 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.
[0078] In any of the embodiments herein, the enrichment steps performed have a specificity and/or 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% The retention rate of the enrichment module(s) herein is such that >50, 60, 70, 80, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 99.9 % of the analytes or cells of interest (e.g., nucleated cells or nucleated red blood cells or nucleated from red blood cells) are retained. Simultaneously, the enrichment modules are configured to remove >50, 60, 70, 80, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 99.9 % of all unwanted analytes (e.g., red blood-platelet enriched cells) from a sample.
[0079] For example, in some embodiments the analytes of interest are retained in an enriched 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. In some embodiments, any or all of the enrichment steps increase the concentration of the analyte of interest (fetal cell), for example, by transferring them from the fluid sample to an enriched fluid sample (sometimes in a new fluid medium, such as a buffer). III. Samp e Ana ysis
[0080] In some embodiments, the methods herein are used for detecting the presence or conditions of rare cells that are in a mixed sample (optionally even after enrichment) at a concentration of up to 90%, 80%, 70%, 60%, 50 %, 40%, 30%, 20%, 10%, 5% or 1% of all cells in the mixed sample, or at a concentration of less than 1:2, 1:4, 1:10, 1:50, 1:100, 1:200, 1:500, 1:1000, 1:2000, 1:5000, 1:10,000, 1:20,000, 1:50,000, 1:100,000, 1:200,000, 1:1,000,000, 1:2,000,000, 1:5,000,000, 1:10,000,000, 1:20,000,000, 1:50,000,000 or 1:100,000,000 of all cells in the sample, or at a concentration of less than 1 x 103, 1 x 104, I x 10~5, 1 x 10~6, or 1 x 10 7 cells/μL of a fluid sample. In some embodiments, the mixed sample has a total of up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, or 100 rare cells. [0081] The rare cells can be, for example, fetal cells derived from a maternal sample (e.g., blood sample), or epithelial, endothelial, CTCs or other cells derived from an animal to be diagnosed.
[0082] Fetal conditions that can be determined based on the methods and systems herein include the presence of a fetus and/or a condition of the fetus such as fetal aneuploidy e.g , trisomy 13, trisomy 18, trisomy 21 (Down Syndrome), Klinefelter Syndrome (XXY) and other irregular number of sex or autosomal chromosomes. Other fetal conditions that can be detected using the methods herein include segmental aneuploidy, such as Ip36 duplication, dup(17)(pl l.2pl l.2) syndrome, Down syndrome, Pelizaeus-Merzbacher disease, dup(22)(ql l.2ql l.2) syndrome, Cat eye syndrome. In some embodiment, the fetal abnormality to be detected is due to one or more deletions in sex or autosomal chromosomes, including Cπ-du-chat syndrome, Wolf-Hirschhorn syndrome, Williams-Beuren syndrome, Charcot-Maπe-Tooth disease, Hereditary neuropathy with liability to pressure palsies, Smith-Magenis syndrome, Neurofibromatosis, Alagille syndrome, Velocardiofacial syndrome, DiGeorge syndrome, steroid sulfatase deficiency, Kallmann syndrome, Microphthalmia with linear skin defects, Adrenal hypoplasia, Glycerol kinase deficiency, Pelizaeus-Merzbacher disease, testis-determrning factor on Y, Azospermia (factor a), Azospermia (factor b), Azospermia (factor c) and Ip36 deletion. In some cases, the fetal abnormality is an abnormal decrease in chromosomal number, such as XO syndrome. [0083] Conditions in a patient that can be detected using the systems and methods herein include, infection (e.g., bacterial, viral, or fungal infection), neoplastic or cancer conditions (e.g., acute lymphoblastic leukemia, acute or chronic lymphocyctic or granulocytic tumor, acute myeloid leukemia, acute promyelocytic leukemia, adenocarcinoma, adenoma, adrenal cancer, basal cell carcinoma, bone cancer, brain cancer, breast cancer, bronchi cancer, cervical dysplasia, chronic myelogenous leukemia, colon cancer, epidermoid carcinoma, Ewing's sarcoma, gallbladder cancer, gallstone tumor, giant cell tumor, glioblastoma multiforma, hairy-cell tumor, head cancer, hyperplasia, hyperplastic corneal nerve tumor, in situ carcinoma, intestinal ganglioneuroma, islet cell tumor, Kaposi's sarcoma, kidney cancer, larynx cancer, leiomyomater tumor, liver cancer, lung cancer, lymphomas, malignant carcinoid, malignant hypercalcemia, malignant melanomas, marfanoid habitus tumor, medullary carcinoma, metastatic skin carcinoma, mucosal neuromas, mycosis fungoide, myelodysplastic syndrome, myeloma, neck cancer, neural tissue cancer, neuroblastoma, osteogenic sarcoma, osteosarcoma, ovarian tumor, pancreas cancer, parathyroid cancer, pheochromocytoma, polycythemia vera, primary brain tumor, prostate cancer, rectum cancer, renal cell tumor, retinoblastoma, rhabdomyosarcoma, seminoma, skin cancer, small-cell lung tumor, soft tissue sarcoma, squamous cell carcinoma, stomach cancer, thyroid cancer, topical skm lesion, veticulum cell sarcoma, or Wilm's tumor), inflammation, etc. J0084] In some cases, sample analyses involves performing one or more genetic analyses or detection steps on nucleic acids from the enriched product (e.g., enriched cells or nuclei) Nucleic acids from enriched cells or enriched nuclei that can be analyzed by the methods herein include: double-stranded DNA, single-stranded DNA, single-stranded DNA hairpins, DNA/RNA hybπds, RNA (e.g. mRNA) and RNA hairpins. Examples of genetic analyses that can be performed on enriched cells or nucleic acids include, e.g., SNP detection, STR detection, and
RNA expression analysis.
[0085] In some embodiments, less than 1 μg, 500 ng, 200 ng, 100 ng, 50 ng, 40 ng, 30 ng, 20 ng, 10 ng, 5ng, 1 ng , 500 pg, 200 pg, 100 pg, 50 pg, 40 pg, 30 pg, 20 pg, 10 pg, 5pg, or 1 pg of nucleic acids are obtained from the enriched sample for further genetic analysis. In some cases, about 1-5 μg, 5-10 μg, or 10-100 μg of nucleic acids are obtained from the enriched sample for further genetic analysis. In some embodiments, the nucleic acid to be analyzed is from a "rare cell-associated gene," i.e., a gene the expression of which is much higher in a particular type of rare cells (e.g., epithelial cells, circulating tumor cells, or endothelial cells) than in non-rare cells (e.g., red blood cells, white blood cells, or platelets) found in a biological sample from a patient. Examples of rare cell- associated genes include, but are not limited to, the genes listed in figure 5. In some embodiments, a rare cell- associated gene is EGFR, EpCAM , MUC-I, HER-2, or Claudin-7.
[0086] When analyzing, for example, a sample such as a blood sample from a patient to diagnose a condition such as cancer, the genetic analyses can be performed on one or more genes encoding or regulating a polypeptide listed in Figure 5. In some cases, a diagnosis is made by comparing results from such genetic analyses with results from similar analyses from a reference sample (one without fetal cells or CTCs, as the case may be). For example, a maternal blood sample enriched for fetal cells can be analyzed to determine the presence of fetal cells and/or a condition in such cells by comparing the ratio of maternal to paternal genomic DNA (or alleles) in control and test samples. [0087] In some embodiments, target nucleic acids from a test sample are amplified and optionally results are compared with amplification of similar target nucleic acids from a non-rare cell population (reference sample).
Amplification of target nucleic acids can be performed by any means known in the art. In some cases, target nucleic acids are amplified by polymerase chain reaction (PCR). Examples of PCR techniques that can be used include, but are not limited to, quantitative PCR, quantitative fluorescent PCR (QF-PCR), multiplex fluorescent PCR (MF-PCR), real time PCR (RT-PCR), single cell PCR, restriction fragment length polymorphism PCR (PCR-RFLP), PCR- RFLP/RT-PCR-RFLP, hot start PCR, nested PCR, in situ polonony PCR, in situ rolling circle amplification (RCA), bridge PCR, picotiter PCR and emulsion PCR. Other suitable amplification methods include the ligase chain reaction (LCR), transcription amplification, self-sustained sequence replication, selective amplification of target polynucleotide sequences, consensus sequence primed polymerase chain reaction (CP-PCR), arbitrarily primed polymerase chain reaction (AP-PCR), degenerate oligonucleotide-primed PCR (DOP-PCR) and nucleic acid based sequence amplification (NABSA). Other amplification methods that can be used herein include those described in U.S. Patent Nos. 5,242,794; 5,494,810; 4,988,617; and 6,582,938.
[0088] In any of the embodiments, amplification of target nucleic acids occurs on a bead. In any of the embodiments herein, target nucleic acids are obtained from a single cell. [0089] In any of the embodiments herein, the nucleic acid(s) of interest can be pre-amplified prior to the amplification step (e.g., PCR). In some cases, a nucleic acid sample may be pre-amplified to increase the overall abundance of genetic material to be analyzed (e.g., DNA). Pre-amplification can therefore include whole genome amplification such as multiple displacement amplification (MDA) or amplifications with outer primers in a nested PCR approach. [0090] In some embodiments amplified nucleic acid(s) are quantified. Methods for quantifying nucleic acids are known in the art and include, but are not limited to, gas chromatography, supercritical fluid chromatography, liquid chromatography (including partition chromatography, adsorption chromatography, ion exchange chromatography, size-exclusion chromatography, thin-layer chromatography, and affinity chromatography), electrophoresis (including capillary electrophoresis, capillary zone electrophoresis, capillary isoelectric focusing, capillary electrochromatography, micellar electrokinetic capillary chromatography, isotachophoresis, transient isotachophoresis and capillary gel electrophoresis), comparative genomic hybridization (CGH), microarrays, bead arrays, and high-throughput genotyping such as with the use of molecular inversion probe (MIP). [0091] Quantification of amplified target nucleic acid can be used to determine gene/or allele copy number, gene or exon-level expression, methylation-state analysis, or detect a novel transcript in order to diagnose or condition, i.e. fetal abnormality or cancer.
[0092] In some embodiments, analysis involves detecting one or more mutations or SNPs in DNA from e.g., enriched rare cells or enriched rare DNA. Such detection can be performed using, for example, DNA microarrays. Examples of DNA microarrays include those commercially available from Affymetrix, Inc. (Santa Clara,
California), including the GeneChip™ Mapping Arrays including Mapping IOOK Set, Mapping 1OK 2.0 Array, Mapping 1OK Array, Mapping 500K Array Set, and GeneChip™ Human Mitochondrial Resequencing Array 2.0. The Mapping 1OK array, Mapping IOOK array set, and Mapping 500K array set interrogate more than 10,000, 100,000 and 500,000 different human SNPs, respectively. SNP detection and analysis using GeneChip™ Mapping Arrays is described in part in Kennedy, G.C., et al., Nature Biotechnology 21, 1233-1237, 2003; Liu, W.M.,
Biomformatics 19, 2397-2403, 2003; Matsuzaki, H., Genome Research 3, 414-25, 2004; and Matsuzaki, H., Nature Methods, 1, 109-111, 2004 as well as in US Patent Nos. 5,445,934; 5,744,305; 6,261,776; 6,291,183; 5,799,637; 5,945,334; 6,346,413, 6,399,365; and 6,610,482, and EP 619 321; 373 203. In some embodiments, a microarray is used to detect at least 5, 10, 20, 50, 100, 200, 500, 1,000, 2,000, 5,000 10,000, 20,000, 50,000, 100,000, 200,000, or 500,000 different nucleic acid target(s) (e.g., SNPs, mutations or STRs) in a sample.
[0093] Methods for analyzing chromosomal copy number using mapping arrays are disclosed, for example, in Bignell et al., Genome Res. 14:287-95 (2004), Lieberfarb, et al., Cancer Res. 63:4781-4785 (2003), Zhao et al., Cancer Res. 64:3060-71 (2004), Nannya et al., Cancer Res. 65:6071-6079 (2005) and Ishikawa et al., Biochem. and Biophys. Res. Comm., 333:1309-1314 (2005). Computer implemented methods for estimation of copy number based on hybπdization intensity are disclosed in U S. Publication Application Nos. 20040157243; 20050064476; and 20050130217.
[0094] In preferred aspects, mapping analysis using fixed content arrays, for example, 10K, IOOK or 500K arrays, preferably identify one or a few regions that show linkage or association with the phenotype of interest. Those linked regions may then be more closely analyzed to identify and genotype polymorphisms within the identified region or regions, for example, by designing a panel of MIPs targeting polymorphisms or mutations in the identified region. The targeted regions may be amplified by hybridization of a target specific primer and extension of the primer by a highly processive strand displacing polymerase, such as phi29 and then analyzed, for example, by genotyping. [0095] A quick overview for the process of using a SNP detection microarray (such as the Mapping IOOK Set) is illustrated in Figure 6. First, in step 600 a sample comprising one or more rare cells (e.g., fetal or CTC) and non- rare cells (e.g., RBCs) is obtained from an animal such as a human. In step 601, rare cells or rare DNA (e.g., rare nuclei) are enriched using one or more methods disclosed herein or known m the art. Preferably, rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets. In some cases, gDNA is obtained from both rare and non-rare cells enriched by the methods herein.
[0096] In step 602, genomic DNA is obtained from the rare cell(s) or nuclei and optionally one or more non-rare cells remaining in the enriched mixture. In step 603, the genomic DNA obtained from the enriched sample is digested with a restriction enzyme, such as Xbal or Hind III. Other DNA microarrays may be designed for use with other restriction enzymes, e.g., Sty I or Nspl. In step 604 all fragments resulting from the digestion are ligated on both ends with an adapter sequence that recognizes the overhangs from the restriction digest In step 605, the DNA fragments are diluted. Subsequently, in step 606 fragments having the adapter sequence at both ends are amplified using a generic primer that recognizes the adapter sequence. The PCR conditions used for amplification preferentially amplify fragments that have a unique length, e.g., between 250 and 2,000 base pairs in length. In steps 607, amplified DNA sequences are fragmented, labeled and hybridized with the DNA microarray (e.g., IOOK Set Array or other array). Hybridization is followed by a step 608 of washing and staining. [0097] In step 609 results are visualized using a scanner that enables the viewing of intensity of data collected and a software "calls" the bases present at each of the SNP positions interrogated. Computer implemented methods for determining genotype using data from mapping arrays are disclosed, for example, in Lm, et al., Bioinformatics 19:2397-2403, 2003; and Di et al., Bioinformatics 21:1958-63, 2005. Computer implemented methods for linkage analysis using mapping array data are disclosed, for example, in Ruschendorf and Nurnberg, Bioinformatics 21:2123-5, 2005; and Leykin et al., BMC Genet. 6:7, 2005; and in US Patent No. 5,733,729. [0098] In some cases, genotyping microarrays that are used to detect SNPs can be used in combination with molecular inversion probes (MIPs) as described in Hardenbol et al., Genome Res. 15(2) :269-275, 2005, Hardenbol, P. et al. Nature Biotechnology 21(6), 673-8, 2003; Faham M, et al. HumMol Genet. Aug l;10(16):1657-64, 2001; Maneesh Jam, Ph.D., et all. Genetic Engineering News V24: No. 18, 2004; and Fakhrai-Rad H, et al. Genome Res. JuI; 14(7): 1404-12, 2004; and m U.S. Pat. No. 6,858,412. Universal tag arrays and reagent kits for performing such locus specific genotyping using panels of custom MIPs are available from Affymetrix and ParAllele. MIP technology involves the use enzymological reactions that can score up to 10,000; 20,000, 50,000; 100,000; 200,000; 500,000; 1,000,000; 2,000,000 or 5,000,000 SNPs (target nucleic acids) m a single assay. The enzymological reactions are insensitive to cross-reactivity among multiple probe molecules and there is no need for pre- amphfication pπor to hybridization of the probe with the genomic DNA. In any of the embodiments, the target nucleic acid(s) or SNPs are obtained from a single cell.
[0099] Thus, the present invention contemplate obtaining a sample enriched for fetal cells, epithelial cells or CTCs and analyzing such enriched sample using the MIP technology or oligonucleotide probes that are precircle probes i.e., probes that form a substantially complete circle when they hybridize to a SNP. The precircle probes comprise a first targeting domain that hybridizes upstream to a SNP position, a second targeting domain that hybridizes downstream of a SNP position, at least a first universal priming site, and a cleavage site. Once the probes are allowed to contact genomic DNA regions of interest (comprising SNPs to be interrogated) hybridization complex forms with a precircle probe and a gap at a SNP position region. Subsequently, ligase enzyme is used to "fill in" the gap or complete the circle. The enzymatic "gap fill" process occurs in an allele-specific manner. The nucleotide added to the probe to fill the gap is complementary to the nucleotide base at the SNP position. Once the probe is circular, it may be separated from cross-reacted or unreacted probes by a simple exonuclease reaction The circular probe is then cleaved at the cleavage site such that it becomes linear again. The cleavage site can be any site in the probe other than the SNP site. Linearization of the circular probe results in the placement of universal primer region at one end of the probe. The universal primer region can be coupled to a tag region. The tag can be detected using amplification techniques known m the art The SNP analyzed can subsequently be detected by amplifying the cleaved (linearized) probe to detect the presence of the target sequence in said sample or the presence of the tag
[00100] Another method contemplated by the present invention to detect SNPs involves the use of bead arrays as is commercially available by Illumina, Inc and as described in US Patent Nos. 7,040,959; 7,035,740; 7033,754; 7,025,935, 6,998,274; 6, 942,968; 6,913,884; 6,890,764; 6,890,741; 6,858,394; 6,846,460; 6,812,005; 6,770,441;
6,663,832; 6,620,584; 6,544,732; 6,429,027; 6,396,995; 6,355,431 and US Publication Application Nos. 20060019258; 20050266432; 20050244870; 20050216207; 20050181394; 20050164246; 20040224353; 20040185482; 20030198573; 20030175773; 20030003490; 20020187515; and 20020177141; as well as Shen, R., et al. Mutation Research 573 70-82 (2005).
[00101] Figure 7 illustrates an overview of one embodiment of detecting mutations or SNPs using bead arrays. In this embodiment, a sample comprising one or more rare cells (e.g., fetal or CTC) and non-rare cells (e.g., RBCs) is obtained from an animal such as a human. Rare cells or rare DNA (e.g., rare nuclei) are enriched using one or more methods disclosed herein or known in the art. Preferably, rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets.
[00102] In step 701, genomic DNA is obtained from the rare cell(s) or nuclei and, optionally, from the one or more non-rare cells remaining in the enriched mixture. The assays in this embodiment require very little genomic DNA starting material, e.g., between 250 ng - 2 μg. Depending on the multiplex level, the activation step may require only 160 pg of DNA per SNP genotype call. In step 702, the genomic DNA is activated such that it may bind paramagnetic particles. In step 703 assay oligonucleotides, hybridization buffer, and paramagnetic particles are combined with the activated DNA and allowed to hybridize (hybridization step). In some cases, three oligonucleotides are added for each SNP to be detected. Two of the three oligos are specific for each of the two alleles at a SNP position and are referred to as Allele-Specific Oligos (ASOs). A third oligo hybridizes several bases downstream from the SNP site and is referred to as the Locus-Specific Oligo (LSO). All three oligos contain regions of genomic complementarity (Cl, C2, and C3) and universal PCR primer sites (Pl, P2 and P3). The LSO also contains a unique address sequence (Address) that targets a particular bead type. (Up to 1,536 SNPs may be interrogated in this manner using GoldenGate™ Assay available by Illumina, Inc. (San Diego, California).) During the primer hybridization process, the assay oligonucleotides hybridize to the genomic DNA sample bound to paramagnetic particles. Because hybridization occurs prior to any amplification steps, no amplification bias is introduced into the assay.
[00103] In step 704, following the hybridization step, several wash steps are performed reducing noise by removing excess and mis-hybridized oligonucleotides. Extension of the appropriate ASO and ligation of the extended product to the LSO joins information about the genotype present at the SNP site to the address sequence on the LSO. In step 705, the joined, full-length products provide a template for performing PCR reactions using universal PCR primers Pl, P2, and P3. Universal primers Pl and P2 are labeled with two different labels (e.g., Cy3 and Cy5). Other labels that can be used include, chromophores, fluorescent moieties, enzymes, antigens, heavy metal, magnetic probes, dyes, phosphorescent groups, radioactive materials, chemiluminescent moieties, scattering or fluorescent nanoparticles, Raman signal generating moieties, or electrochemical detection moieties. [00104] In step 706, the single-stranded, labeled DNAs are eluted and prepared for hybridization. In step 707, the single-stranded, labeled DNAs are hybridized to their complement bead type through their unique address sequence. Hybridization of the GoldenGate Assay™ products onto the Array Matrix™ of Beadchip™ allows for separation of the assay products in solution, onto a solid surface for individual SNP genotype readout.
[00105] In step 708, the array is washed and dried. In step 709, a reader such as the BeadArray Reader™ is used to analyze signals from the label. For example, when the labels are dye labels such as Cy3 and Cy5, the reader can analyze the fluorescence signal on the Sentrix Array Matrix or BeadChip.
[00106] In step 710, a computer program comprising a computer readable medium having a computer executable logic is used to automate genotyping clusters and callings. [00107] In any of the embodiments herein, preferably, more than 1000, 5,000, 10,000, 50,000, 100,000, 500,000, or
1,000,000 SNPs are interrogated in parallel.
[00108] In some embodiments, analysis involves detecting levels of expression of one or more genes or exons in e.g., enriched rare cells or enriched rare mRNA. Such detection can be performed using, for example, expression microarrays. Thus, the present invention contemplates a method comprising the steps of: enriching rare cells from a sample as described herein, isolating nucleic acids from the rare cells, contacting a microarray under conditions such that the nucleic acids specifically hybridize to the genetic probes on the microarray, and determining the binding specificity (and amount of binding) of the nucleic acid from the enriched sample to the probes. The results from these steps can be used to obtain a binding pattern that would reflect the nucleic acid abundance and establish a gene expression profile. In some embodiments, the gene expression or copy number results from the enriched cell population is compared with gene expression or copy number of a non-rare cell population to diagnose a disease or a condition.
[00109] Examples of expression microarrays include those commercially available from Affymetrix, Inc. (Santa
Clara, California), such as the exon arrays (e.g., Human Exon ST Array); tiling arrays (e.g., Chromosome 21/22 1.0 Array Set, ENCODEOl 1.0 Array, or Human Genome Arrays +); and 3' eukaryotic gene expression arrays (e.g., Human Genome Array +, etc.). Examples of human genome arrays include HuGene FL Genome Array, Human Cancer Gl 10 ARray, Human Exon 1.0 ST, Human Genome Focus Array, Human Genome Ul 33 Plus 2.0, Human Genome U133 Set, Human Genome U133A 2.0, Human Promoter U95 SetX, Human Tiling 1.0R Array Set, Human Tiling 2.0R Array Set, and Human X3P Array. [00110] Expression detection and analysis using microarrays is described in part in VaIk, P. J. et al. New England Journal of Medicine 350(16), 1617-28, 2004; Modlich, O. et al. Clinical Cancer Research 10(10), 3410-21, 2004; Onken, Michael D. et al. Cancer Res. 64(20), 7205-7209, 2004; Gardian, et al. J. Biol. Chem. 280(1), 556- 563, 2005; Becker, M. et al. MoI. Cancer Ther. 4(1), 151-170, 2005; and Flechner, SM et al. AmJ Transplant 4(9), 1475-89, 2004; as well as in US Patent Nos. 5,445,934; 5,700,637; 5,744,305; 5,945,334; 6,054,270; 6,140,044; 6,261,776; 6,291,183; 6,346,413; 6,399,365; 6,420,169; 6,551,817; 6,610,482; 6,733,977; and EP 619 321; 323 203.
[00111] An overview of a protocol that can be used to detect RNA expression (e.g., using Human Genome U133A Set) is illustrated in Figure 8. In step 800 a sample comprising one or more rare cells (e.g., fetal or CTC) and non- rare cells (e.g., RBCs) is obtained from an animal, such as a human. In step 801, rare cells or rare DNA (e.g., rare nuclei) are enriched using one or more methods disclosed herein or known in the art. Preferably, rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets such that rare cells and cells larger than rare cells are directed into a first outlet and one or more cells or particles smaller than the rare cells are directed into a second outlet. [00112] In step 802 total RNA or poly-A mRNA is obtained from enriched cell(s) (e.g., fetal, epithelial or CTCs) using purification techniques known in the art. Generally, about 1 μg - 2 μg of total RNA is sufficient. In step 803, a first-strand complementary DNA (cDNA) is synthesized using reverse transcriptase and a single T7-oligo(dT) primer. In step 804, a second-strand cDNA is synthesized using DNA ligase, DNA polymerase, and RNase enzyme. In step 805, the double stranded cDNA (ds-cDNA) is purified. In step 806, the ds-cDNA serves as a template for in vitro transcription reaction. The in vitro transcription reaction is carried out in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix. This generates roughly ten times as many complementary RNA (cRNA) transcripts. [00113] In step 807, biotinylated cRNAs are cleaned up, and subsequently m step 808, they are fragmented randomly. Finally, in step 809 the expression microarray (e.g., Human Genome U133 Set) is washed with the fragmented, biotin-labeled cRNAs and subsequently stained with streptavidin phycoerythπn (SAPE). And in step 810, after final washing, the micrarray is scanned to detect hybπdization of cRNA to probe pairs. [00114] In step 811 a computer program product comprising a computer executable logic analyzes images generated from the scanner to determine gene expression. Such methods are disclosed in part in US Patent No.
6,505,125.
[00115] Another method contemplated by the present invention to detect and quantify gene expression involves the use of bead as is commercially available by Illumina, Inc. (San Diego) and as described in US Patent Nos. 7,035,740; 7033,754; 7,025,935, 6,998,274; 6, 942,968; 6,913,884; 6,890,764; 6,890,741; 6,858,394; 6,812,005; 6,770,441; 6,620,584; 6,544,732; 6,429,027; 6,396,995; 6,355,431 and US Publication Application Nos. 20060019258; 20050266432; 20050244870; 20050216207; 20050181394; 20050164246; 20040224353; 20040185482; 20030198573; 20030175773; 20030003490; 20020187515; and 20020177141; and in B. E. Stranger, et al., Public Library of Science- Genetics, 1 (6), December 2005; Jmgli Cai, et al., Stem Cells, published online November 17, 2005; CM. Schwartz, et al., Stem Cells and Development, 14, 517-534, 2005; Barnes, M., J. et al , Nucleic Acids Research, 33 (18), 5914-5923, October 2005; and Bibikova M, et al. Clinical Chemistry, Volume 50, No.12, 2384-2386, December 2004.
[00116] Figure 9 illustrates an overview of one embodiment of detecting mutations or SNPs using bead arrays. In step 900 a sample comprising one or more rare cells (e g., fetal or CTC) and non-rare cells (e.g., RBCs) is obtained from an animal, such as a human. In step 901, rare cells or rare DNA (e.g., rare nuclei) are enriched using one or more methods disclosed herein or known in the art. Preferably, rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets such that rare cells and cells larger than rare cells are directed into a first outlet and one or more cells or particles smaller than the rare cells are directed into a second outlet. [00117] In step 902, total RNA is extracted from enriched cells (e.g., fetal cells, CTC, or epithelial cells). In step 903, two one-quarter scale Message Amp II reactions (Ambion, Austin, Texas) are performed for each RNA extraction using 200 ng of total RNA. MessageAmp is a procedure based on antisense RNA (aRNA) amplification, and involves a series of enzymatic reactions resulting in linear amplification of exceedingly small amounts of RNA for use in array analysis. Unlike exponential RNA amplification methods, such as NASBA and RT-PCR, aRNA amplification maintains representation of the starting mRNA population. The procedure begins with total or ρoly(A) RNA that is reverse transcribed using a primer containing both ohgo(dT) and a T7 RNA polymerase promoter sequence. After first-strand synthesis, the reaction is treated with RNase H to cleave the mRNA into small fragments. These small RNA fragments serve as primers during a second-strand synthesis reaction that produces a double-stranded cDNA template for transcription. Contaminating rRNA, mRNA fragments and primers are removed and the cDNA template is then used in a large scale in vitro transcription reaction to produce linearly amplified aRNA. The aRNA can be labeled with biotin rNTPS or amino allyl-UTP during transcription [00118] In step 904, biotin-16-UTP (Perkm Elmer, Wellesley, California) is added such that half of the UTP is used in the in vitro transcription reaction In step 905, cRNA yields are quantified using RiboGreen (Invitrogen, Carlsbad, California). In step 906, 1 μg of cRNA is hybridized to a bead array (e.g , Illumina Bead Array). In step 907, one or more washing steps is performed on the array. In step 908, after final washing, the micrarray is scanned to detect hybridization of cRNA. In step 908, a computer program product comprising an executable program analyzes images generated from the scanner to determine gene expression. [00119] Additional description for preparing RNA for bead arrays is described in Kacharmina JE, et al., Methods
Enzymol 303: 3-18, 1999; Pabon C, et al., Biotechniques 31(4): 874-9, 2001; Van Gelder RN, et al., Proc Natl Acad Sci USA 87: 1663-7 (1990); and Murray, SS. BMC Genetics 6(Suppl I):S85 (2005). [00120] Preferably, more than 1000, 5,000, 10,000, 50,000, 100,000, 500,000, or 1,000,000 transcripts are interrogated in parallel.
[00121] In any of the embodiments herein, genotyping (e.g., SNP detection) and/or expression analysis (e.g., RNA transcript quantification) of genetic content from enriched rare cells or enriched rare cell nuclei can be accomplished by sequencing. Sequencing can be accomplished through classic Sanger sequencing methods which are well known in the art. Sequence can also be accomplished using high-throughput systems some of which allow detection of a sequenced nucleotide immediately after or upon its incorporation into a growing strand, i.e., detection of sequence in substantially real time or real time. In some cases, high throughput sequencing generates at least 1,000, at least 5,000, at least 10,000, at least 20,000, at least 30,000, at least 40,000, at least 50,000, at least 100,000 or at least 500,000 sequence reads per hour; with each read being at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 120 or at least 150 bases per read. [00122] In some embodiments, high-throughput sequencing involves the use of technology available by Helicos BioSciences Corporation (Cambridge, Massachusetts) such as the Single Molecule Sequencing by Synthesis (SMSS) method. SMSS is unique because it allows for sequencing the entire human genome in up to 24 hours. This fast sequencing method also allows for detection of a SNP/nucleotide in a sequence in substantially real time or real time. Finally, SMSS is powerful because, like the MIP technology, it does not require a preamplification step prior to hybridization. In fact, SMSS does not require any amplification. SMSS is described in part in US Publication Application Nos. 20060024711; 20060024678; 20060012793; 20060012784; and 20050100932. [00123] An overview the use of SMSS for analysis of enriched cells/nucleic acids (e.g., fetal cells, epithelial cells, CTCs) is outlined in Figure 10. [00124] First, in step 1000 a sample comprising one or more rare cells (e.g., fetal or CTC) and one or more non-rare cells (e.g., RBCs) is obtained from an animal, such as a human. In step 1002, rare cells or rare DNA (e.g., rare nuclei) are enriched using one or more methods disclosed herein or known in the art. Preferably, rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets. In step 1004, genomic DNA is obtained from the rare cell(s) or nuclei and optionally one or more non-rare cells remaining in the enriched mixture. [00125] In step 1006 the genomic DNA is purified and optionally fragmented. In step 1008, a universal priming sequence is generated at the end of each strand. In step 1010, the strands are labeled with a fluorescent nucleotide. These strands will serve as templates in the sequencing reactions.
[00126] In step 1012 universal primers are immobilized on a substrate (e.g., glass surface) inside a flow cell. [00127] In step 1014, the labeled DNA strands are hybridized to the immobilized primers on the substrate. [00128] In step 1016, the hybridized DNA strands are visualized by illuminating the surface of the substrate with a laser and imaging the labeled DNA with a digital TV camera connected to a microscope. In this step, the position of all hybridization duplexes on the surface is recorded.
[00129] In step 1018, DNA polymerase is flowed into the flow cell. The polymerase catalyzes the addition of the labeled nucleotides to the correct primers. [00130] In step 1020, the polymerase and unincorporated nucleotides are washed away in one or more washing procedures. [00131] In step 1022, t e incorporate nuc eoti es are visua ize y i uminating the surface with a laser and imaging the incorporated nucleotides with a camera. In this step, recordation is made of the positions of the incorporated nucleotides.
[00132] In step 1024, the fluorescent labels on each nucleotide are removed. [00133] Steps 1018-1024 are repeated with the next nucleotide such that the steps are repeated for A, G, T, and C. This sequence of events is repeated until the desired read length is achieved.
[00134] SMSS can be used, e.g., to sequence DNA from enriched CTCs to identify genetic mutations (e.g., SNPs) in DNA, or to profile gene expression of mRNA transcπps of such cells or other cells (fetal cells). SMSS can also be used to identify genes in CTCs that are methylated ("turned off) and develop cancer diagnostics based on such methylation. Finally, enriched cells/DNA can be analyzed using SMSS to detect minute levels of DNA from pathogens such as viruses, bacteria or fungi. Such DNA analysis can further be used for serotyping to detect, e.g., drug resistance or susceptibility to disease. Furthermore, enriched stem cells can be analyzed using SMSS to determine if various expression profiles and differentiation pathways are turned "on" or "off. This allows for a determination to be made of the enriched stem cells are prior to or post differentiation. [00135] In some embodiments, high-throughput sequencing involves the use of technology available by 454
Lifesciences, Inc. (Branford, Connecticut) such as the PicoTiterPlate device which includes a fiber optic plate that transmits chemilluminescent signal generated by the sequencing reaction to be recorded by a CCD camera m the instrument. This use of fiber optics allows for the detection of a minimum of 20 million base pairs in 4.5 hours [00136] Methods for using bead amplification followed by fiber optics detection are described in Marguiles, M., et al. "Genome sequencing in microfabπcated high-density pricolitre reactors", Nature, doi:10.1038/nature03959; and well as in US Publication Application Nos. 20020012930; 20030068629; 20030100102; 20030148344 ; 20040248161; 20050079510, 20050124022; and 20060078909. [00137] An overview of this embodiment is illustrated in Figure 11. [00138] First, in step 1100 a sample comprising one or more rare cells (e.g., fetal or CTC) and one or more non-rare cells (e.g., RBC's) is obtained from an animal, such as a human. In step 1102, rare cells or rare DNA (e.g., rare nuclei) are enriched using one or more methods disclosed herein or known in the art. Preferably, rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets. In step 1104, genomic DNA is obtained from the rare cell(s) or nuclei and optionally one or more non-rare cells remaining m the enriched mixture. [00139] In step 1112, the enriched genomic DNA is fragmented to generate a library of hundreds of DNA fragments for sequencing runs. Genomic DNA (gDNA) is fractionated into smaller fragments (300-500 base pairs) that are subsequently polished (blunted). In step 1113, short adaptors (e g., A and B) are ligated onto the ends of the fragments. These adaptors provide priming sequences for both amplification and sequencing of the sample-library fragments. One of the adaptors (e.g , Adaptor B) contains a 5'-biotin tag or other tag that enables immobilization of the library onto beads (e g., streptavidin coated beads). In step 1114, only gDNA fragments that include both
Adaptor A and B are selected using avidin-blottmg purification. The sstDNA library is assessed for its quality and the optimal amount (DNA copies per bead) needed for subsequent amplification is determined by titration. In step 1115, the sstDNA library is annealed and immobilized onto an excess of capture beads (e.g., streptavidin coated beads). The latter occurs under conditions that favor each bead to carry only a single sstDNA molecule. In step 1116, each bead is captured in its own microreactor, such as a well, which may optionally be addressable, or a picohtre-sized well. In step 1117, the bead-bound library is amplified using, e.g , emPCR. This can be accomplished by capturing each bead within a droplet of a PCR- reaction-mixture-m-oil-emulsion. Thus, the bead- bound library can be emulsified with the amplification reagents in a water-in-oil mixture. EmPCR enables the amplification of a DNA fragment immobilized on a bead from a single fragment to 10 million identical copies. This amplification step generates sufficient identical DNA fragments to obtain a strong signal in the subsequent sequencing step. The amplification step results m bead-immobilized, clonally amplified DNA fragments. The amplification on the bead results can result in each bead carrying at least one million, at least 5 million, or at least 10 million copies of the unique target nucleic acid.
[00140] The emulsion droplets can then be broken, genomic material on each bead may be denatured, and single- stranded nucleic acids clones can be deposited into wells, such as picolitre-sized wells, for further analysis including, but are not limited to quantifying said amplified nucleic acid, gene and exon-level expression analysis, methylation-state analysis, novel transcript discovery, sequencing, genotyping or resequencing. In step 1118, the sstDNA library beads are added to a DNA bead incubation mix (containing DNA polymerase) and are layered with enzyme beads (containing sulfurylase and luciferase as is described in US Patent Nos. 6,956,114 and 6,902,921) onto a fiber optic plate such as the PicoTiterPlate device. The fiber optic plate is centπfuged to deposit the beads mto wells (~up to 50 or 45 μm in diameter). The layer of enzyme beads ensures that the DNA beads remain positioned in the wells during the sequencing reaction. The bead-deposition process maximizes the number of wells that contain a single amplified library bead (avoiding more than one sstDNA library bead per well). Preferably, each well contains a single amplified library bead. In step 1119, the loaded fiber optic plate (e g., PicoTiterPlate device) is then placed into a sequencing apparatus (e.g., the Genome Sequencer 20 Instrument). Fluidics subsystems flow sequencing reagents (containing buffers and nucleotides) across the wells of the plate. Nucleotides are flowed sequentially in a fixed order across the fiber optic plate during a sequencing run In step 1120, each of the hundreds of thousands of beads with millions of copies of DNA is sequenced in parallel during the nucleotide flow. If a nucleotide complementary to the template strand is flowed into a well, the polymerase extends the existing DNA strand by addmg nucleotide(s) which transmits a chemilluminescent signal. In step 1122, the addition of one (or more) nucleotide(s) results in a reaction that generates a chemilluminescent signal that is recorded by a digital camera or CCD camera in the instrument The signal strength of the chemilluminescent signal is proportional to the number of nucleotides added. Finally, in step 1124, a computer program product comprising an executable logic processes the chemilluminescent signal produced by the sequencing reaction. Such logic enables whole genome sequencing for de novo or resequencing projects. [00141] In some embodiments, high-throughput sequencing is performed using Clonal Single Molecule Array (Solexa, Inc.) or sequencmg-by-synthesis (SBS) utilizing reversible terminator chemistry. These technologies are described in part in US Patent Nos. 6,969,488; 6,897,023; 6,833,246; 6,787,308; and US Publication Application Nos. 20040106110; 20030064398; 20030022207; and Constans, A., The Scientist 2003, 17(13) 36. [00142] Figure 12 illustrates a first embodiment using the SBS approach described above. [00143] First, in step 1200 a sample comprising one or more rare cells (e.g , fetal or CTC) and one or more non-rare cells (e g., RBCs) is obtained from an animal, such as a human. In step 1202, rare cells, rare DNA (e.g., rare nuclei), or rare mRNA is enriched using one or more methods disclosed herein or known in the art. Preferably, rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes into different outlets. [00144] In step 1204, enriched genetic material e g., gDNA is obtained using methods known in the art or disclosed herein In step 1206, the genetic material e g., gDNA is randomly fragmented. In step 1222, the randomly fragmented gDNA is ligated with adapters on both ends. In step 1223, the genetic material, e.g., ssDNA are bound randomly to inside surface of a flow cell channels. In step 1224, unlabeled nucleotides and enzymes are added to initiate solid phase bridge amplification. The above step results in genetic material fragments becoming double stranded and bound at either end to the substrate. In step 1225, the double stranded bridge is denatured to create to immobilized smgle stranded genomic DNA (e.g., ssDNA) sequencing complementary to one another. The above bπdge amplification and denaturation steps are repeated multiple times (e.g., at least 10, 50, 100, 500, 1,000, 5,000, 10,000, 50,000, 100,000, 500,000, 1,000,000, 5,000,000 times) such that several million dense clusters of dsDNA (or immobilized ssDNA pairs complementary to one another) are generated in each channel of the flow cell. In step 1226, the first sequencing cycle is initiated by adding all four labeled reversible terminators, primers, and DNA polymerase enzyme to the flow cell. This sequencing-by-synthesis (SBS) method utilizes four fluorescently labeled modified nucleotides that are especially created to posses a reversible termination property, which allow each cycle of the sequencing reaction to occur simultaneously in the presence of all four nucleotides (A, C, T, G). In the presence of all four nucleotides, the polymerase is able to select the correct base to incorporate, with the natural competition between all four alternatives leading to higher accuracy than methods where only one nucleotide is present m the reaction mix at a time which require the enzyme to reject an incorrect nucleotide. In step 1227, all unincorporated labeled terminators are then washed off. In step 1228, laser is applied to the flow cell. Laser excitation captures an image of emitted fluorescence from each cluster on the flow cell. In step 1229, a computer program product comprising a computer executable logic records the identity of the first base for each cluster. In step 1230, before initiated the next sequencing step, the 3' terminus and the fluorescence from each incorporated base are removed. [00145] Subsequently, a second sequencing cycle is initiated, just as the first was by adding all four labeled reversible terminators, primers, and DNA polymerase enzyme to the flow cell. A second sequencing read occurs by applying a laser to the flow cell to capture emitted fluorescence from each cluster on the flow cell which is read and analyzed by a computer program product that comprises a computer executable logic to identify the first base for each cluster. The above sequencing steps are repeated as necessary to sequence the entire gDNA fragment. In some cases, the above steps are repeated at least 5, 10, 50, 100, 500, 1,000, 5,000, to 10,000 times. [00146] In some embodiments, high-throughput sequencing of mRNA or gDNA can take place using AnyDot.chips (Genovoxx, Germany), which allows for the momtoπng of biological processes (e.g., mRNA expression or allele variability (SNP detection). In particular, the AnyDot chips allow for 10x — 50x enhancement of nucleotide fluorescence signal detection. AnyDot.chips and methods for using them are described in part in International Publication Application Nos. WO 02088382, WO 03020968, WO 03031947, WO 2005044836, PCT/EP 05/05657, PCT/EP 05/05655; and German Patent Application Nos. DE 101 49 786, DE 102 14 395, DE 103 56 837, DE 10
2004 009 704, DE 10 2004 025 696, DE 10 2004 025 746, DE 10 2004 025 694, DE 10 2004 025 695, DE 10 2004
025 744, DE 10 2004 025 745, and DE 10 2005 012 301.
[00147] An overview of one embodiment of the present invention is illustrated in Figure 13.
[00148] First, in step 1300 a sample comprising one or more rare cells (e.g., fetal or CTC) and one or more non-rare cells (e g., RBCs) is obtained from an animal, such as a human. In step 1302, rare cells or rare genetic material
(e.g., gDNA or RNA) is enriched using one or more methods disclosed herein or known in the art. Preferably, rare cells are enriched by flowing the sample through an array of obstacles that selectively directs particles or cells of different hydrodynamic sizes mto different outlets. In step 1304, genetic material is obtained from the enriched sample. In step 1306, the genetic material (e.g , gDNA) is fragmented mto millions of individual nucleic acid molecules and in step 1308, a universal primer binding site is added to each fragment (nucleic acid molecule). In step 1332, the fragments are randomly distributed, fixed and primed on a surface of a substrate, such as an AnyDot.chip. Distance between neighboring molecules averages 0.1-10 μm or about 1 μm. A sample is applied by simple liquid exchange within a microfluidic system. Each mm2 contains 1 million single DNA molecules ready for sequencing. In step 1334, unbound DNA fragments are removed from the substrate; and in step 1336, a solution containing polymerase and labeled nucleotide analogs having a reversible terminator that limits extension to a single base, such as AnyBase. nucleotides are applied to the substrate. When incorporated into the primer-DNA hybrid, such nucleotide analogs cause a reversible stop of the primer-extension (terminating property of nucleotides). This step represents a single-base extension. During the stop, incorporated bases, which include a fluorescence label, can be detected on the surface of the substrate.
[00149] In step 1338, fluorescent dots are detected by a single-molecule fluorescence detection system (e.g., fluorescent microscope). In some cases, a single fluorescence signal (300 nm in diameter) can be properly tracked over the complete sequencing cycles (see below). After detection of the single-base, in step 1340, the terminating property and fluorescent label of the incorporated nucleotide analogs (e.g., AnyBase.nucleotides) are removed. The nucleotides are now extendable similarly to native nucleotides. Thus, steps 1336-1340 are thus repeated, e.g., at least 2, 10, 20, 100, 200, 1,000, 2,000 times. For generating sequence data that can be compared with a reference database (for instance human mRNA database of the NCBI), length of the sequence snippets has to exceed 15-20 nucleotides. Therefore, steps 1 to 3 are repeated until the majority of all single molecules reaches the required length. This will take, on average, 2 offers of nucleotide incorporations per base.
[00150] Other high-throughput sequencing systems include those disclosed in Venter, J., et al. Science 16 February 2001; Adams, M. et al. Science 24 March 2000; and M. J. Levene, et al. Science 299:682-686, January 2003; as well as US Publication Application No. 20030044781 and 2006/0078937. Overall such system involve sequencing a target nucleic acid molecule having a plurality of bases by the temporal addition of bases via a polymerization reaction that is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. Sequence can then be deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labeled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labeled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined. [00151] Analyzing the rare cells to determine the existence of condition or disease may also include detecting mitochondrial DNA, telomerase, or a nuclear matrix protein in the enriched rare cell sample; detecting the presence or absence of perinuclear compartments in a cell of the enriched sample; or performing gene expression analysis, determining nucleic acid copy number, in-cell PCR, or fluorescence in-situ hybridization of the enriched sample. [00152] In some embodiments, PCR-amplified single-strand nucleic acid is hybridized to a primer and incubated with a polymerase, ATP sulfurylase, Iuciferase, apyrase, and the substrates luciferin and adenosine 5' phosphosulfate. Next, deoxynucleotide triphosphates corresponding to the bases A, C, G, and T (U) are added sequentially. Each base incorporation is accompanied by release of pyrophosphate, converted to ATP by sulfurylase, which drives synthesis of oxyluciferin and the release of visible light. Since pyrophosphate release is equimolar with the number of incorporated bases, the light given off is proportional to the number of nucleotides adding in any one step. The process repeats until the entire sequence is determined. In one embodiment, pyrosequencing analyzes DNA methylations, mutation and SNPs. In another embodiment, pyrosequencing also maps surrounding sequences as an internal quality control. Pyrosequencing analysis methods are known in the art. [00153J In some embodiments, sequence analysis of the rare cell's genetic material may include a four-color sequencing by ligation scheme (degenerate ligation), which involves hybridizing an anchor primer to one of four positions. Then an enzymatic ligation reaction of the anchor primer to a population of degenerate nonamers that are labeled with fluorescent dyes is performed. At any given cycle, the population of nonamers that is used is structure such that the identity of one of its positions is correlated with the identity of the fluorophore attached to that nonamer. To the extent that the ligase discriminates for complementarily at that queried position, the fluorescent signal allows the inference of the identity of the base. After performing the ligation and four-color imaging, the anchor primer: nonamer complexes are stripped and a new cycle begins. Methods to image sequence information after performing ligation are known in the art. [00154] In some embodiments described herein, the efficacy of a cancer treatment in a cancer patient is determined by measuring the expression level of a rare-cell associated gene over time (a temporal gene expression profile) in rare cell-enriched samples obtained from patient samples collected at a series of timepoints, including during and/or after cancer treatment. A temporal expression profile starting from the beginning of treatment and showing decreasing expression levels of the rare cell-associated gene over time indicates that the cancer treatment is efficacious in the patient. Conversely, a trend of constant or increasing expression of the rare cell-associated gene indicates that the cancer treatment is not effective in the patient. In some embodiments, determining the temporal expression profile includes determining the expression level of the rare-cell associated gene prior to the beginning of the cancer treatment. In some embodiments, determining the temporal expression profile includes determining the expression level of the rare cell-associated gene at the end of the cancer treatment period, after the end of the cancer treatment period, or both. In
[00155J Another embodiment includes kits for performing some or all of the steps of the invention. The kits may include devices and reagents in any combination to perform any or all of the steps. For example, the kits may include the arrays for the size-based separation or enrichment, the device and reagents for magnetic separation and the reagents needed for the genetic analysis, e.g., reagents to determine an expression level of a rare cell-associated gene, e.g., EGFR.
EXAMPLES
Example 1. Separation of Fetal Cord Blood
[00156] Figures 14A-14D shows a schematic of the device used to separate nucleated cells from fetal cord blood. [00157] Dimensions: 100 mm x 28 mm x lmm
[00158] Array design: 3 stages, gap size = 18, 12 and 8 μm for the first, second and third stage, respectively. [00159] Device fabrication: The arrays and channels were fabricated in silicon using standard photolithography and deep silicon reactive etching techniques. The etch depth is 140 μm. 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).
[00160] 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. [00161] Device operation: 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.
[00162] Experimental conditions: Human fetal cord blood was drawn into phosphate buffered saline containing Acid Citrate Dextrose anticoagulants. ImL of blood was processed at 3 mL/hr using the device described above at room temperature and within 48 hrs of draw. 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). [00163] 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).
[00164] Performance: Fetal nucleated red blood cells were observed in the product fraction (Figure 15A) and absent from the waste fraction (Figure 15B).
Example 2. Isolation of Fetal Cells from Maternal blood [00165] 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.
[00166] Experimental conditions: blood from consenting maternal donors carrying male fetuses was collected into K2EDTA vacutainers (366643, Becton Dickinson, Franklin Lakes, NJ) immediately following elective termination of pregnancy. The undiluted blood was processed using the device described in Example 1 at room temperature and within 9 hrs of draw. 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). Subsequently, the nucleated cell fraction was labeled with anti-CD71 microbeads (130-046-201, Miltenyi Biotech Inc., Auburn, CA) and enriched using the MiniMACS™ 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.
[00167] 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. [00168] Performance: Isolation of fetal cells was confirmed by the reliable presence of male cells in the CD71- positive population prepared from the nucleated cell fractions (Figure 16). In the single abnormal case tested, the trisomy 21 pathology was also identified (Figure 17).
Example 3. Amplification and Sequencing of STRs for Fetal Diagnosis [00169] Fetal cells or nuclei can be isolated as describe in the enrichment section or as described in example 1 and 2. DNA from the fetal cells or isolated nuclei from fetal cells can be obtained using any methods known in the art. STR loci can be chosen on the suspected trisomic chromosomes (X, 13, 18, or 21) and on other control chromosomes. These would be selected for high heterozygosity (variety of alleles) so that the paternal allele of the fetal cells is more likely to be distinct in length from the maternal alleles, with resulting improved power to detect. Di-, tri-, or terra- nucleotide repeat loci can be used. The STR loci can then be amplified according the methods described in the amplification section.
[00170] For instance, the genomic DNA from the enriched fetal cells and a maternal control sample can be fragmented, and separated into single strands. The single strands of the target nucleic acids would be bound to beads under conditions that favor each single strand molecule of DNA to bind a different bead. Each bead would then be captured within a droplet of a PCR- reaction-mixture-in-oil-emulsion and PCR amplification occurs within each droplet. The amplification on the bead could results in each bead carrying at least one 10 million copies of the unique single stranded target nucleic acid. The emulsion would be broken, the DNA is denatured and the beads carrying single-stranded nucleic acids clones would be deposited into a picolitre-sized well for further analysis. [00171] The beads can then be placed into a highly parallel sequencing by synthesis machine which can generate over 400,000 reads (~100bp per read) in a single 4 hour run. Sequence by synthesis involves inferring the sequence of the template by synthesizing a strand complementary to the target nucleic acid sequence. The identity of each nucleotide would be detected after the incorporation of a labeled nucleotide or nucleotide analog into a growing strand of a complementary nucleic acid sequence in a polymerase reaction. After the successful incorporation of a label nucleotide, a signal would be measured and then nulled and the incorporation process would be repeated until the sequence of the target nucleic acid is identified. The allele abundances for each of the STRs loci can then be determined. The presence of trisomy would be determined by comparing abundance for each of the STR loci in the fetal cells with the abundance for each of the SRTs loci in a maternal control sample. The enrichment, amplification and sequencing methods described in this example allow for the analysis of rare alleles from fetal cells, even in circumstances where fetal cells are in a mixed sample comprising other maternal cells, and even in circumstances where other maternal cells dominate the mixture.
Example 4. Detection of Mutations Related to Fetal Abnormalities [00172] Fetal cells or nuclei can be isolated as describe in the Enrichment section or as described in example 1 and 2. DNA from the fetal cells or isolated nuclei from fetal cells can be obtained using any methods known in the art. The presence of mutations of DNA or RNA from the genes listed in Figure 4 can then be analyzed. DNA or RNA of any of the genes listed in table 2 can then be amplified according the methods described in the amplification section. [00173] For instance, the genomic DNA from the enriched fetal cells and a maternal control sample can be fragmented, and separated into single strands. The single strands of the target nucleic acids would be bound to beads under conditions that favor each single strand molecule of DNA to bind a different bead. Each bead would then be captured within a droplet of a PCR- reaction-mixture-in-oil-emulsion and PCR amplification occurs within each droplet. The amplification on the bead could results in each bead carrying at least one 10 million copies of the unique single stranded target nucleic acid. The emulsion would be broken, the DNA would be denatured and the beads carrying single-stranded nucleic acids clones would be deposited into a picolitre-sized well for further analysis.
[00174] The beads can then be placed into a highly parallel sequencing by synthesis machine which can generate over 400,000 reads (—lOObp per read) in a single 4 hour run. Sequence by synthesis involves inferring the sequence of the template by synthesizing a strand complementary to the target nucleic acid sequence. The identity of each nucleotide would be detected after the incorporation of a labeled nucleotide or nucleotide analog into a growing strand of a complementary nucleic acid sequence in a polymerase reaction. After the successful incorporation of a label nucleotide, a signal would be measured and then nulled and the incorporation process would be repeated until the sequence of the target nucleic acid is identified. The presence of a mutation can then be determined. The enrichment, amplification and sequencing methods described in this example allow for the analysis of rare nucleic acids from fetal cells, even in circumstances where fetal cells are in a mixed sample comprising other maternal cells and even in circumstances where maternal cells dominate the mixture. Example 5. Quantitative Genotyping Using Molecular Inversion Probes for Trisomy Diagnosis on
Fetal Cells
[00175] Fetal cells or nuclei can be isolated as descπbed in the enrichment section or as described in example 1 and 2. Quantitative genotyping can then be used to detect chromosome copy number changes. The output of the enrichment procedure would be divided into separate wells of a microtiter plate with the number of wells chosen so no more than one cell or genome copy is located per well, and where some wells may have no cell or genome copy at all.
[00176] Perform multiplex PCR and Genotyping using MIP technology with bin specific tags: PCR primer pairs for multiple (40 - 100) highly polymorphic SNPs can then be added to each well m the microtiter plate For example, SNPs primers can be designed along chromosomes 13, 18, 21 and X to detect the most frequent aneuploidies, and along control regions of the genome where aneuploidy is not expected. Multiple (~10) SNPs would be designed for each chromosome of interest to allow for non-informative genotypes and to ensure accurate results. PCR primers would be chosen to be multiplexible with other pairs (fairly uniform melting temperature, absence of cross-priming on the human genome, and absence of primer-primer interaction based on sequence analysis). The primers would be designed to generate amplicons 70 - 100 bp in size to mcrease the performance of the multiplex PCR. The pπmers would contam a 22 bp tag on the 5' which is used in the genotyping analysis. A second of round of PCR using nested primers may be performed to ensure optimal performance of the multiplex amplification. [00177] The Molecular Inversion Probe (MIP) technology developed by Affymetrix (Santa Clara, CA) can genotype 20,000 SNPs or more in a single reaction. In the typical MIP assay, each SNP would be assigned a 22bp DNA tag which allows the SNP to be uniquely identified during the highly parallel genotyping assay. In this example, the DNA tags serve two roles: 1) determine the identity of the different SNPs and 2) determine the identity of the well from which the genotype was derived. [00178] The tagged MIP probes would be combined with the amplicons from the initial multiplex single-cell PCR and the genotyping reactions would be performed. The probe/template mix would be divided into 4 tubes each containing a different nucleotide (e.g. G, A, T or C). Following an extension and ligation step, the mixture would be treated with exonuclease to remove all linear molecules and the tags of the surviving circular molecules would be amplified using PCR. The amplified tags form all of the bins would then be pooled and hybridized to a single DNA microarray contaimng the complementary sequences to each of the 20,000 tags. [00179] Identify bins with non-maternal alleles (e g. fetal cells'): The first step m the data analysis procedure would be to use the 22bp tags to sort the 20,000 genotypes into bins which correspond to the individual wells of the original microtiter plates. The second step would be to identify bins contain non-maternal alleles which correspond to wells that contained fetal cells. Determining the number bms with non-maternal alleles relative to the total number of bins would provide an accurate estimate of the number of fnRBCs that were present in the original enriched cell population. When a fetal cell is identified in a given bin, the non-maternal alleles would be detected by 40 independent SNPs which provide an extremely high level of confidence in the result. [00180] Detect ploidv for chromosomes 13. 18, and 21: After identifying approximately 10 bins that contain fetal cells, the next step would be to determine the ploidy of chromosomes 13, 18, 21 and X by comparing ratio of maternal to paternal alleles for each of the 10 SNPs on each chromosome. The ratios for the multiple SNPs on each chromosome can be combined (averaged) to increase the confidence of the aneuploidy call for that chromosome. In addition, the information from the approximate 10 independent bins containing fetal cells can also be combined to further increase the confidence of the call. Example 6. Fetal Diagnosis with CGH
[00181] Fetal cells or nuclei can be isolated as described m the enrichment section or as described in example 1 and 2 Comparative genomic hybridization (CGH) can be used to determine copy numbers of genes and chromosomes DNA extracted from the enriched fetal cells would be hybridized to immobilized reference genomic DNA which can be in the form of bacteπal artificial chromosome (BAC) clones, or PCR products, or synthesized DNA oligos representing specific genomic sequence tags Comparing the strength of hybridization fetal cells and maternal control cells to the immobilized DNA segments gives a copy number ratio between the two samples. To perform CGH effectively starting with small numbers of cells, the DNA from the enriched fetal cells can be amplified according to the methods described in the amplification section [00182] A ratio-preserving amplification of the DNA would be done to minimize these errors, i e. this amplification method would be chosen to produce as close as possible the same amplification factor for all target regions of the genome Appropπate methods would include multiple displacement amplification, the two-stage PCR, and linear amplification methods such as in vitro transcription [00183] To the extent the amplification errors are random their effect can be reduced by averaging the copy number or copy number ratios determined at different loci over a genomic region in which aneuploidy is suspected For example, a microarray with 1000 ohgo probes per chromosome could provide a chromosome copy number with error bars ~sqrt(1000) times smaller than those from the determination based on a single probe It is also important to perform the probe averaging over the specific genomic region(s) suspected for aneuploidy For example, a common known segmental aneuploidy would be tested for by averaging the probe data only over that known chromosome region rather than the entire chromosome Random errors could be reduced by a very large factor using DNA microarrays such as Affymetrix arrays that could have a million or more probes per chromosome [00184] In practice other biases will dominate when the random amplification errors have been averaged down to a certain level, and these biases in the CGH experimental technique must be carefully controlled. For example, when the two biological samples being compared are hybridized to the same array, it is helpful to repeat the expeπment with the two different labels reversed and to average the two results - this technique of reducing the dye bias is called a 'fluor reversed pair' To some extent the use of long 'clone' segments, such as BAC clones, as the immobilized probes provides an analog averaging of these kinds of errors, however, a larger number of shorter ohgo probes should be superior because errors associated with the creation of the probe features are better averaged out [00185] Differences in amplification and hybridization efficiency from sequence region to sequence region may be systematically related to DNA sequence. These differences can be minimized by constraining the choices of probes so that they have similar melting temperatures and avoid sequences that tend to produce secondary structure. Also, although these effects are not truly 'random', they will be averaged out by averaging the results from a large number of array probes However, these effects may result in a systematic tendency for certain regions or chromosomes to have slightly larger signals than others, after probe averaging, which may mimic aneuploidy. When these particular biases are in common between the two samples being compared, they divide out if the results are normalized so that control genomic regions believed to have the same copy number in both samples yield a unity ratio [00186] After performing CGH analysis trisomy can be diagnosed by comparing the strength of hybridization fetal cells and maternal control cells to the immobilized DNA segments which would give a copy number ratio between the two samples Example 7. Isolation of Epithelial Cells from Blood
[00187] Microfluidic devices of the invention were designed by computer-aided design (CAD) and microfabπcated by photolithography. A two-step process was developed in which a blood sample is first debulked to remove the large population of small cells, and then the rare target epithelial cells target cells are recovered by immunoaffmity capture. The devices were defined by photolithography and etched into a silicon substrate based on the CAD- generated design. The cell enrichment module, which is approximately the size of a standard microscope slide, contains 14 parallel sample processing sections and associated sample handling channels that connect to common sample and buffer inlets and product and waste outlets. Each section contains an array of microfabricated obstacles that is optimized to enrich the target cell type by hydrodynamic size via displacement of the larger cells into the product stream. In this example, the microchip was designed to separate red blood cells (RBCs) and platelets from the larger leukocytes and CTCs. Enriched populations of target cells were recovered from whole blood passed through the device. Performance of the cell enrichment microchip was evaluated by separating RBCs and platelets from white blood cells (WBCs) in normal whole blood (Figure 18). In cancer patients, CTCs are found in the larger WBC fraction. Blood was minimally diluted (30%), and a 6 ml sample was processed at a flow rate of up to 6 ml/hr. The product and waste stream were evaluated in a Coulter Model "Ac-T diff ' clinical blood analyzer, which automatically distinguishes, sizes, and counts different blood cell populations. The enrichment chip achieved separation of RBCs from WBCs, in which the WBC fraction had >99% retention of nucleated cells, >99% depletion of RBCs, and >97% depletion of platelets. Representative histograms of these cell fractions are shown in Figure 19. Routine cytology confirmed the high degree of enrichment of the WBC and RBC fractions (Figure 20). [00188] Next, epithelial cells were recovered by affinity capture in a microfluidic module that is functionalized with immobilized antibody. A capture module with a single chamber containing a regular array of antibody-coated microfabricated obstacles was designed. These obstacles are disposed to maximize cell capture by increasing the capture area approximately four- fold, and by slowing the flow of cells under laminar flow adjacent to the obstacles to increase the contact time between the cells and the immobilized antibody. The capture modules may be operated under conditions of relatively high flow rate but low shear to protect cells against damage. The surface of the capture module was functionalized by sequential treatment with 10% silane, 0.5% gluteraldehyde, and avidin, followed by biotinylated anti-EpCAM. Active sites were blocked with 3% bovine serum albumin in PBS, quenched with dilute Tris HCl, and stabilized with dilute L-histidine. Modules were washed in PBS after each stage and finally dried and stored at room temperature. Capture performance was measured with the human advanced lung cancer cell line NCI-H1650 (ATCC Number CRL-5883). This cell line has a heterozygous 15 bp in-frame deletion in exon 19 of EGFR that renders it susceptible to gefϊtinib. Cells from confluent cultures were harvested with trypsin, stained with the vital dye Cell Tracker Orange (CMRA reagent, Molecular Probes, Eugene, OR), resuspended in fresh whole blood, and fractionated in the microfluidic chip at various flow rates. In these initial feasibility experiments, cell suspensions were processed directly in the capture modules without prior fractionation in the cell enrichment module to debulk the red blood cells; hence, the sample stream contained normal blood red cells and leukocytes as well as tumor cells. After the cells were processed in the capture module, the device was washed with buffer at a higher flow rate (3ml/hr) to remove the nonspecifϊcally bound cells. The adhesive top was removed and the adherent cells were fixed on the chip with paraformaldehyde and observed by fluorescence microscopy. Cell recovery was calculated from hemacytometer counts; representative capture results are shown in Table 1. Initial yields in reconstitution studies with unfractionated blood were greater than 60% with less than 5% of non-specific binding. Table 1
Figure imgf000032_0001
[00189] Next, NCI-H 1650 cells that were spiked into whole blood and recovered by size fractionation and affinity capture as described above were successfully analyzed in situ. In a trial run to distinguish epithelial cells from leukocytes, 0.5 ml of a stock solution of fluorescein-labeled CD45 pan-leukocyte monoclonal antibody were passed into the capture module and incubated at room temperature for 30 minutes. The module was washed with buffer to remove unbound antibody, and the cells were fixed on the chip with 1% paraformaldehyde and observed by fluorescence microscopy. As shown in Figure 21 the epithelial cells were bound to the obstacles and floor of the capture module. Background staining of the flow passages with CD45 pan-leukocyte antibody is visible, as are several stained leukocytes, apparently because of a low level of non-specific capture.
Example 8. Method for detection of EGFR mutations
[00190] A blood sample from a cancer patient is processed and analyzed using the devices and methods of the invention, e.g., those of Example 6, resulting in an enriched sample of epithelial cells containing CTCs. This sample is then analyzed to identify potential EGFR mutations. The method permits both identification of known, clinically relevant EGFR mutations as well as discovery of novel mutations. An overview of this process is shown in Figure 22. (00191] Below is an outline of the strategy for detection and confirmation of EGFR mutations:
1) Sequence CTC EGFR mRNA a) Purify CTCs from blood sample; b) Purify total RNA from CTCs; c) Convert RNA to cDNA using reverse transcriptase; d) Use resultant cDNA to perform first and second PCR reactions for generating sequencing templates; and e) Purify the nested PCR amplicon and use as a sequencing template to sequence EGFR exons 18-21.
2) Confirm RNA sequence using CTC genomic DNA a) Purify CTCs from blood sample; b) Purify genomic DNA (gDNA) from CTCs; c) Amplify exons 18, 19, 20, and/or 21 via PCR reactions; and d) Use the resulting PCR amplicon(s) in real-time quantitative allele-specific PCR reactions in order to confirm the sequence of mutations discovered via RNA sequencing. [00192] Further details for each step outlined above are as follows: 1) Sequence CTC EGFR mRNA a) Purify CTCs from blood sample. CTCs are isolated using any of the size-based enrichment and/or affinity purification devices of the invention. b) Purify total RNA from CTCs. Total RNA is then purified from isolated CTC populations using, e.g., the Qiagen Micro RNeasy kit, or a similar total RNA purification protocol from another manufacturer; alternatively, standard RNA purification protocols such as guanidium isothiocyanate homogenization followed by phenol/chloroform extraction and ethanol precipitation may be used. c) Convert RNA to cDNA using reverse transcriptase. cDNA reactions are carried out based on the protocols of the supplier of reverse transcriptase. Typically, the amount of input RNA into the cDNA reactions is in the range of 10 picograms (pg) to 2 micrograms (μg) total RNA. First-strand DNA synthesis is carried out by hybridizing random 7mer DNA primers, or oligo-dT primers, or gene-specific primers, to RNA templates at 65°C followed by snap-chilling on ice. cDNA synthesis is initiated by the addition of iScript Reverse Transcriptase (BioRad) or Superscript Reverse Transcriptase (Invitrogen) or a reverse transcriptase from another commercial vendor along with the appropriate enzyme reaction buffer. For iScript, reverse transcriptase reactions are carried out at 42°C for 30-45 minutes, followed by enzyme inactivation for 5 minutes at 85°C. cDNA is stored at -200C until use or used immediately in PCR reactions. Typically, cDNA reactions are carried out in a final volume of 20 μl, and 10% (2 μl) of the resultant cDNA is used in subsequent PCR reactions. d) Use resultant cDNA to perform first and second PCR reactions for generating sequencing templates. cDNA from the reverse transcriptase reactions is mixed with DNA primers specific for the region of interest (Figure 23). See Table 2 for sets of primers that may be used for amplification of exons 18-21. In Table 2, primer set M13(+)/M12(-) is internal to primer set Ml l(+)/M14(-). Thus primers M13(+) and M12(-) may be used in the nested round of amplification, if primers Ml 1(+) and M14(-) were used in the first round of expansion. Similarly, primer set Ml l(+)/M14(-) is internal to primer set M15(+)/M16(-), and primer set M23(+)/M24(-) is internal to primer set M21(+)/M22(-). Hot Start PCR reactions are performed using Qiagen Hot-Star Taq Polymerase kit, or Applied Biosystems HotStart TaqMan polymerase, or other Hot Start thermostable polymerase, or without a hot start using Promega GoTaq Green Taq Polymerase master mix, TaqMan DNA polymerase, or other thermostable DNA polymerase. Typically, reaction volumes are 50 μl, nucleotide triphosphates are present at a final concentration of 200 μM for each nucleotide, MgCl2 is present at a final concentration of 1-4 mM, and oligo primers are at a final concentration of 0.5 μM. Hot start protocols begin with a 10-15 minute incubation at 95°C, followed by 40 cycles of 94°C for one minute (denaturation), 52°C for one minute (annealing), and 72°C for one minute (extension). A lO minute terminal extension at 72°C is performed before samples are stored at 4°C until they are either used as template in the second (nested) round of PCRs, or purified using QiaQuick Spin Columns (Qiagen) prior to sequencing. If a hot-start protocol is not used, the initial incubation at 95°C is omitted. If a PCR product is to be used in a second round of PCRs, 2 μl (4%) of the initial PCR product is used as template in the second round reactions, and the identical reagent concentrations and cycling parameters are used.
Table 2. Primer Sets for expanding EGFR mRNA around Exons 18-21
Figure imgf000034_0001
e) Purify the nested PCR amplicon and use as a sequencing template to sequence EGFR exons 18-21 Sequencing is performed by ABI automated fluorescent sequencing machines and fluorescence-labeled DNA sequencing ladders generated via Sanger-style sequencing reactions using fluorescent dideoxynucleotide mixtures PCR products are purified using Qiagen QuickSpm columns, the Agencourt AMPure PCR Purification System, or PCR product purification kits obtained from other vendors After PCR products are purified, the nucleotide concentration and purity is determined with a Nanodrop 7000 spectrophotometer, and the PCR product concentration is brought to a concentration of 25 ng/μl As a quality control measure, only PCR products that have a UV-light absorbance ratio (A26c/A28o) greater than 1 8 are used for sequencing Sequencing primers are brought to a concentration of 3 2 pmol/μl
2) Confirm RNA sequence using CTC genomic DNA a) Purify CTCs from blood sample As above, CTCs are isolated using any of the size-based enrichment and/or affinity purification devices of the invention b) Purify genomic DNA (gDNA) from CTCs Genomic DNA is purified using the Qiagen DNeasy Mini kit, the Invitrogen ChargeSwitch gDNA kit, or another commercial kit, or via the following protocol:
1 Cell pellets are either lysed fresh or stored at -80°C and are thawed immediately before lysis.
2 Add 500 μl 5OmM Tns pH 7.9/10OmM EDTA/0 5%SDS (TES buffer). 3 Add 12 5 μl Proteinase K (IBI5406, 20mg/ml), generating a final [ProtK] = 0 5 mg/ml
4 Incubate at 55°C overnight in rotating incubator.
5 Add 20 μl of RNase cocktail (500 U/ml RNase A + 20,000 U/ml RNase Tl, Ambion #2288) and incubate four hours at 37°C
6 Extract with Phenol (Kodak, Tns pH 8 equilibrated), shake to mix, spin 5 mm in tabletop centrifuge
7 Transfer aqueous phase to fresh tube
8 Extract with Phenol/Chloroform/Isoamyl alcohol (EMD, 25 24 1 ratio, Tns pH 8 equilibrated), shake to mix, spm five minutes in tabletop centrifuge
9 Add 50 μl 3M NaOAc pH = 6 10. Add 500 μl EtOH.
11. Shake to mix. Strings of precipitated DNA may be visible If anticipated DNA concentration is very low, add carrier nucleotide (usually yeast tRNA)
12. Spin one minute at max speed in tabletop centrifuge
13. Remove supernatant.
14. Add 500 μl 70% EtOH, Room Temperature (RT)
15. Shake to mix.
16. Spin one minute at max speed in tabletop centrifuge.
17. Air dry 10-20 minutes before adding TE.
18. Resuspend in 400 μl TE. Incubate at 65°C for 10 minutes, then leave at RT overnight before quantitation on Nanodrop. c) Amplify exons 18, 19, 20, and/or 21 via PCR reactions. Hot start nested PCR amplification is carried out as described above in step Id, except that there is no nested round of amplification The initial PCR step may be stopped during the log phase in order to minimize possible loss of allele-specific information during amplification The primer sets used for expansion of EGFR exons 18-21 are listed in Table 3 (see also Paez et al., Science 304:1497-1500 (Supplementary Material) (2004)).
Table 3. Primer sets for expanding EGFR genomic DNA
Figure imgf000035_0001
d) Use the resulting PCR amplιcon(s) in real-time quantitative allele-specific PCR reactions in order to confirm the sequence of mutations discovered via RNA sequencing. An aliquot of the PCR amplicons is used as template in a multiplexed allele-specific quantitative PCR reaction using TaqMan PCR 5' Nuclease assays with an Applied Biosystems model 7500 Real Time PCR machine (Figure 24). This round of PCR amplifies subregions of the initial PCR product specific to each mutation of interest Given the very high sensitivity of Real Time PCR, it is possible to obtain complete information on the mutation status of the EGFR gene even if as few as 10 CTCs are isolated Real Time PCR provides quantification of allelic sequences over 8 logs of input DNA concentrations, thus, even heterozygous mutations in impure populations are easily detected using this method [00193] Probe and primer sets are designed for all known mutations that affect gefitmib responsiveness in NSCLC patients, including over 40 such somatic mutations, including point mutations, deletions, and insertions, that have been reported in the medical literature For illustrative purposes, examples of pπmer and probe sets for five of the point mutations are listed in Table 4 In general, oligonucleotides may be designed using the primer optimization software program Primer Express (Applied Biosystems), with hybridization conditions optimized to distinguish the wild type EGFR DNA sequence from mutant alleles EGFR genomic DNA amplified from lung cancer cell lines that are known to carry EGFR mutations, such as H358 (wild type), H1650 (15-bp deletion, Δ2235-2249), and H1975 (two point mutations, 2369 C→ T, 2573 T→ G), is used to optimize the allele-specific Real Time PCR reactions. Using the TaqMan 5 ' nuclease assay, allele-specific labeled probes specific for wild type sequence or for known EGFR mutations are developed The oligonucleotides are designed to have meltmg temperatures that easily distinguish a match from a mismatch, and the Real Time PCR conditions are optimized to distinguish wild type and mutant alleles All Real Time PCR reactions are carried out in triplicate
[00194] Initially, labeled probes containing wild type sequence are multiplexed in the same reaction with a single mutant probe Expressing the results as a ratio of one mutant allele sequence versus wild type sequence may identify samples containing or lacking a given mutation After conditions are optimized for a given probe set, it is then possible to multiplex probes for all of the mutant alleles within a given exon within the same Real Time PCR assay, increasing the ease of use of this analytical tool in clinical settmgs
[00195] A unique probe is designed for each wild type allele and mutant allele sequence. Wild-type sequences are marked with the fluorescent dye VIC at the 5' end, and mutant sequences with the fluorophore FAM A fluorescence quencher and Minor Groove Binding moiety are attached to the 3' ends of the probes ROX is used as a passive reference dye for normalization purposes. A standard curve is generated for wild type sequences and is used for relative quantitation Precise quantitation of mutant signal is not required, as the input cell population is of unknown, and varying, purity The assay is set up as described by ABI product literature, and the presence of a mutation is confirmed when the signal from a mutant allele probe rises above the background level of fluorescence (Figure 25), and this threshold cycle gives the relative frequency of the mutant allele in the input sample
Table 4. Probes and Primers for Allele-Specific qPCR
Figure imgf000036_0001
Figure imgf000037_0001
Example 9: Absence of EGFR expression in leukocytes
[00196] The protocol of Example 7 would be most useful if EGFR were expressed in target cancer cells but not in background leukocytes. To test whether EGFR mRNA is present in leukocytes, several PCR experiments were performed. Four sets of primers, shown in Table 5, were designed to amplify four corresponding genes:
1) BCKDK (branched-chain a-ketoacid dehydrogenase complex kinase) - a "housekeeping" gene expressed in all types of cells, a positive control for both leukocytes and tumor cells;
2) CD45 - specifically expressed in leukocytes, a positive control for leukocytes and a negative control for tumor cells;
3) EpCaM - specifically expressed in epithelial cells, a negative control for leukocytes and a positive control for tumor cells; and
4) EGFR - the target mRNA to be examined. Table 5
Figure imgf000038_0001
[00197] Total RNAs of approximately 9xlO6 leukocytes isolated using a cell enrichment device of the invention (cutoff size 4 μm) and 5x106 H 1650 cells were isolated by using RNeasy mini kit (Qiagen). Two micrograms of total RNAs from leukocytes and H1650 cells were reverse transcribed to obtain first strand cDNAs using 100 pmol random hexamer (Roche) and 200 U Superscript II (Invitrogen) in a 20 μl reaction. The subsequent PCR was carried out using 0.5 μl of the first strand cDNA reaction and 10 pmol of forward and reverse primers in total 25 μl of mixture. The PCR was ran for 40 cycles of 950C for 20 seconds, 56°C for 20 seconds, and 700C for 30 seconds. The amplified products were separated on a 1% agarose gel. As shown in Figure 26A, BCKDK was found to be expressed in both leukocytes and Hl 650 cells; CD45 was expressed only in leukocytes; and both EpCAM and EGFR were expressed only in H1650 cells. These results, which are fully consistent with the profile of EGFR expression shown in Figure 26B, confirmed that EGFR is a particularly useful target for assaying mixtures of cells that include both leukocytes and cancer cells, because only the cancer cells will be expected to produce a signal.

Claims

WHAT IS CLAIMED IS:
I. A method for detecting cancer in a subject comprising: enriching a sample from said subject for rare cells by flowing said sample through an array of obstacles coated with antibodies that specifically bind to one or more cell populations in said sample to obtain a rare cell-enriched sample, wherein said rare cells in said sample are in a concentration of less than 1 in 100,000 cells prior to said enrichment, and detecting the presence or absence of a rare cell nucleic acid in said rare cell-enriched sample, wherein the presence of said rare cell nucleic acid in said rare cell-enriched sample indicates the presence of said cancer in said subject.
2. The method of claim 1, wherein said rare cell-enriched sample is not eluted from said array prior to said detecting.
3. The method of claim 1, wherein outflow from said array occurs in a single direction.
4. The method of claim 1, wherein said array of obstacles comprises between 5,000 to 100,000 obstacles.
5 The method of claim 1, wherein said array of obstacles comprises 20-500 rows.
6. The method of claim 5, wherein said rows have a continuous offset.
7. The method of claim 1, wherein said sample is a blood sample.
8. The method of claim 1, wherem said sample is treated with a stabilizer, a preservative, or a fixant prior to said enriching.
9. The method of claim 1, wherein said rare cells comprise circulating tumor cells, epithelial cells, endothelial cells, or progenitor stem cells.
10. The method of claim 9, wherem said rare cells comprise epithelial cells.
I I. The method of claim 9, wherem said detecting comprises detecting the expression of a gene identified in Figure 5.
12. The method of claim 11 , further comprising detecting the presence or absence of a mutation in said gene.
13. The method of claim 12, wherem said mutation occurs m any of exons 18-21 of an EGFR gene.
14 The method of claim 11, wherein a level of expression of said gene is determined.
15. The method of claim 11, wherein said gene is EGFR, EGF, EpCAM , MUC-I, HER-2, or Claudin-7.
16. The method of claim 15, wherein said gene is EpCAM.
17. The method of claim 15, wherem said gene is EGFR or EGF.
18 The method of claim 1, wherem said cancer is acute lymphoblastic leukemia, acute or chrome lymphocyctic or granulocytic tumor, acute myeloid leukemia, acute promyelocytic leukemia, adenocarcinoma, adenoma, adrenal cancer, basal cell carcinoma, bone cancer, brain cancer, breast cancer, bronchi cancer, cervical dysplasia, chronic myelogenous leukemia, colon cancer, epidermoid carcinoma, Ewing's sarcoma, gallbladder cancer, gallstone tumor, giant cell tumor, glioblastoma multiforma, hairy-cell tumor, head cancer, hyperplasia, hyperplastic corneal nerve tumor, in situ carcinoma, intestinal ganglioneuroma, islet cell tumor, Kaposi's sarcoma, kidney cancer, larynx cancer, leiomyomater tumor, liver cancer, lung cancer, lymphomas, malignant carcinoid, malignant hypercalcemia, malignant melanomas, marfanoid habitus tumor, medullary carcinoma, metastatic skin carcinoma, mucosal neuromas, mycosis fungoide, myelodysplastic syndrome, myeloma, neck cancer, neural tissue cancer, neuroblastoma, osteogenic sarcoma, osteosarcoma, ovarian tumor, pancreas cancer, parathyroid cancer, pheochromocytoma, polycythemia vera, primary brain tumor, prostate cancer, rectum cancer, renal cell tumor, retinoblastoma, rhabdomyosarcoma, seminoma, skin cancer, small-cell lung tumor, soft tissue sarcoma, squamous cell carcinoma, stomach cancer, thyroid cancer, topical skin lesion, veticulum cell sarcoma, or Wilm's tumor.
19. The method of claim 1, wherein said enriching step comprises flowing said sample or a fraction thereof through one or more magnetic fields that selectively retain paramagnetic components.
20. The method of claim 1 , further comprising (i) applying hyperbaric pressure to said sample or a fraction thereof prior to said enriching to selectively eject nuclei of said rare cells; or (ii) applying hyperbaric pressure to said enriched sample or a fraction thereof to selectively eject nuclei of said rare cells.
21. The method of claim 1 , wherein said antibodies bind to said rare cells.
22. The method of claim 1, wherein said antibodies comprise an anti-EpCAM antibody, an anti-E-cadherin antibody, or an anti-Muc-1 antibody.
23. The method of claim 22, wherein said antibodies comprise an anti-EpCAM antibody.
24. The method of claim 22, wherein said antibodies comprise at least two antibodies from said anti-EpCAM antibody, said anti-E-cadherin antibody, or said anti-Muc-1 antibody.
25. The method of claim 1, wherein said antibodies bind to cells in said sample other than said rare cells.
26. The method of claim 1, wherein said antibodies comprise an anti-CD71 antibody, anti-CD235a antibody, anti-CD36 antibody, an anti-selectin antibody, an anti-CD45 antibody, or an anti-GPA antibody.
27. The method of claim 1, comprising performing said enriching and detecting on samples obtained at two or more time points.
28. The method of claim 27, wherein said two or more time points occur at an interval between one day and one year of each other.
29. The method of claim 27, wherein said two or more time points occur at a regular time interval.
30. The method of claim 29, wherein said regular time interval is two weeks, one month, two months, three months, six months, or one year.
31. The method of claim 1, wherein said biological sample was obtained from a subject that has not undergone cancer therapy.
32. The method of claim 1, wherein said biological sample was obtained from a subject that has undergone or is undergoing cancer therapy.
33. The method of claim 1, further comprising flowing said sample or said enriched sample through an array of obstacles that selectively directs cells larger than a predetermined size in to a first outlet and cells equal to or smaller than said predetermined size to a second outlet.
34. The method of claim 33, wherein said predetermined size is about the size of a red blood cell, a white blood cell, a circulating tumor cell, an epithelial cell, an endothelial cell, or a progenitor stem cell.
35. The method of claim 1, wherein said predetermined size is about 2 to about 10 μm.
36. A method for detecting cancer in a subject comprising:
(i) enriching a sample from said subject for rare cells by flowing said sample through an array of obstacles that selectively directs cells smaller than a predetermined size to a first outlet and cells equal to or larger than said predetermined size to a second outlet to obtain a first rare cell-enriched sample , wherein said rare cells in said sample are in a concentration of less than 1 in 100,000 cells;
(ii) flowing said first rare cell-enriched sample through an array of obstacles coated with antibodies that specifically bind to one or more cell populations in said sample to obtain a second rare cell-enriched sample; and (iii) detecting the presence or absence of a rare cell nucleic acid in said second rare-cell enriched sample, wherein the presence of said rare cell nucleic acid in said second rare-cell enriched sample indicates the presence of said cancer in said subject.
37. The method of claim 36, wherein said sample is a blood sample.
38. The method of claim 36, wherein said sample is treated with a stabilizer, a preservative, or a fixant prior to said enriching.
39. The method of claim 36, wherein said predetermined size is about the size of a red blood cell, a white blood cell, a circulating tumor cell, an epithelial cell, an endothelial cell, or a progenitor stem cell.
40. The method of claim 36, wherein said predetermined size is about 1 to about 10 μm.
41. The method of claim 40, wherein said predetermined size is about 2 to about 8 μm.
42. The method of claim 36, wherein said predetermined size is about 4 μm.
43. The method of claim 36, wherein said rare cell nucleic acid is from a circulating tumor cell, an epithelial cell, an endothelial cell, or a progenitor stem cell.
44. The method of claim 43, wherein said rare cell nucleic acid is from an epithelial cell.
45. The method of claim 36, wherein said detecting comprises detecting the expression of a gene identified in Figure 5.
46. The method of claim 36, wherein said rare cell nucleic acid is EGFR, EGF, EpCAM, MUC-I , HER-2, or Claudin-7.
47. The method of claim 46, wherein said rare cell nucleic acid is EpCAM.
48. The method of claim 36, wherein said rare cell nucleic acid is EGFR or EGF.
49. The method of claim 36, wherein said cancer is breast cancer, lung cancer, or prostate cancer.
50. The method of claim 36, further comprising flowing said sample or said enriched sample through an array of obstacles coated with antibodies that specifically bind to one or more cell populations in said sample.
51. A method for determining cancer treatment efficacy in a patient, comprising:
(i) enriching, for epithelial cells, each of a plurality of blood samples from said patient by flowing each blood sample in said plurality through an array of obstacles coated with one or more antibodies that specifically bind to epithelial cells to obtain a plurality of epithelial cell-enriched blood samples, wherein said plurality of blood samples was generated by obtaining a blood sample from said patient at a series of time points during said cancer treatment, and said series of time points includes at least a first time point at the beginning of said treatment and at least two points subsequent to said first time point; (ii) quantifying in each epithelial-cell enriched sample of said plurality, the expression level of at least one gene expressed in epithelial cells and not expressed in other cells present in blood, to obtain a temporal expression profile for said at least one gene in said plurality of epithelial cell-enriched blood samples; and
(iii) determining that said cancer treatment is efficacious if said temporal expression profile indicates a decreasing trend of expression levels for said at least one gene.
52. The method of claim 51 , wherein said expression level of is an mRNA expression level.
53. The method of claim 51, wherein said antibodies comprise an anti-EpCAM antibody, an anti-E-cadherin antibody, or an anti-Muc-1 antibody.
54. The method of claim 51 , wherein said sample is treated with a stabilizer, a preservative, or a fixant prior to said enriching.
55. The method of claim 53, wherein said antibodies comprise an anti-EpCAM antibody.
56. The method of claim 55, wherein said antibodies comprise at least two antibodies from said anti-EpCAM antibody, said anti-E-cadherin antibody, or said anti-Muc-1 antibody.
57. The method of claim 51 , wherein said detecting comprises detecting the expression of a gene identified in Figure 5.
58. The method of claim 57, wherein said gene is EGFR, EGF, EpCAM , MUC-I, HER-2, or
Claudin-7.
59. The method of claim 57, wherein said gene is EpCAM.
60. The method of claim 59, wherein said gene is EGFR.
61. The method of claim 60, further comprising detecting the presence of a mutation in said EGFR gene.
62. The method of claim 51 , wherein said time points occur at an interval of about one week to about one month from each other.
63. The method of claim 51 , wherein at least one of said time points occurs after the end of said cancer treatment.
64. A kit for detecting cancer cells in a subject, comprising a device comprising an array of obstacles coated with antibodies that specifically bind to one or more cell populations and a set of reagents for detecting the expression of a gene identified in Figure 5.
65. The kit of claim 64, wherein said gene is EGFR, EGF, EpCAM , MUC- 1 , HER-2, or Claudin-7.
66. The kit of claim 65, wherein said gene is EpCAM.
67. The kit of claim 64, wherein said gene is EGFR.
68. The kit of claim 64, wherein said expression of a gene is mRNA expression of said gene.
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