Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information

Author:

Ju JiaORCID,Li Jia,Liu Siyang,Zhang Haiqiang,Xu Jinjin,Lin Yu,Gao Ya,Zhou Yulin,Jin XinORCID

Abstract

AbstractCell-free fetal DNA fraction (FF) in maternal plasma is a key parameter affecting the performance of noninvasive prenatal testing (NIPT). Accurate quantitation of FF plays a pivotal role in these tests. However, there are few methods that could determine FF with high accuracy using shallow‐depth whole‐genome sequencing data. In this study, we hypothesized that the actual FF in maternal plasma should be proportional to the discrepancy rate between the observed genotypes and inferred genotypes based on the linkage disequilibrium rule in certain polymorphism sites. Based on this hypothesis, we developed a method named Linkage Disequilibrium information-based cell-free Fetal DNA Fraction (LDFF) to accurately quantify FF in maternal plasma. This method achieves a high performance and outperforms existing methods in the fetal DNA fraction estimation. As LDFF is a gender-independent method and developed on shallow-depth samples, it can be easily incorporated into routine NIPT test and may enhance the current NIPT performance.

Funder

Natural Science Foundation of Guangdong Province

National Natural Science Foundation of China

Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases

Publisher

Springer Science and Business Media LLC

Subject

Genetics(clinical),Genetics,Molecular Biology

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