Bioinformatics Pipeline for Accurate Quantification of Fetal DNA Fraction in Maternal Plasma

The discovery of circulating cell-free fetal DNA has profoundly transformed the landscape of noninvasive prenatal testing (NIPT) and rapidly found its way into global clinical applications. The fractional concentration of cell-free fetal DNA in plasma DNA of a pregnant woman is an important parameter for understanding and interpreting analytical results of NIPT. Thus, the accurate quantification of fetal DNA fraction is indispensable when NIPT is involved. In this protocol, we describe the bioinformatics workflow to calculate fetal DNA fraction using two programs developed by our group, which provide accurate estimation.