Determination of fetal aneuploidy by quantification of genomic dna from mixed samples

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 determining the presence or absence of a fetal aneuploidy using a maternal blood sample comprising fetal and maternal genomic DNA obtained from a female pregnant, the method comprising:
 (a) enriching a maternal blood sample comprising fetal and maternal genomic DNA for fetal genomic DNA to produce an enriched sample comprising fetal and maternal genomic DNA;   (b) obtaining fetal and maternal genomic DNA from the enriched sample;   (c) selectively amplifying and sequencing a plurality of genomic DNA regions of the fetal and maternal genomic DNA of (b), wherein said genomic DNA regions are selected from each of two or more chromosomes, wherein said two or more chromosomes comprises at least one chromosome that is suspected of being aneuploid and at least one control chromosome that is not suspected of being aneuploid;   (d) quantifying amplified and sequenced genomic DNA regions of at least one chromosome that is suspected of being aneuploid and at least one chromosome that is not suspected of being aneuploid of (c); and   (e) comparing quantities of at least amplified and sequenced genomic DNA regions of the at least one chromosome suspected of being aneuploid with quantities of at least amplified, sequenced genomic DNA regions of the at least one control chromosome that is not suspected of being aneuploid without performing a single nucleotide polymorphism (SNP) analysis or a short tandem repeat (STR) analysis to thereby determine the presence or absence of said fetal aneuploidy.   
     
     
         103 . The method of  claim 102 , wherein said fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of one or more chromosomes. 
     
     
         104 . The method of  claim 102 , wherein said at least one chromosome that is suspected of being aneuploid is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y. 
     
     
         105 . The method of  claim 104 , wherein said fetal aneuploidy comprises trisomy. 
     
     
         106 . The method of  claim 105 , wherein said trisomy comprises trisomy 13, trisomy 18, or trisomy 21. 
     
     
         107 . The method of  claim 102 , wherein said fetal aneuploidy comprises XXX, XXY, or XYY. 
     
     
         108 . The method of  claim 102 , wherein said genomic DNA regions selected from each of two or more chromosomes are selectively amplified by PCR amplification. 
     
     
         109 . The method of  claim 108 , wherein said PCR amplification comprises using oligonucleotide primers that do not interact with one another. 
     
     
         110 . The method of  claim 108 , wherein said PCR amplification comprises using oligonucleotide primers having uniform melting temperatures. 
     
     
         111 . The method of  claim 108 , wherein said PCR amplification comprises using oligonucleotide primer pairs that do not cross-prime with the human genome. 
     
     
         112 . The method of  claim 102 , wherein said genomic DNA regions selected from each of two or more chromosomes do not overlap with one another. 
     
     
         113 . A method of determining the presence or absence of a fetal aneuploidy in a fetus, the method comprising:
 (a) enriching a maternal blood sample comprising fetal and maternal genomic DNA for fetal genomic DNA to produce an enriched sample comprising fetal and maternal genomic DNA;   (b) obtaining fetal and maternal genomic DNA from the enriched sample;   (c) selectively amplifying a plurality of genomic DNA regions of the fetal and maternal genomic DNA of (b), wherein said genomic DNA regions are selected from each of two or more chromosomes, wherein said two or more chromosomes includes at least one suspected aneuploid chromosome and at least one non-aneuploid chromosome;   (d) sequencing said selectively amplified genomic DNA regions of (c) to produce sequences corresponding to selectively amplified genomic DNA regions of at least one suspected aneuploid chromosome and sequences corresponding to selectively amplified genomic DNA regions of at least one non-aneuploid chromosome; and   (e) quantifying sequences corresponding to selectively amplified genomic DNA regions of at least one suspected aneuploid chromosome and quantifying sequences corresponding to selectively amplified genomic DNA regions of at least one non-aneuploid chromosome; and   (f) conducting an analysis of the quantified sequences of (e) comprising comparing quantities of at least selectively amplified genomic DNA regions of at least one suspected aneuploid chromosome with quantities of at least selectively amplified genomic DNA regions of at least one non-aneuploid chromosome without performing a single nucleotide polymorphism (SNP) analysis or a short tandem repeat (STR) analysis, thereby determining the presence or absence of said fetal aneuploidy.   
     
     
         114 . The method of  claim 113 , wherein said fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of one or more chromosomes. 
     
     
         115 . The method of  claim 113 , wherein said at least one suspected aneuploid chromosome is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y. 
     
     
         116 . The method of  claim 115 , wherein said fetal aneuploidy comprises trisomy. 
     
     
         117 . The method of  claim 116 , wherein said trisomy comprises trisomy 13, trisomy 18, or trisomy 21. 
     
     
         118 . The method of  claim 113 , wherein said fetal aneuploidy comprises XXX, XXY, or XYY. 
     
     
         119 . The method of  claim 113 , wherein said genomic DNA regions selected from each of two or more chromosomes are selectively amplified by PCR amplification. 
     
     
         120 . The method of  claim 119 , wherein said PCR amplification comprises using oligonucleotide primer pairs that do not interact with one another. 
     
     
         121 . The method of  claim 119 , wherein said PCR amplification comprises using oligonucleotide primer pairs having uniform melting temperatures. 
     
     
         122 . The method of  claim 119 , wherein said PCR amplification comprises using oligonucleotide primer pairs that do not cross-prime with the human genome. 
     
     
         123 . The method of  claim 113 , wherein said genomic DNA regions selected from two or more chromosomes do not overlap with one another. 
     
     
         124 . The method of  claim 113 , wherein said at least one suspected aneuploid chromosome comprises at least one suspected trisomic chromosome and said at least one non-aneuploid chromosome comprises at least one non-trisomic chromosome. 
     
     
         125 . The method of  claim 124 , wherein said at least one suspected trisomic chromosome comprises chromosome 21 and said at least one non-trisomic chromosome comprises chromosome 18. 
     
     
         126 . The method of  claim 102 , wherein said at least one chromosome that is suspected of being aneuploid comprises chromosome 21.