Inferring fetal fractions from read heterozygosity empowers the noninvasive prenatal screening.

ABSTRACT:

Purpose

Fetal fraction (FF) is the percent of cell-free DNA (cfDNA) in the mother's peripheral blood that is of fetal origin, which plays a pivotal role in noninvasive prenatal screening (NIPS). We present a method that can reliably estimate FFs by examining autosome single-nucleotide polymorphisms (SNPs).

Methods

Even at a very low sequencing depth, there are plenty of SNPs covered by more than one read. At those SNPs, we define read heterozygosity and demonstrate that the percent of read heterozygosity is a function of FF, which allows FF to be inferred.

Results

We first demonstrated the effectiveness of our method in inferring FF. Then we used the inferred FF as an informative alternative prior to computing Bayes factors to test for aneuploidy, and observed better

SUBMITTER: Dang M 

PROVIDER: S-EPMC7000331 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature