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

PLoS One. 2016 Sep 15;11(9):e0159385. doi: 10.1371/journal.pone.0159385. eCollection 2016.


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.

MeSH terms

  • DNA / blood*
  • Female
  • Humans
  • Male
  • Microsatellite Repeats
  • Paternity*
  • Pilot Projects
  • Polymorphism, Single Nucleotide


  • DNA

Grant support

Project The Establishment of 30 National Standards about Key Nucleic Acid Biotechnology (201510208), Shenzhen Municipal Government of China (NO.JCYJ20140414170821214), Shenzhen Municipal Government of China (NO.ZDSYS20140509153457495) and Shenzhen Municipal Government of China (NO.CXZZ20140808170655268) supported this study. BGI-Shenzhen provided support in the form of salaries for F. Chen, H. J. Ge, and X. 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.