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 sample of DNA from the mother of the fetus and from the fetus, and from genotypic data from the mother and optionally also from the father. The ploidy state is determined by using a joint distribution model to create a set 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. In an embodiment, the mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias.
1 . A method for estimating the fetal fraction of fetal cell-free DNA in a maternal blood sample from a pregnant mother of a fetus, comprising:
a) isolating DNA from the maternal blood sample, wherein the DNA comprises fetal and maternal cell-free DNA from the fetus and from the pregnant mother, wherein the cell-free DNA comprises target loci, and wherein the target loci comprise at least 1,000 polymorphic loci;
b) performing multiplex PCR to amplify the cell-free DNA comprising target loci;
c) measuring an amount of the target loci by performing next generation sequencing; and
d) estimating the fetal fraction of fetal cell-free DNA in the maternal blood sample using the measured amounts of target loci.
2 . The method of claim 1 , wherein the method further comprises a universal PCR before the measuring step and wherein a sample barcode is attached to the DNA during one of the PCR reactions.
3 . The method of claim 1 , wherein the target loci comprise one or more single nucleotide polymorphisms (SNPs).
4 . The method of claim 3 , wherein the method further comprises determining allele ratios at the SNPs.
5 . The method of claim 4 , wherein estimating the fetal fraction uses the allele ratios.
6 . The method of claim 1 , wherein the method further comprises determining a ploidy state of a target chromosome of the fetus comprising at least two of the target loci.
7 . The method of claim 6 , wherein one or more of the target loci map to chromosomes 13, 18, and/or 21 and the method further comprises determining a ploidy state for chromosomes 13, 18, and/or 21 using the measured amounts of the target loci.
8 . The method of claim 7 , wherein one or more of the target loci map to a reference chromosome.
9 . The method of claim 6 , wherein measuring the amounts of target loci comprises performing read count analysis using the measured amounts of at least one of the target loci, and wherein the ploidy state determination uses the read count analysis.
10 . The method of claim 2 , wherein during one or both of the amplifications a sequencing compatible adaptor is appended to the amplified DNA.
11 . The method of claim 6 , wherein the measuring provides bulk genotypic measurements of at least some of the target loci, and wherein the bulk genotypic measurements are used to determine the ploidy state of the target chromosome.
12 . The method of claim 6 , wherein the target loci comprise one or more single nucleotide polymorphisms (SNPs) and wherein the estimating comprises using allele calls at the SNPs.
13 . The method of claim 12 , wherein the measuring comprises quantitative allele measurements.
14 . The method of claim 13 , wherein the quantitative allele measurements are used for determining the ploidy state and for estimating the fetal fraction.
15 . The method of claim 6 , wherein one or more of the target loci map to a reference chromosome.
16 . The method of claim 15 , wherein the target loci comprise one or more single nucleotide polymorphisms (SNPs).
17 . The method of claim 16 , wherein a Z score is determined using measurements of the amounts of target loci on the target chromosome and the reference chromosome, and the Z score is used to determine the ploidy state of the target chromosome.