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

  • Meng Ni
  • Xianlu Laura Peng
  • Peiyong JiangEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1909)


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.

Key words

Fetal DNA fraction Maternal plasma DNA Noninvasive prenatal testing Bioinformatics pipeline 



P.J. is currently funded by the Innovation and Technology Fund (ITS/401/17), Hong Kong.

Conflict of Interest

P.J. is a consultant to GRAIL. P.J. has filed patents/patent applications regarding cell-free DNA molecules. The remaining authors declare no conflict of interest.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Li Ka Shing Institute of Health SciencesThe Chinese University of Hong KongShatinHong Kong
  2. 2.Department of Chemical PathologyThe Chinese University of Hong Kong, Prince of Wales HospitalShatinHong Kong
  3. 3.Lineberger Comprehensive Cancer CenterUniversity of North CarolinaChapel HillUSA

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