METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING
The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.
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 without prior knowledge of fetal genotypes, the method comprising:
a) binding a plurality of probes to a mixture of free-floating maternal and fetal DNA isolated 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, without prior knowledge of fetal genotypes;
b) amplifying at least 1000 loci from the free-floating maternal and fetal DNA having a bound probe in one reaction mixture 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) determining a bias of a technique used to measure an amount of the amplified products, wherein the bias is used to statistically correct 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) performing microarray analysis to measure the amount of amplified products derived from the free-floating fetal DNA in the blood, serum, or plasma sample using a statistically corrected, measured quantity of each allele at the plurality of the polymorphic loci on the at least one chromosome that is expected to be disomic; and
e) determining, on a computer, the risk of aneuploidy of the at least one chromosome or chromosome segment of interest in the genome of the fetus using the measured amount of amplified products derived from the free-floating fetal DNA and the measured genetic data for the at least one chromosome or chromosome segment of interest.
2 . The method of claim 1 , wherein a maximum likelihood estimate is used to determine the amount of amplified products derived from the fetal DNA.
3 . The method of claim 2 , wherein the maximum likelihood estimate is performed using a gradient descent method.
4 . The method of claim 2 , wherein the maximum likelihood estimate is performed using a Newton-Raphson optimization method.
5 . The method of claim 1 , wherein prior probabilities of aneuploidy given maternal age and/or gestational age 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 amount of amplified products derived from the fetal DNA in the sample.
6 . The method of claim 1 , 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.
7 . The method of claim 1 , 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, and chromosome Y.
8 . 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.