Patent ID: 9447453
Filing Date: 2016-09-20
CPC Classification: C12Q,G16B

Claim Text:
1. A method of estimating a fraction of fetal DNA in DNA obtained from a bodily fluid of a pregnant individual carrying a fetus, the method comprising: (a) receiving a sample of the bodily fluid; (b) extracting DNA from the sample under conditions that extract DNA of both a maternal genome and a fetal genome present in the bodily fluid; (c) sequencing the extracted DNA with a nucleic acid sequencer under conditions that produce DNA sequence reads containing a plurality of polymorphisms; (d) mapping the DNA sequence reads to a plurality of polymorphism sites on a reference sequence corresponding to the plurality of polymorphisms, wherein the mapping is performed using a computational apparatus programmed to map nucleic acid sequences to polymorphism sites of the reference sequence; (e) determining allele frequencies of the mapped DNA sequence reads for the plurality of polymorphisms; and (f) estimating the fraction of fetal DNA in the extracted DNA, wherein the estimating comprises performing a calculation or calculations using the allele frequencies determined in (e) for polymorphisms of two or more of the following zygosity cases: (i) the pregnant individual is homozygous and the fetus is homozygous, (ii) the pregnant individual is homozygous and the fetus is heterozygous, (iii) the pregnant individual is heterozygous and the fetus is homozygous, and (iv) the pregnant individual is heterozygous and the fetus is heterozygous; wherein (e)-(f) are performed on one or more processors running under program instructions for the determining and estimating.