Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study.

Haojun Jiang,Huijuan Ge,Xuchao Li,Fang Chen,Nongyue He,Lu Yin,Haofang Mu,Yifan Xie,Xiaoli Feng,Zhou Du,Yongqiang Deng,H Sunny Sun

doi:10.1371/journal.pone.0159385

Abstract

Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels in order to verify the performance in clinical cases. Combining targeted deep sequencing of selective SNP and informative bioinformatics pipeline, we calculated the combined paternity index (CPI) of 17 cases to determine paternity. Sequencing-based NIPAT results fully agreed with invasive prenatal paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future.

Highlights

The discovery of cell-free fetal DNA in maternal blood in 1997 provides the possibility to develop novel noninvasive prenatal paternity testing, which can avoid the procedureassociated fetal loss as well as the restriction of sampling time [1]
The binomial distribution was suited to the frequency distribution of the effective single nucleotide polymorphisms (SNPs) in noninvasive prenatal paternity testing (NIPAT)
We showed that maternal plasma sequencing-based NIPAT could obtained 93.546% (86.21~98.82%) of total effective SNPs in maternal plasma DNA to calculate combined paternity index (CPI) and determine paternity, which means that sequencing-based NIPAT can obtain similar number of effective SNPs from plasma as from amniotic fluid

Summary

Introduction

The discovery of cell-free fetal DNA (cffDNA) in maternal blood in 1997 provides the possibility to develop novel noninvasive prenatal paternity testing, which can avoid the procedureassociated fetal loss as well as the restriction of sampling time [1]. BGI-Shenzhen provided support in the form of salaries for F. C. Li. The specific roles of these authors are articulated in the ‘author contributions’ section. The funders did not play a role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript

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Results

Conclusion