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 - 101 . (canceled) 
     
     
         102 . A method of analyzing a fetal cell in a mixed sample obtained from a pregnant human female, the method comprising:
 (a) obtaining a mixed sample comprising fetal and maternal cells;   (b) enriching the mixed sample for fetal cells to produce an enriched sample comprising fetal cells and maternal cells, wherein the enrichment increases the ratio of fetal cells to maternal cells to about 1/10,000 to about 1/10;   (c) lysing fetal cells in the enriched sample and separating nuclei of the fetal cells from other cells and cell components in the enriched sample to produce isolated fetal nuclei;   (d) isolating genomic DNA from the isolated fetal nuclei;   (e) amplifying genomes of the isolated fetal nuclei to produce amplified nucleic acids; and   (f) analyzing the amplified nucleic acids for aneuploidy using ultra-deep sequencing.   
     
     
         103 . The method of  claim 102 , wherein the analyzing comprises analyzing for fetal aneuploidy, wherein the fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of one or more chromosomes. 
     
     
         104 . The method of  claim 103 , wherein the fetal aneuploidy is a fetal aneuploidy of a chromosome selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y. 
     
     
         105 . The method of  claim 103 , wherein the fetal aneuploidy comprises trisomy or monosomy. 
     
     
         106 . The method of  claim 105 , wherein the fetal aneuploidy comprises trisomy, and wherein the trisomy comprises trisomy 13, trisomy 18, or trisomy 21. 
     
     
         107 . The method of  claim 105 , wherein the fetal aneuploidy comprises monosomy X and the chromosome suspected of being aneuploid comprises chromosome X. 
     
     
         108 . The method of  claim 102 , wherein the fetal aneuploidy comprises XXX, XXY, or XYY. 
     
     
         109 . The method of  claim 102 , wherein the ultra-deep sequencing produces partial genome sequences for analysis. 
     
     
         110 . The method of  claim 102 , wherein the ultra-deep sequencing produces complete genome sequences for analysis. 
     
     
         111 . The method of  claim 102 , wherein amplifying the genomes of the lysed fetal cells comprises amplifying whole genomes of the lysed fetal cells. 
     
     
         112 . The method of  claim 102 , further comprising binning fetal cells prior to the step of lysing fetal cells in the enriched sample. 
     
     
         113 . The method of  claim 112 , wherein binning comprises use of a nanofluidic system that separates samples into droplets. 
     
     
         114 . The method of  claim 102 , further comprising positive selection for fetal cells prior to binning. 
     
     
         115 . The method of  claim 102 , further comprising negative selection for non-target cells prior to binning. 
     
     
         116 . The method of  claim 102 , wherein the enrichment increases the ratio of fetal cells to maternal cells to about 1/100 to about 1/10. 
     
     
         117 . The method of  claim 102 , wherein the enrichment increases the ratio of fetal cells to maternal cells to about 1/50 to about 1/10. 
     
     
         118 . The method of  claim 102 , wherein the enrichment increases the ratio of fetal cells to maternal cells to about 1/10. 
     
     
         119 . The method of  claim 102 , wherein the mixed sample is obtained from whole blood, bone marrow suspension, vaginal flow, milk, or genitourinary tracts fluid. 
     
     
         120 . The method of  claim 102 , wherein the enriching comprises contacting the mixed sample with particles coupled to antibodies that selectively bind to fetal cells. 
     
     
         121 . The method of  claim 120 , wherein the particles are magnetic particles.