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.

1 . A method for determining the copy number of a chromosome of interest in a target individual, using genotypic measurements made on genetic material from the target individual, wherein the genetic material of the target individual is mixed with genetic material from the mother of the target individual, the method comprising:
 obtaining genotypic data for a set of SNPs of the parents of the target individual;   making genotypic measurements for the set of SNPs on a mixed sample that comprises DNA from the target individual and also DNA from the mother of the target individual;   creating, on a computer, a set of ploidy state hypothesis for the chromosome of interest of the target individual;   determining, on the computer, the probability of each of the hypotheses given the genetic measurements of the mixed sample and the genetic data of the parents of the target individual; and   using the determined probabilities of each hypothesis to determine the most likely copy number of the chromosome of interest in the target individual.   
     
     
         2 . The method of  claim 1  wherein the target individual is a fetus. 
     
     
         3 . The method of  claim 1  wherein the copy number determination is used to make a clinical decision. 
     
     
         4 . The method of  claim 3  wherein the target individual is a fetus, and the clinical decision is to terminate a pregnancy where the fetus is found to have a genetic abnormality, or to not terminate the pregnancy where the fetus is not found to have a genetic abnormality. 
     
     
         5 . The method of  claim 1  wherein the set of SNPs comprises a plurality of SNPs from the chromosome of interest, and a plurality of SNPs from at least one chromosome that is expected to be disomic on the target individual. 
     
     
         6 . The method of  claim 5  wherein the step of determining, on the computer, the probability of each of the hypotheses comprises:
 using the genotypic data of the parents to determine parental contexts for each of the SNPs; 
 grouping the genotypic measurements of the mixed sample into the parental contexts; 
 using the grouped genotypic measurements from the at least one chromosome that is expected to be disomic to determine a platform response; 
 using the grouped genotypic measurements from the at least one chromosome that is expected to be disomic to determine a ratio of fetal to maternal DNA in the mixed sample; 
 using the determined platform response and the determined ratio to predict an expected distribution of SNP measurements for each set of SNPs in each parental context under each hypothesis; and 
 calculating the probabilities that each of the hypotheses is true given the platform response, and given the ratio, and given the grouped genotypic measurements of the mixed sample, and given the predicted expected distributions, for each parental context, for each hypothesis. 
 
     
     
         7 . The method of  claim 1  wherein the chromosome of interest is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, the X chromosome, the Y chromosome, and combinations thereof. 
     
     
         8 . The method of  claim 1  wherein the method is used to determine the copy number of a number of chromosomes in the target individual, where the number is taken from the group consisting of one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty, twenty one, twenty two, and twenty three. 
     
     
         9 . The method of  claim 1  wherein the mixed sample is maternal blood, maternal plasma or some other substance taken from a pregnant mother. 
     
     
         10 . The method of  claim 1  wherein the target individual's genetic material is free floating DNA found in maternal blood or serum. 
     
     
         11 . The method of  claim 1  wherein the target individual's genetic material is nuclear DNA found in one or more cells from the target individual. 
     
     
         12 . The method of  claim 1  wherein a confidence is computed for the chromosome copy number determination. 
     
     
         13 . The method of  claim 1  wherein a ratio of fetal to maternal DNA in the mixed sample is determined for individual chromosomes. 
     
     
         14 . The method of  claim 1  wherein the step of obtaining of genotypic data, and/or the step of making genetotypic measurements is done by measuring genetic material using techniques selected from the group consisting of padlock probes, circularizing probes, genotyping microarrays, SNP genotyping assays, chip based microarrays, bead based microarrays, other SNP microarrays, other genotyping methods, Sanger DNA sequencing, pyrosequencing, high throughput sequencing, reversible dye terminator sequencing, sequencing by ligation, sequencing by hybridization, other methods of DNA sequencing, other high throughput genotyping platforms, fluorescent in situ hybridization (FISH), comparative genomic hybridization (CGH), array CGH, and multiples or combinations thereof. 
     
     
         15 . The method of  claim 14  wherein the step of measuring genetic material is done on genetic material that is amplified, prior to being measured, using a technique that is selected from the group consisting of Polymerase Chain Reaction (PCR), ligand mediated PCR, degenerative oligonucleotide primer PCR, Multiple Displacement Amplification (MDA), allele-specific PCR, allele-specific amplification techniques, bridge amplification, padlock probes, circularizing probes, and combinations thereof. 
     
     
         16 . The method of  claim 1  wherein the step of determining the copy number of the chromosome of interest is performed for the purpose of screening for a chromosomal condition, wherein the chromosomal condition is selected from the group consisting of nullsomy, monosomy, disomy, uniparental disomy, euploidy, trisomy, matched trisomy, unmatched trisomy, maternal trisomy, paternal trisomy, tetrasomy, matched tetrasomy, unmatched tetrasomy, other aneuploidy, unbalanced translocation, balanced translocation, recombination, deletion, insertion, mosaicism, and combinations thereof. 
     
     
         17 . The method of  claim 1  wherein the method is used for the purpose of paternity testing. 
     
     
         18 . A method for determining the copy number of a chromosome of interest in a target individual, using genotypic measurements made on genetic material from the target individual, wherein the genetic material of the target individual is mixed with genetic material from the mother of the target individual, the method comprising:
 obtaining genotypic data for a set of SNPs of the mother of the target individual;   making genotypic measurements for the set of SNPs on a mixed sample that comprises DNA from the target individual and also DNA from the mother of the target individual;   creating, on a computer, a set of ploidy state hypothesis for the chromosome of interest of the target individual;   determining, on the computer, the probability of each of the hypotheses given the genetic measurements of the mixed sample and the genetic data of the mother of the target individual; and   using the determined probabilities of each hypothesis to determine the most likely copy number of the chromosome of interest in the target individual.