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 whether a chromosome or chromosome segment of interest in the genome of a gestating fetus is euploid or aneuploid, the method comprising:
 obtaining measured genetic data at a plurality of loci in a mixed sample of DNA comprising fetal DNA and maternal DNA, and wherein the plurality of loci comprises single nucleotide polymorphisms (SNPs);   determining, on a computer, a ratio of fetal to maternal DNA in the mixed sample using the measured genetic data;   creating, on a computer, a distribution of expected data for the mixed sample for the case where the chromosome or chromosome segment of interest is euploid;   creating, on a computer, a distribution of expected data for the mixed sample for the case where the chromosome or chromosome segment of interest is aneuploid using the ratio of fetal to maternal DNA in the mixed sample;   calculating, on a computer, (i) a data fit between the measured genetic data and the distribution of expected data for the euploid case and (ii) a data fit between the measured genetic data and the distribution of expected data for the aneuploid case; and   selecting the case for which the data fit is best, thereby determining whether the chromosome or chromosome segment of interest in the fetus is euploid or aneuploid.   
     
     
         2 . The method of  claim 1 , further comprising obtaining measured genetic data at the plurality of loci from genetic material from the mother and/or father of the fetus, wherein the distribution of expected data for the aneuploidy case is determined using the measured genetic data of the mother and/or father, the measured genetic data of the mixed sample, and the ratio of fetal to maternal DNA. 
     
     
         3 . The method of  claim 1 , wherein a confidence is computed for the determination of whether the chromosome or chromosome segment of interest in the fetus is euploid or aneuploid. 
     
     
         4 . The method of  claim 1 , wherein the plurality of loci comprises (i) a plurality of SNPs from the chromosome or chromosome segment of interest and (ii) a plurality of SNPs from at least one chromosome or chromosome segment that is expected to be disomic in the fetus. 
     
     
         5 . The method of  claim 4 , wherein the method comprises:
 obtaining genotypic measurements at each of the SNPs from genetic material from the mother and the father of the fetus;   using the genotypic data of the mother and father 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 calculate a distribution of expected SNP measurements for the set of SNPs in at least one parental context under each hypothesis; and   calculating, on a computer, the probability that each of the hypotheses is true from the platform response, the determined ratio, the grouped genotypic measurements of the mixed sample, and the distribution of expected SNP measurements for the at least one parental context.   
     
     
         6 . The method of  claim 1 , wherein the ratio of fetal to maternal DNA in the mixed sample is determined for individual chromosomes. 
     
     
         7 . The method of  claim 1 , wherein the mixed sample is derived from maternal blood or maternal plasma. 
     
     
         8 . The method of  claim 1 , wherein the fetal DNA is free floating DNA found in maternal blood or serum. 
     
     
         9 . The method of  claim 1 , wherein the fetal DNA is nuclear DNA found in one or more cells from the fetus. 
     
     
         10 . The method of  claim 1 , wherein the step of obtaining measured genetic data is performed by measuring genetic material using a technique 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 combinations thereof. 
     
     
         11 . The method of  claim 10 , wherein the step of measuring genetic material is performed 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), ligation-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. 
     
     
         12 . The method of  claim 1 , wherein the method further comprises taking a clinical action based on the determination of whether the fetus is euploid or aneuploid, wherein the clinical action is termination of a pregnancy. 
     
     
         13 . The method of  claim 1 , wherein the method further comprises performing amniocentesis or chorion villus biopsy. 
     
     
         14 . 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. 
     
     
         15 . The method of  claim 1 , wherein the step of determining whether the chromosome or chromosome segment of interest in the fetus is euploid or aneuploid is performed for the purpose of screening for a chromosomal condition 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. 
     
     
         16 . The method of  claim 1 , wherein the method comprises determining whether the fetus has Down syndrome, Klinefelters syndrome, Edwards syndrome, or Turner syndrome. 
     
     
         17 . The method of  claim 1 , wherein the method is used for paternity testing. 
     
     
         18 . A method for determining the number of copies of a chromosome or chromosome segment of interest in the genome of a gestating fetus, the method comprising:
 obtaining measured genetic data at a plurality of loci in a mixed sample of DNA comprising fetal DNA and maternal DNA, and wherein the plurality of loci comprises SNPs;   determining, on a computer, a ratio of fetal to maternal DNA in the mixed sample from the measured genetic data;   creating, on a computer, a plurality of hypotheses specifying the number of copies of the chromosome or chromosome segment of interest in the fetus;   determining, on the computer, the probability of each of the hypotheses using the measured genetic data and the ratio of fetal to maternal DNA; and   selecting the hypothesis with the greatest probability, thereby determining the number of copies of the chromosome or chromosome segment of interest in the genome of the fetus.   
     
     
         19 . The method of  claim 18 , further comprising obtaining measured genetic data at the plurality of loci from genetic material from the mother and/or father of the fetus, wherein the probability of each of the hypotheses is determined using the measured genetic data of the mother and/or father, the measured genetic data of the mixed sample, and the ratio of fetal to maternal DNA. 
     
     
         20 . The method of  claim 18 , wherein a confidence is computed for the determination of the number of copies of the chromosome or chromosome segment of interest in the genome of the target individual. 
     
     
         21 . The method of  claim 18 , wherein the plurality of loci comprises (i) a plurality of SNPs from the chromosome or chromosome segment of interest and (ii) a plurality of SNPs from at least one chromosome or chromosome segment that is expected to be disomic in the fetus. 
     
     
         22 . The method of  claim 21 , wherein the method comprises:
 obtaining genotypic measurements at each of the SNPs from genetic material from the mother and the father of the fetus;   using the genotypic data of the mother and father 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 calculate a distribution of expected SNP measurements for the set of SNPs in at least one parental context under each hypothesis; and   calculating, on a computer, the probability that each of the hypotheses is true from the platform response, the determined ratio, the grouped genotypic measurements of the mixed sample, and the distribution of expected SNP measurements for the at least one parental context.   
     
     
         23 . The method of  claim 18 , wherein the method further comprises performing amniocentesis or chorion villus biopsy. 
     
     
         24 . The method of  claim 18 , wherein the method is used for paternity testing. 
     
     
         25 . A method for determining a ratio of fetal to maternal DNA in a mixed sample comprising DNA from a fetus and DNA from the mother of the fetus, the method comprising:
 obtaining measured genetic data from the mixed sample by measuring the quantity of each allele at a plurality of polymorphic loci on at least one chromosome that is expected to be disomic in both the mother and the fetus;   building, on a computer, a model for expected allele measurements in the mixed sample at the plurality of polymorphic loci on the at least one chromosome for possible ratios of fetal to maternal DNA;   calculating, on a computer, a relative probability of each of the possible ratios using the model and the measured quantity of each allele at the plurality of polymorphic loci from the mixed sample; and   selecting the possible ratio with the greatest probability, thereby determining the ratio of fetal to maternal DNA in the mixed sample.   
     
     
         26 . The method of  claim 25 , further comprising
 obtaining measured genetic data from the mother by measuring the quantity of each allele at the plurality of polymorphic loci in genetic material from the mother;   optionally obtaining measured genetic data from the father of the fetus by measuring the quantity of each allele at the plurality of polymorphic loci in genetic material from the father; and   determining, on a computer, the ratio of fetal to maternal DNA in the mixed sample given the measured genetic data of the mixed sample, the measured genetic data of mother, and optionally the measured genetic data of the father.   
     
     
         27 . The method of  claim 25 , wherein the ratio of fetal to maternal DNA in the mixed sample is determined by:
 identifying the polymorphic loci where the mother is homozygous for a first allele at the polymorphic locus, and the father is (i) heterozygous for the first allele and a second allele or (ii) homozygous for a second allele at the polymorphic locus; and   using the amount of the second allele in the mixed sample for each of the identified polymorphic loci to determine the ratio of fetal to maternal DNA in the mixed sample.   
     
     
         28 . The method of  claim 25 , further comprising:
 determining the number of copies of a chromosome or chromosome segment of interest in the genome of the fetus using the selected ratio of fetal to maternal DNA in the mixed sample.   
     
     
         29 . The method of  claim 25 , further comprising:
 determining the likelihood that the fetal genome contains three copies of a chromosome or chromosome segment of interest using the selected ratio of fetal to maternal DNA in the mixed sample.   
     
     
         30 . The method of  claim 25 , wherein the polymorphic loci are SNPs.