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 whether one or more mutations are present in free floating DNA in a maternal blood sample, comprising:
(i) isolating free floating DNA from the maternal blood sample,
(ii) performing PCR to amplify the isolated DNA,
(iii) performing hybrid capture using hybrid capture probes directed to genetic loci associated with one or more diseases or genetic states of interest to enrich the amplified DNA,
(iv) performing PCR to amplify the enriched DNA,
(v) performing high throughput DNA sequencing to generate nucleic acid sequence data for the amplified enriched DNA, and
(vi) determining from the sequence data whether the one or more mutations are present in the DNA.
2 . A method for sequencing DNA derived from a maternal blood sample, comprising:
(i) isolating free floating DNA from a maternal blood sample,
(ii) performing PCR to amplify the isolated DNA,
(iii) performing hybrid capture using hybrid capture probes directed to genetic loci associated with one or more diseases or genetic states of interest to enrich the amplified DNA,
(iv) performing PCR to amplify the enriched DNA, and
(v) performing high throughput DNA sequencing to sequence the amplified enriched DNA.