Diagnosis of fetal abnormalities using polymorphisms including short tandem repeats

Abstract

The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, i.e. aneuploidy. In addition, the present invention provides methods to determine when there are insufficient fetal cells for a determination and report a non-informative case. The present invention involves quantifying regions of genomic DNA from a mixed sample. More particularly the invention involves quantifying DNA polymorphisms from the mixed sample.

1 . A method for diagnosing a fetal abnormality comprising: enriching one or more fetal cells from a maternal blood sample using size-based separation, identifying said one or more fetal cells using biomarkers, further enriching said one or more identified individual fetal cells using laser microdissection, analyzing one or more regions of genomic DNA from said identified individual fetal cells for polymorphic DNA regions, and determining a fetal abnormality based on analysis of said polymorphic DNA regions. 
     
     
         2 . The method of  claim 1 , wherein said analysis of polymorphic DNA regions is comprised of single-nucleotide polymorphism (SNP) analysis or short tandem repeats (STR) analysis. 
     
     
         3 . The method of  claim 1 , further comprising treating maternal blood sample with one or more reagents prior to first enriching step, said reagents comprising: 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. 
     
     
         4 . The method of  claim 1 , wherein said analyzing step involves the amplification of one or more regions of genomic DNA by single cell PCR. 
     
     
         5 . The method of  claim 1 , wherein said analyzing step involves whole genome amplification. 
     
     
         6 . The method of  claim 1 , wherein said first enriching step comprises applying said sample to a device comprising an array of obstacles on a substrate. 
     
     
         7 . The method of  claim 1 , wherein said first enriching step further comprises enriching one or more fetal cells by magnetic separation. 
     
     
         8 . The method of  claim 7 , wherein said magnetic separation comprises labeling one or more fetal cells with anti-CD71 microbeads and applying said labeled one or more fetal cells to a magnetic column. 
     
     
         9 . The method of  claim 1 , wherein said first enriching step comprises applying said sample into a system that separates a first component of said mixed sample in a first direction and a second component of said mixed sample in a second direction, and wherein said first component has a larger hydrodynamic size than said second component. 
     
     
         10 . The method of  claim 1 , wherein said fetal abnormality is aneuploidy. 
     
     
         11 . The method of  claim 10 , wherein said aneuploidy is trisomy selected from the group consisting of: trisomy 13, trisomy 18, trisomy 21 (Down Syndrome), Klinefelter Syndrome (XXY), other irregular number of sex or autosomal chromosomes, and a combination thereof. 
     
     
         12 . The method of  claim 1 , wherein said fetal abnormality is a segmental aneuploidy. 
     
     
         13 . The method of  claim 1 , wherein said regions of genomic DNA are localized in a specific chromosome. 
     
     
         14 . The method of  claim 13 , wherein said chromosome is selected from the group consisting of: X chromosome, Y chromosome, chromosome 21, chromosome 13 and chromosome 18.