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

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

Jiang H1,2, Xie Y3,2, Li X3, Ge H3, Deng Y4, Mu H3,5, Feng X3,5, Yin L6,7, Du Z6,7, Chen F3,6,7,8,9,10, He N1.

Author information

1
State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
2
BGI-Shenzhen, Shenzhen, 518000, China.
3
BGI Education Center, University of Chinese Academy of Sciences, Beijing, 100049, China.
4
Department of stomatology, The Second People's Hospital of Shenzhen, Shenzhen, 518000, China.
5
Center of Forensic Sciences, Beijing Genomics Institute, Beijing, 100049, China.
6
Public Security Bureau of Shenzhen Municipality, Shenzhen, 518000, China.
7
Joint Laboratory of Gene-associated Application Research in Forensics, Shenzhen, 518000, China.
8
Shenzhen Municipal Key Laboratory of Birth Defects Screening and Engineering, BGI-Shenzhen, Shenzhen, 518000, China.
9
Guangdong Provincial Key Laboratory of human diseases genome, BGI-Shenzhen, Shenzhen, 518000, China.
10
Section of Molecular Disease Biology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1165 KĂžbenhavn K, Denmark.

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.

PMID:
27631491
PMCID:
PMC5025199
DOI:
10.1371/journal.pone.0159385
[Indexed for MEDLINE]
Free PMC Article

Conflict of interest statement

F. Chen, H. J. Ge, and X. C. Li are employed by BGI-Shenzhen. There are no patents, products in development, or marketed products to declare. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.

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