Methods for non-invasive prenatal ploidy calling

A method for determining a ploidy status of a chromosome or chromosome segment in a gestating fetus, the method comprising:

• measuring the DNA in a sample that comprises maternal DNA from the mother of the fetus and fetal DNA from the fetus at a plurality of at least 10 polymorphic loci on the chromosome or chromosome segment;
• determining, on a computer, allele counts at the plurality of polymorphic loci from the DNA measurements made on the sample;
• generating, on a computer, a plurality of ploidy hypotheses each specifying a different possible ploidy state of the chromosome or chromosome segment;
• generating, on a computer, a joint distribution model for the expected allele counts and for the expected linkage between the expected allele counts at the plurality of polymorphic loci on the chromosome or chromosome segment for each ploidy hypothesis;
• determining, on a computer, a relative probability of each of the ploidy hypotheses by comparing (i) the joint distribution model for the expected allele counts and for the expected linkage between the expected allele counts at the plurality of polymorphic loci to (ii) the allele counts measured on the sample at the plurality of polymorphic loci;
• and
• outputting the hypothesis with the greatest probability of being true as an indication of the ploidy state of the fetus.