Methods For The Diagnosis Of Fetal Abnormalities

Abstract

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

1 . A method for determining a condition in a patient or a fetus of a patient comprising:
 enriching one or more cells from a sample from said patient using size-based separation,   obtaining one or more nucleic acid molecules from said enriched cells;   detecting said one or more nucleotides in said nucleic acid molecules by high throughput sequencing.   
     
     
         2 . The method of  claim 1 , wherein said sample is a blood sample. 
     
     
         3 . The method of  claim 2 , wherein said blood sample is a maternal blood sample. 
     
     
         4 . The method of  claim 1 , wherein said one or more cells are selected from the group consisting of fetal cells, epithelial cells, endothelial cells, progenitor stem cells, or a combination thereof. 
     
     
         5 . The method of  claim 1 , wherein said cells are in said sample at a concentration of less than 1 in 100,000 cells prior to said enrichment. 
     
     
         6 . The method of  claim 1 , wherein said one or more cells are fetal cells and said condition is selected from the group consisting of trisomy 13, trisomy 18, trisomy 21, Klinefelter Syndrome, dup(17)(p11.2p11.2) syndrome, Down syndrome, Pre-eclampsia, Pre-term labor, Edometriosis, Pelizaeus-Merzbacher disease, dup(22)(q11.2q11.2) syndrome, Cat eye syndrome, Cri-du-chat syndrome, Wolf-Hirschhorn syndrome, Williams-Beuren syndrome, Charcot-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), 1 p36 deletion, or a combination thereof. 
     
     
         7 . The method of  claim 1  wherein said condition is selected from the group consisting of 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, Wilm's tumor, or a combination thereof. 
     
     
         8 . The method of  claim 1 , wherein said detecting step occurs in substantially real-time. 
     
     
         9 . The method of  claim 1 , wherein said size-based separation is performed by flowing said sample or a fraction thereof through an array of obstacles that selectively directs cells larger than a predetermined size to a first outlet and cells smaller than said predetermined size to a second outlet. 
     
     
         10 . The method of  claim 9 , wherein at least a portion of said obstacles are coated with binding moieties that specifically bind to one or more cell populations in said sample. 
     
     
         11 . The method of  claim 9 , wherein said binding moieties are one selected from the group consisting of antibodies, receptors, ligands, proteins, nucleic acids, sugars, carbohydrates and combinations thereof. 
     
     
         12 . The method of  claim 1  wherein said enriching step further comprises one or more of the following steps:
 (i) flowing said sample or a fraction thereof through one or more magnetic fields that selectively retain paramagnetic components; and 
 (ii) applying hyperbaric or hypobaric pressure to said sample or a fraction thereof. 
 
     
     
         13 . A method for determining a condition in a patient or a fetus of a patient comprising:
 enriching one or more cells from a sample from said patient by flowing said sample or a fraction thereof through an array of obstacles, wherein at least a portion of said obstacles are coated with binding moieties that specifically bind to one or more cell populations in said sample,   obtaining one or more nucleic acid molecules from said enriched cells;   detecting said one or more nucleotides in said nucleic acid molecules by high throughput sequencing.   
     
     
         14 . The method of  claim 13 , wherein said sample is a blood sample. 
     
     
         15 . The method of  claim 14 , wherein said blood sample is a maternal blood sample. 
     
     
         16 . The method of  claim 13 , wherein said one or more cells are selected from the group consisting of fetal cells, epithelial cells, endothelial cells, progenitor stem cells, or a combination thereof. 
     
     
         17 . The method of  claim 13 , wherein said cells are in said sample at a concentration of less than 1 in 100,000 cells prior to said enrichment. 
     
     
         18 . The method of  claim 13 , wherein said one or more cells are fetal cells and said condition is selected from the group consisting of trisomy 13, trisomy 18, trisomy 21, Klinefelter Syndrome, dup(17)(p11.2p11.2) syndrome, Down syndrome, Pre-eclampsia, Pre-term labor, Edometriosis, Pelizaeus-Merzbacher disease, dup(22)(q11.2q11.2) syndrome, Cat eye syndrome, Cri-du-chat syndrome, Wolf-Hirschhorn syndrome, Williams-Beuren syndrome, Charcot-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), 1p36 deletion, or a combination thereof. 
     
     
         19 . The method of  claim 13 , wherein said condition is selected from the group consisting of 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, glioblastorxia 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, Wilm's tumor, or a combination thereof. 
     
     
         20 . The method of  claim 13 , wherein said detecting step occurs in substantially real-time. 
     
     
         21 - 57 . (canceled)