Methods for non-invasive prenatal ploidy calling

Abstract

Disclosed herein are methods for determining the copy number of a chromosome in a fetus in the context of non-invasive prenatal diagnosis. In an embodiment, the measured genetic data from a sample of genetic material that contains both fetal DNA and maternal DNA is analyzed, along with the genetic data from the biological parents of the fetus, and the copy number of the chromosome of interest is determined. In an embodiment, the maternal serum is measured using a single-nucleotide polymorphism (SNP) microarray, along with parental genomic data, and the determination of the chromosome copy number is used to make clinical decisions pertaining to the fetus.

What is claimed is: 
     
         1 . A method for determining the risk of aneuploidy of at least one chromosome or chromosome segment of interest in the genome of a gestating fetus, the method comprising:
 a) obtaining a plurality of probes to each of a plurality of loci (i) that are known to be polymorphic in the human population and (ii) that are likely to be informative based on the rate of SNP heterozygosity in the human population for the locus; wherein each of the plurality of loci is a SNP locus on at least one chromosome that is expected to be disomic in both the mother and the fetus where the mother is homozygous for a first allele at that locus, and the father is (i) heterozygous for the first allele and a second allele or (ii) homozygous for a second allele at that locus;   b) amplifying free floating maternal and fetal DNA from a blood, serum, or plasma sample from the mother of the gestating fetus, using the plurality of probes to obtain amplified products comprising the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic;   c) measuring an amount of the amplified products to obtain a measured quantity of each allele at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic;   d) determining a ratio of fetal to maternal DNA in the blood, serum, or plasma sample using (i) the measured quantity of the second allele or (ii) the measured quantity of the first and second alleles for each of the polymorphic loci on the at least one chromosome that is expected to be disomic;   e) measuring genetic data at a plurality of loci on at least one chromosome or chromosome segment of interest in the blood, serum, or plasma sample;   f) creating one or more hypotheses specifying the number of copies of the at least one chromosome or chromosome segment of interest in the genome of the fetus; and   g) determining, on a computer, the probability of each of the hypotheses using the measured genetic data for the at least one chromosome or chromosome segment of interest and the ratio of fetal to maternal DNA, and thereby the risk of aneuploidy of the at least one chromosome or chromosome segment of interest in the genome of the fetus.   
     
     
         2 . The method of  claim 1 , wherein a maximum likelihood estimate is used to determine the ratio of fetal to maternal DNA. 
     
     
         3 . The method of  claim 2 , wherein the maximum likelihood estimate is performed using a gradient descent method or a Newton-Raphson optimization method. 
     
     
         4 . The method of  claim 1 , wherein prior probabilities of aneuploidy given maternal age and/or gestational age of the mother are used in determining the risk of aneuploidy, in addition to the measured genetic data from the at least one chromosome or chromosome segment of interest and the determined ratio of fetal to maternal DNA in the sample. 
     
     
         5 . The method of  claim 1 , wherein measuring the amplified products at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic, and measuring the genetic data at the plurality of loci on the at least one chromosome or chromosome segment of interest, are performed in the same reaction using a microarray. 
     
     
         6 . The method of  claim 1 , wherein the fetal DNA in the sample is not preferentially enriched over the maternal DNA before performance of the method. 
     
     
         7 . A method for determining the risk of aneuploidy of at least one chromosome or chromosome segment of interest in the genome of a gestating fetus, the method comprising:
 a) binding a plurality of probes to maternal and fetal DNA from a blood, serum, or plasma sample from the mother of the gestating fetus at a plurality of loci on a chromosome or chromosome segment of interest, and at each of a plurality of SNP loci on at least one chromosome that is expected to be disomic in both the mother and the fetus, wherein each of the plurality of loci on the at least one chromosome that is expected to be disomic is a locus where the mother is homozygous for a first allele at that locus, and the father is (i) heterozygous for the first allele and a second allele or (ii) homozygous for a second allele at that locus;   b) amplifying each of the plurality of loci having a bound probe to obtain amplified products comprising the plurality of loci on the at least one chromosome or chromosome segment of interest and the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic;   c) measuring an amount of the amplified products to obtain a measured quantity of each allele at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic;   d) determining a ratio of fetal to maternal DNA in the blood, serum, or plasma sample using (i) the measured quantity of the second allele or (ii) the measured quantity of the first and second alleles for each of the polymorphic loci on the at least one chromosome that is expected to be disomic;   e) measuring an amount of the amplified products to obtain genetic data at the plurality of loci on the at least one chromosome or chromosome segment of interest;   f) creating one or more hypotheses specifying the number of copies of the at least one chromosome or chromosome segment of interest in the genome of the fetus; and   g) determining, on a computer, the probability of each of the hypotheses using the measured genetic data for the at least one chromosome or chromosome segment of interest and the ratio of fetal to maternal DNA, and thereby the risk of aneuploidy of the at least one chromosome or chromosome segment of interest in the genome of the fetus.   
     
     
         8 . The method of  claim 7 , wherein a maximum likelihood estimate is used to determine the ratio of fetal to maternal DNA. 
     
     
         9 . The method of  claim 8 , wherein the maximum likelihood estimate is performed using a gradient descent method. 
     
     
         10 . The method of  claim 7 , wherein prior probabilities of aneuploidy given maternal age and/or gestational age of the mother are used in determining the risk of aneuploidy, in addition to the measured genetic data from the at least one chromosome or chromosome segment of interest and the determined ratio of fetal to maternal DNA in the sample. 
     
     
         11 . The method of  claim 7 , wherein measuring the amplified products at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic, and measuring the genetic data at the plurality of loci on the at least one chromosome or chromosome segment of interest, are performed in the same reaction using a microarray, and wherein the fetal DNA in the sample is not preferentially enriched over the maternal DNA before performance of the method. 
     
     
         12 . A method for determining the risk of aneuploidy of at least one chromosome or chromosome segment of interest in the genome of a gestating fetus, the method comprising:
 a) binding a plurality of probes to maternal and fetal DNA from a blood, serum, or plasma sample from the mother of the gestating fetus, at each of a plurality of loci on a chromosome or chromosome segment of interest, and at each of a plurality of polymorphic loci on at least one chromosome that is expected to be disomic in both the mother and the fetus where the mother is homozygous for a first allele at that locus, and the father is (i) heterozygous for the first allele and a second allele or (ii) homozygous for a second allele at that locus;   b) amplifying each of the plurality of loci having a bound probe to obtain amplified products comprising the plurality of loci on the at least one chromosome or chromosome segment of interest and the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic;   c) measuring the amplified products in the same reaction to obtain a measured genetic data at the plurality of loci on the chromosome or chromosome segment of interest and a measured quantity of each allele at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic;   d) determining a bias of a technique used to measure the amount of the amplified products, wherein the bias is used to statistically correct the measured genetic data at the plurality of loci on the chromosome or chromosome segment of interest and the measured quantity of each allele at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic;   e) determining a ratio of fetal to maternal DNA in the blood, serum, or plasma sample using (i) the statistically corrected, measured quantity of the second allele or (ii) the statistically corrected, measured quantity of the first and second alleles for each of the polymorphic loci on the at least one chromosome that is expected to be disomic;   f) creating one or more hypotheses specifying the number of copies of the at least one chromosome or chromosome segment of interest in the genome of the fetus; and   g) determining, on a computer, the probability of each of the hypotheses using the statistically corrected, measured genetic data for the at least one chromosome or chromosome segment of interest and the ratio of fetal to maternal DNA, and thereby the risk of aneuploidy of the at least one chromosome or chromosome segment of interest in the genome of the fetus.   
     
     
         13 . The method of  claim 12 , wherein a maximum likelihood estimate is used to determine the ratio of fetal to maternal DNA. 
     
     
         14 . The method of  claim 13 , wherein the maximum likelihood estimate is performed using a gradient descent method. 
     
     
         15 . The method of  claim 13 , wherein the maximum likelihood estimate is performed using a Newton-Raphson optimization method. 
     
     
         16 . The method of  claim 12 , wherein prior probabilities of aneuploidy given maternal age and/or gestational age of the mother are used in determining the risk of aneuploidy, in addition to the statistically corrected, measured genetic data from the at least one chromosome or chromosome segment of interest and the determined ratio of fetal to maternal DNA in the sample. 
     
     
         17 . The method of  claim 12 , wherein the measuring is performed using a microarray. 
     
     
         18 . The method of  claim 12 , further comprising aggregating the statistically corrected, measured genetic data from the plurality of loci on the at least one chromosome or chromosome segment of interest to determine an aggregated value, and using the aggregated value to determine the risk of aneuploidy of the at least one chromosome or chromosome segment of interest. 
     
     
         19 . The method of  claim 12 , wherein determining the risk of aneuploidy of the at least one chromosome or chromosome segment of interest comprises comparing a mean value for the statistically corrected, measured genetic data from the plurality of loci on each of the at least one chromosome or chromosome segment of interest to a mean value for the measured genetic data from the plurality of loci on one or more of the at least one chromosome that is expected to be disomic. 
     
     
         20 . The method of  claim 12 , wherein at least one of the at least one chromosome or chromosome segment of interest is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, chromosome Y, and combinations thereof. 
     
     
         21 . The method of  claim 12 , wherein the fetal DNA in the sample is not preferentially enriched over the maternal DNA before performance of the method. 
     
     
         22 . A method for determining the risk of aneuploidy of at least one chromosome or chromosome segment of interest in the genome of a gestating fetus, the method comprising:
 a) binding a plurality of probes to maternal and fetal DNA from a blood, serum, or plasma sample from the mother of the gestating fetus, at each of a plurality of loci on a chromosome or chromosome segment of interest, and at each of a plurality of polymorphic loci on at least one chromosome that is expected to be disomic in both the mother and the fetus where the mother is homozygous for a first allele at that locus, and the father is (i) heterozygous for the first allele and a second allele or (ii) homozygous for a second allele at that locus;   b) amplifying each of the plurality of loci having a bound probe to obtain amplified products comprising the plurality of loci on the at least one chromosome or chromosome segment of interest and the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic;   c) measuring an amount of the amplified products in the same reaction to obtain measured genetic data at the plurality of loci on the chromosome or chromosome segment of interest and of each allele at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic, wherein the fetal DNA in the sample is not preferentially enriched over the maternal DNA before performance of the method;   d) determining a ratio of fetal to maternal DNA in the blood, serum, or plasma sample using (i) the measured quantity of the second allele or (ii) the measured quantity of the first and second alleles for each of the polymorphic loci on the at least one chromosome that is expected to be disomic;   e) creating one or more hypotheses specifying the number of copies of the at least one chromosome or chromosome segment of interest in the genome of the fetus; and   f) determining, on a computer, the probability of each of the hypotheses using the measured genetic data for the at least one chromosome or chromosome segment of interest and the ratio of fetal to maternal DNA, and thereby the risk of aneuploidy of the at least one chromosome or chromosome segment of interest in the genome of the fetus.   
     
     
         23 . The method of  claim 22 , wherein a maximum likelihood estimate is used to determine the ratio of fetal to maternal DNA. 
     
     
         24 . The method of  claim 23 , wherein the maximum likelihood estimate is performed using a gradient descent method. 
     
     
         25 . The method of  claim 23 , wherein the maximum likelihood estimate is performed using a Newton-Raphson optimization method. 
     
     
         26 . The method of  claim 22 , wherein prior probabilities of aneuploidy given maternal age and/or gestational age of the mother are used in determining the risk of aneuploidy, in addition to the measured genetic data from the at least one chromosome or chromosome segment of interest and the determined ratio of fetal to maternal DNA in the sample. 
     
     
         27 . The method of  claim 22 , wherein the measuring is performed using a microarray. 
     
     
         28 . The method of  claim 22 , further comprising aggregating the measured genetic data from the plurality of loci on the at least one chromosome or chromosome segment of interest to determine an aggregated value, and using the aggregated value to determine the risk of aneuploidy of the at least one chromosome or chromosome segment of interest. 
     
     
         29 . The method of  claim 22 , wherein determining the risk of aneuploidy of the at least one chromosome or chromosome segment of interest comprises comparing a mean value for the measured genetic data from the plurality of loci on each of the at least one chromosome or chromosome segment of interest to a mean value for the measured genetic data from the plurality of loci on one or more of the at least one chromosome that is expected to be disomic. 
     
     
         30 . The method of  claim 22 , wherein at least one of the at least one chromosome or chromosome segment of interest is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, chromosome Y, and combinations thereof.