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

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 devel...

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Autores principales: Jiang, Haojun, Xie, Yifan, Li, Xuchao, Ge, Huijuan, Deng, Yongqiang, Mu, Haofang, Feng, Xiaoli, Yin, Lu, Du, Zhou, Chen, Fang, He, Nongyue
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025199/
https://www.ncbi.nlm.nih.gov/pubmed/27631491
http://dx.doi.org/10.1371/journal.pone.0159385
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author Jiang, Haojun
Xie, Yifan
Li, Xuchao
Ge, Huijuan
Deng, Yongqiang
Mu, Haofang
Feng, Xiaoli
Yin, Lu
Du, Zhou
Chen, Fang
He, Nongyue
author_facet Jiang, Haojun
Xie, Yifan
Li, Xuchao
Ge, Huijuan
Deng, Yongqiang
Mu, Haofang
Feng, Xiaoli
Yin, Lu
Du, Zhou
Chen, Fang
He, Nongyue
author_sort Jiang, Haojun
collection PubMed
description 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.
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spelling pubmed-50251992016-09-27 Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study Jiang, Haojun Xie, Yifan Li, Xuchao Ge, Huijuan Deng, Yongqiang Mu, Haofang Feng, Xiaoli Yin, Lu Du, Zhou Chen, Fang He, Nongyue PLoS One Research Article 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. Public Library of Science 2016-09-15 /pmc/articles/PMC5025199/ /pubmed/27631491 http://dx.doi.org/10.1371/journal.pone.0159385 Text en © 2016 Jiang et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Jiang, Haojun
Xie, Yifan
Li, Xuchao
Ge, Huijuan
Deng, Yongqiang
Mu, Haofang
Feng, Xiaoli
Yin, Lu
Du, Zhou
Chen, Fang
He, Nongyue
Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study
title Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study
title_full Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study
title_fullStr Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study
title_full_unstemmed Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study
title_short Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study
title_sort noninvasive prenatal paternity testing (nipat) through maternal plasma dna sequencing: a pilot study
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025199/
https://www.ncbi.nlm.nih.gov/pubmed/27631491
http://dx.doi.org/10.1371/journal.pone.0159385
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