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 . A method of analyzing the presence or absence of a fetal aneuploidy in a fetus using a maternal blood sample comprising fetal and maternal genomic DNA obtained from a pregnant human female, the method comprising:
 (a) enriching the 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 DNA regions of the fetal and maternal genomic DNA of (b), wherein said plurality of DNA regions comprises DNA regions selected from each of two chromosomes, wherein said two chromosomes comprise a chromosome suspected of being aneuploid and a control chromosome that is not suspected of being aneuploid, to generate amplified DNA regions corresponding to said plurality of DNA regions;   (d) sequencing said amplified DNA regions of (c) to produce sequences corresponding to DNA regions selected from the chromosome suspected of being aneuploid and sequences corresponding to DNA regions selected from the control chromosome;   (e) quantifying sequences corresponding to DNA regions selected from the chromosome suspected of being aneuploid and quantifying sequences corresponding to DNA regions selected from the control chromosome; and   (f) analyzing the presence or absence of a fetal aneuploidy by analyzing the quantity of sequences corresponding to DNA regions selected from the chromosome suspected of being aneuploid and the quantity of sequences corresponding to DNA regions selected from the control chromosome without performing a single nucleotide polymorphism (SNP) analysis or a short tandem repeat (STR) analysis.   
     
     
         2 . The method of  claim 1 , wherein said analyzing of (f) comprises comparing the quantity of sequences corresponding to DNA regions selected from the chromosome suspected of being aneuploid with the quantity of sequences corresponding to DNA regions selected from the control chromosome. 
     
     
         3 . The method of  claim 1 , wherein said fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of one or more chromosomes. 
     
     
         4 . The method of  claim 1 , wherein the chromosome suspected of being aneuploid is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y. 
     
     
         5 . The method of  claim 4 , wherein said fetal aneuploidy comprises trisomy or monosomy of the chromosome suspected of being aneuploid. 
     
     
         6 . The method of  claim 5 , wherein said trisomy comprises trisomy 13, trisomy 18, or trisomy 21. 
     
     
         7 . The method of  claim 5 , wherein said fetal aneuploidy comprises monosomy X and the chromosome suspected of being aneuploid comprises chromosome X. 
     
     
         8 . The method of  claim 1 , wherein said fetal aneuploidy comprises XXX, XXY, or XYY. 
     
     
         9 . The method of  claim 1 , wherein said selectively amplifying of (c) comprises amplifying DNA regions selected from each of the two chromosomes by polymerase chain reaction (PCR) amplification. 
     
     
         10 . The method of  claim 9 , wherein said PCR amplification comprises using oligonucleotide primers that do not interact with one another. 
     
     
         11 . The method of  claim 9 , wherein said PCR amplification comprises using oligonucleotide primers having uniform melting temperatures. 
     
     
         12 . The method of  claim 9 , wherein said PCR amplification comprises using oligonucleotide primer pairs that do not cross-prime with the human genome. 
     
     
         13 . The method of  claim 1 , wherein the DNA regions selected from each of the two chromosomes do not overlap with one another. 
     
     
         14 . The method of  claim 1 , wherein the control chromosome is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y. 
     
     
         15 . A method of determining the presence or absence of a fetal aneuploidy in a fetus using a maternal blood sample comprising fetal and maternal genomic DNA obtained from a pregnant human female, the method comprising:
 (a) obtaining fetal and maternal genomic DNA from the maternal blood sample;   (b) selectively amplifying a plurality of DNA regions of the fetal and maternal genomic DNA of (a), wherein said DNA regions are selected from each of two or more chromosomes, wherein said two or more chromosomes comprise at least one chromosome suspected of being aneuploid and at least one control chromosome that is not suspected of being aneuploid, to generate amplified DNA regions corresponding to the plurality of DNA regions,   (c) sequencing said selectively amplified DNA regions of (b) to produce sequences corresponding to DNA regions selected from the at least one chromosome suspected of being aneuploid and sequences corresponding to DNA regions selected from the at least one control chromosome;   (d) quantifying sequences corresponding to DNA regions selected from the at least one chromosome suspected of being aneuploid and quantifying sequences corresponding to DNA regions selected from the at least one control chromosome; and   (e) conducting an analysis of the quantity of sequences corresponding to DNA regions selected from the at least one chromosome suspected to be aneuploid and the quantity of sequences corresponding to DNA regions selected from the at least one control chromosome without performing a single nucleotide polymorphism (SNP) analysis or a short tandem repeat (STR) analysis to thereby determine the presence or absence of a fetal aneuploidy.   
     
     
         16 . The method of  claim 15 , wherein conducting an analysis of (e) comprises comparing the quantity of sequences corresponding to DNA regions selected from the chromosome suspected of being aneuploid with the quantity of sequences corresponding to DNA regions selected from the control chromosome. 
     
     
         17 . The method of  claim 15 , wherein the chromosome suspected of being aneuploid is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y. 
     
     
         18 . The method of  claim 15 , wherein the control chromosome is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, and chromosome Y. 
     
     
         19 . (canceled) 
     
     
         20 . The method of  claim 15 , wherein said fetal aneuploidy comprises monosomy, trisomy, tetrasomy, or pentasomy of one or more chromosomes. 
     
     
         21 . The method of  claim 20 , wherein said fetal aneuploidy comprises trisomy 13, trisomy 18, or trisomy 21. 
     
     
         22 .- 29 . (canceled)