title: Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study.
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.
authors.affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.|BGI-Shenzhen, Shenzhen, 518000, China.
authors.forename: Haojun
authors.initials: H
authors.lastname: Jiang
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China.|BGI-Shenzhen, Shenzhen, 518000, China.
authors.forename: Yifan
authors.initials: Y
authors.lastname: Xie
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Xuchao
authors.initials: X
authors.lastname: Li
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China.
authors.forename: Huijuan
authors.initials: H
authors.lastname: Ge
authors.affiliation: Department of stomatology, The Second People's Hospital of Shenzhen, Shenzhen, 518000, China.
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Deng
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China.|Center of Forensic Sciences, Beijing Genomics Institute, Beijing, 100049, China.
authors.forename: Haofang
authors.initials: H
authors.lastname: Mu
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China.|Center of Forensic Sciences, Beijing Genomics Institute, Beijing, 100049, China.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Feng
authors.affiliation: Public Security Bureau of Shenzhen Municipality, Shenzhen, 518000, China.|Joint Laboratory of Gene-associated Application Research in Forensics, Shenzhen, 518000, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Yin
authors.affiliation: Public Security Bureau of Shenzhen Municipality, Shenzhen, 518000, China.|Joint Laboratory of Gene-associated Application Research in Forensics, Shenzhen, 518000, China.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Du
authors.affiliation: BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China.|Public Security Bureau of Shenzhen Municipality, Shenzhen, 518000, China.|Joint Laboratory of Gene-associated Application Research in Forensics, Shenzhen, 518000, China.|Shenzhen Municipal Key Laboratory of Birth Defects Screening and Engineering, BGI-Shenzhen, Shenzhen, 518000, China.|Guangdong Provincial Key Laboratory of human diseases genome, BGI-Shenzhen, Shenzhen, 518000, China.|Section of Molecular Disease Biology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1165 København K, Denmark.
authors.forename: Fang
authors.initials: F
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
authors.forename: Nongyue
authors.initials: N
authors.lastname: He
mesh_terms: D004247:DNA / Q000097:blood*; D005260:Female; D006801:Humans; D008297:Male; D018895:Microsatellite Repeats; D010334:Paternity; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide
chemical_list: D004247:DNA