Non-invasive prenatal diagnosis of fetal trisomy by analyzing allelic relationship using massively directed parallel sequencing

摘要

A method of analyzing a biological sample of a pregnant woman with a fetus, to determine if the fetus has an aneuploidy associated with a first chromosome, the biological sample containing a mixture of DNA molecules from the fetus and the mother, the method comprising: enrich the biological sample in DNA molecules from a plurality of target regions; sequencing the DNA molecules of the biological sample to obtain a plurality of sequence readings; analyze the plurality of sequence readings, including the analysis of a sequence reading: identify a location of the sequence reading in a reference genome by aligning the sequence reading with respect to the reference genome; and determine a respective allele of the sequence reading; identify a plurality of first locus of the first chromosome, the plurality of first locus corresponding to a part of the target regions; identify a plurality of second locus in one or more reference chromosomes, the plurality of the second locus corresponding to a part of the target regions, the pregnant woman being homozygous for a respective maternal allele in each of the first and second locus, and the heterozygous fetus for the respective maternal allele and a respective paternal allele of each of the first and second locus, the respective paternal alleles being different from the respective maternal alleles; determine a first maternal amount of the respective maternal alleles in the plurality of first locus; determine a first paternal amount of the respective paternal alleles in the plurality of first locus; calculate a first ratio of the first maternal amount and the first paternal amount; determine a second maternal amount of the respective maternal alleles in the plurality of second locus; determine a second paternal amount of the respective paternal alleles in the plurality of second locus; calculate a second ratio of the second maternal amount and the second paternal amount; calculate a third relation of the first relation and the second relation; and compare the third relationship with one or more cut-off values to determine if the fetus has an aneuploidy associated with the first chromosome.