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 probability of trisomy of a chromosome or chromosome segment of interest in the genome of a fetus, the method comprising:
 amplifying DNA derived from free floating DNA in maternal blood, maternal serum, or maternal plasma of the mother of the fetus;   determining for the amplified DNA, using a microarray or a high throughput sequencing platform a quantity of DNA for each locus at a plurality of loci on the chromosome or chromosome segment of interest and a quantity of DNA for each allele at a plurality of SNP loci on one or more chromosomes or chromosome segments expected to be disomic in the mother and the fetus, where the SNP loci comprise an allele present in the fetus but not the mother;   estimating a ratio of fetal to maternal DNA in the maternal blood, maternal serum, or maternal plasma using the quantity of each allele at the SNP loci and an expected quantity of each allele at the SNP loci for different fetal fractions, thereby determining the ratio of fetal to maternal DNA in the maternal blood, maternal serum, or maternal plasma; and   determining, on a computer, the probability of trisomy of the chromosome or chromosome segment of interest using the quantity of the amplified DNA at the plurality of loci on the chromosome or chromosome segment of interest and the estimated ratio of fetal to maternal DNA in the maternal blood, maternal serum, or maternal plasma.   
     
     
         2 . The method of  claim 1 , further comprising determining a bias of one or more techniques used to amplify the DNA and/or determine the quantity of DNA, and using the bias to statistically correct the quantity of the amplified DNA at the plurality of loci on the chromosome or chromosome segment of interest before the determined quantity of amplified DNA on the chromosome or chromosome segment of interest is used for determining the probability of trisomy. 
     
     
         3 . The method of  claim 1 , wherein a maximum likelihood estimate is used to estimate the ratio of fetal to maternal DNA. 
     
     
         4 . The method of  claim 1 , wherein prior probabilities of trisomy given maternal age and/or gestational age of the mother are used in determining the probability of trisomy in the chromosome or chromosome segment of interest in the fetus, in addition to the quantity of the amplified DNA at the plurality of loci on the chromosome or chromosome segment of interest and the estimated ratio of fetal to maternal DNA in the maternal blood, maternal serum, or maternal plasma. 
     
     
         5 . The method of  claim 1 , wherein the quantities of amplified DNA at the plurality of loci on the chromosome or chromosome segment of interest and for each allele at the plurality of SNP loci on one or more chromosomes or chromosome segments expected to be disomic in the mother and the fetus, are determined using a method comprising a microarray. 
     
     
         6 . The method of  claim 1 , wherein DNA derived from the fetus in the maternal blood, maternal serum, or maternal plasma is not preferentially enriched over the DNA derived from the mother before performance of the method. 
     
     
         7 . The method of  claim 1 , further comprising aggregating the quantities of amplified DNA from the plurality of loci on the chromosome or chromosome segment of interest to determine an aggregated value, and using the aggregated value to determine the probability of trisomy of the chromosome or chromosome segment of interest. 
     
     
         8 . The method of  claim 1 , wherein determining the probability of trisomy of the chromosome or chromosome segment of interest comprises comparing a mean value for the quantities of amplified DNA from the plurality of loci on each of the chromosome or chromosome segment of interest to a mean value for the quantities of amplified DNA from a plurality of loci on one or more disomic chromosome or chromosome segments. 
     
     
         9 . The method of  claim 1 , wherein the chromosome or chromosome segment of interest is chromosome 13, chromosome 18, chromosome 21, chromosome X, chromosome Y, or combinations thereof. 
     
     
         10 . The method of  claim 1 , wherein the amplifying is performed using an allele-specific amplification technique. 
     
     
         11 . A method for determining the probability of trisomy for a chromosome or chromosome segment of interest in the genome of a fetus, the method comprising:
 a) amplifying DNA derived from free floating DNA in maternal blood, maternal serum, or maternal plasma of the mother of the fetus, using PCR and/or an allele-specific amplification technique;   b) analyzing the amplified DNA using a microarray or a high throughput sequencing platform to determine a quantity of each allele at a plurality of SNP loci on one or more chromosomes or chromosome segments expected to be disomic in both the mother and the fetus, where the SNP loci comprise an allele present in the fetus but not the mother;   c) making genotypic measurements on the chromosome or chromosome segment of interest in the amplified DNA for alleles present in the mother and in the fetus;   d) estimating a ratio of fetal to maternal DNA using the quantity of each allele at the SNP loci and an expected quantity of each allele at the SNP loci for different fetal fractions; and   e) using the estimated ratio of fetal to maternal DNA and the genotypic measurements on the chromosome or chromosome segment of interest, to determine the probability of trisomy for the chromosome or chromosome segment of interest.   
     
     
         12 . The method of  claim 11 , wherein determining the quantity of each allele at the plurality of SNP loci on the one or more chromosomes or chromosome segments expected to be disomic and making genotypic measurements on the chromosome or chromosome segment of interest, are performed in the same reaction using the same measuring technique. 
     
     
         13 . The method of  claim 11 , further comprising determining a bias of the PCR and/or allele-specific amplification or a bias of the microarray or high throughput sequencing platform, and using the bias to statistically correct the determined quantity of each allele at the plurality of SNP loci on the one or more chromosomes or chromosome segments expected to be disomic before the quantity of each allele is used to estimate the ratio of fetal to maternal DNA. 
     
     
         14 . The method of  claim 11 , further comprising determining a bias of the PCR and/or allele-specific amplification or a bias of the microarray or high throughput sequencing platform, and using the bias to statistically correct the genotypic measurements on the chromosome or chromosome segment of interest before the genotypic measurements on the chromosome or chromosome segment of interest are used to determine the probability of trisomy for the chromosome or chromosome segment of interest. 
     
     
         15 . The method of  claim 11 , wherein a maximum likelihood estimate is used to estimate the ratio of fetal to maternal DNA. 
     
     
         16 . The method of  claim 15 , wherein the maximum likelihood estimate is performed using a gradient descent method. 
     
     
         17 . The method of  claim 15 , wherein the maximum likelihood estimate is performed using a Newton-Raphson optimization method. 
     
     
         18 . The method of  claim 11 , wherein the quantity of each allele is determined using a method comprising a microarray. 
     
     
         19 . The method of  claim 11 , wherein the DNA derived from the fetus in the maternal blood, maternal serum, or maternal plasma is not preferentially enriched over the DNA derived from the mother before performance of the method. 
     
     
         20 . The method of  claim 11 , wherein the amplifying is performed using a method comprising an allele-specific amplification technique that uses probes. 
     
     
         21 . A method for determining the probability of trisomy for a chromosome or chromosome segment of interest in the genome of a fetus, the method comprising:
 a) amplifying DNA derived from free floating DNA in maternal blood, maternal serum, or maternal plasma of the mother of the fetus, using PCR and/or an allele-specific amplification technique;   b) analyzing the amplified DNA using a microarray or a high throughput sequencing platform to determine a quantity of each allele at a plurality of loci on one or more chromosomes or chromosome segments expected to be disomic in both the mother and the fetus and a plurality of loci on the chromosome or chromosome segment of interest, where the loci on the one or more chromosomes or chromosome segments expected to be disomic comprise SNP loci having an allele that is present in the fetus but not in the mother, and the plurality of loci on the chromosome or chromosome segment of interest comprise alleles that are present in the fetus and the mother in differing ratios if trisomy is present or absent in the chromosome or chromosome segment of interest in the fetus;   c) estimating a ratio of fetal to maternal DNA using the quantity of each allele at the plurality of loci on the one or more chromosomes or chromosome segments expected to be disomic; and   d) using the estimated ratio of fetal to maternal DNA and the quantity of the plurality of loci on the chromosome or chromosome segment of interest to determine the probability of trisomy for the chromosome or chromosome segment of interest.   
     
     
         22 . The method of  claim 21 , further comprising determining a bias of the PCR and/or allele-specific amplification or a bias of the microarray or high throughput sequencing platform, and using the bias to statistically correct the determined quantity of each allele at the plurality of loci on the one or more chromosomes or chromosome segments expected to be disomic before the quantity of each allele is used to estimate the ratio of fetal to maternal DNA. 
     
     
         23 . The method of  claim 21 , further comprising determining a bias of the PCR and/or allele-specific amplification or a bias of the microarray or high throughput sequencing platform, and using the bias to statistically correct the determined quantity of the plurality of loci on the chromosome or chromosome segment of interest before the quantity is used to determine the probability of trisomy for the chromosome or chromosome segment of interest. 
     
     
         24 . The method of  claim 21 , wherein the DNA derived from the fetus in the maternal blood, maternal serum, or maternal plasma is not preferentially enriched over the DNA derived from the mother before performance of the method. 
     
     
         25 . The method of  claim 21 , wherein the amplifying is performed using a method comprising an allele-specific amplification technique. 
     
     
         26 . A method for determining a ratio of fetal to maternal DNA in maternal blood, maternal serum, or maternal plasma of a mother of a fetus, the method comprising:
 a) amplifying DNA derived from free floating DNA in the maternal blood, maternal serum, or maternal plasma, using PCR and/or an allele-specific amplification technique;   b) analyzing the amplified DNA using a microarray or a high throughput sequencing platform to determine a quantity of each allele at a plurality of SNP loci on one or more chromosomes or chromosome segments expected to be disomic in both the mother and the fetus, where the SNP loci comprise an allele present in the fetus but not the mother; and   c) estimating the ratio of fetal to maternal DNA using the quantity of each allele at the SNP loci and an expected quantity of each allele for different fetal fractions.   
     
     
         27 . The method of  claim 26 , further comprising determining a bias of the PCR and/or allele-specific amplification or a bias of the microarray or high throughput sequencing platform, and using the bias to statistically correct the determined quantity of each allele at the plurality of SNP loci on the one or more chromosomes or chromosome segments expected to be disomic before the quantity of each allele is used to estimate the ratio of fetal to maternal DNA. 
     
     
         28 . The method of  claim 26 , wherein a maximum likelihood estimate is used to estimate the ratio of fetal to maternal DNA. 
     
     
         29 . The method of  claim 26 , wherein the DNA derived from the fetus in the maternal blood, maternal serum, or maternal plasma is not preferentially enriched over the DNA derived from the mother before performance of the method. 
     
     
         30 . The method of  claim 26 , wherein the amplifying is performed using a method comprising an allele-specific amplification technique.