Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing
Cell-free fetal DNA (cffDNA) from maternal plasma has made it possible to develop noninvasive prenatal paternity testing (NIPPT). However, most studies have focused on customized single nucleotide polymorphism (SNP) typing systems and few have used conventional short tandem repeat (STR) markers. Bas...
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MDPI AG
2021-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/3/454 |
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| author | Xuefeng Shen Ran Li Haixia Li Yu Gao Hui Chen Ning Qu Dan Peng Riga Wu Hongyu Sun |
| author_facet | Xuefeng Shen Ran Li Haixia Li Yu Gao Hui Chen Ning Qu Dan Peng Riga Wu Hongyu Sun |
| author_sort | Xuefeng Shen |
| collection | DOAJ |
| description | Cell-free fetal DNA (cffDNA) from maternal plasma has made it possible to develop noninvasive prenatal paternity testing (NIPPT). However, most studies have focused on customized single nucleotide polymorphism (SNP) typing systems and few have used conventional short tandem repeat (STR) markers. Based on massively parallel sequencing (MPS), this study used a widely-accepted forensic multiplex assay system to evaluate the effect of noninvasive prenatal paternity testing with a combination of well-established SNP and STR markers. Using a ForenSeq DNA Signature Prep Kit, NIPPT was performed in 17 real parentage cases with monovular unborn fetuses at 7 to 24 gestational weeks. Different analytical strategies for the identification of paternally inherited allele (PIA) were developed to deal with SNPs and STRs. Combined paternity index (CPI) for 17 real trios as well as 272 unrelated trios was calculated. With the combination of SNPs and A-STRs, 82.35% (14/17), 88.24% (15/17), 94.12% (16/17), and 94.12% (16/17) of real trios could be accurately determined when the likelihood ratio (LR) threshold for paternity inclusion was set to 10,000, 1000, 100, and 10, respectively. This reveals that simultaneous surveys of SNP and STR markers included in the ForenSeq DNA Signature Prep Kit offer a promising method for NIPPT using MPS technology. |
| first_indexed | 2024-03-10T13:00:16Z |
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| id | doaj.art-b3c89b9369b541fe964e0f41ae549c44 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T13:00:16Z |
| publishDate | 2021-03-01 |
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| series | Genes |
| spelling | doaj.art-b3c89b9369b541fe964e0f41ae549c442023-11-21T11:33:56ZengMDPI AGGenes2073-44252021-03-0112345410.3390/genes12030454Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel SequencingXuefeng Shen0Ran Li1Haixia Li2Yu Gao3Hui Chen4Ning Qu5Dan Peng6Riga Wu7Hongyu Sun8Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, ChinaFaculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, ChinaFaculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, ChinaDepartment of Obstetrics, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, ChinaFaculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, ChinaFaculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, ChinaFaculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, ChinaGuangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-Sen University, Guangzhou 510080, ChinaFaculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, ChinaCell-free fetal DNA (cffDNA) from maternal plasma has made it possible to develop noninvasive prenatal paternity testing (NIPPT). However, most studies have focused on customized single nucleotide polymorphism (SNP) typing systems and few have used conventional short tandem repeat (STR) markers. Based on massively parallel sequencing (MPS), this study used a widely-accepted forensic multiplex assay system to evaluate the effect of noninvasive prenatal paternity testing with a combination of well-established SNP and STR markers. Using a ForenSeq DNA Signature Prep Kit, NIPPT was performed in 17 real parentage cases with monovular unborn fetuses at 7 to 24 gestational weeks. Different analytical strategies for the identification of paternally inherited allele (PIA) were developed to deal with SNPs and STRs. Combined paternity index (CPI) for 17 real trios as well as 272 unrelated trios was calculated. With the combination of SNPs and A-STRs, 82.35% (14/17), 88.24% (15/17), 94.12% (16/17), and 94.12% (16/17) of real trios could be accurately determined when the likelihood ratio (LR) threshold for paternity inclusion was set to 10,000, 1000, 100, and 10, respectively. This reveals that simultaneous surveys of SNP and STR markers included in the ForenSeq DNA Signature Prep Kit offer a promising method for NIPPT using MPS technology.https://www.mdpi.com/2073-4425/12/3/454forensic geneticsnoninvasive prenatal paternity testingshort tandem repeatsingle nucleotide polymorphism |
| spellingShingle | Xuefeng Shen Ran Li Haixia Li Yu Gao Hui Chen Ning Qu Dan Peng Riga Wu Hongyu Sun Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing Genes forensic genetics noninvasive prenatal paternity testing short tandem repeat single nucleotide polymorphism |
| title | Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing |
| title_full | Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing |
| title_fullStr | Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing |
| title_full_unstemmed | Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing |
| title_short | Noninvasive Prenatal Paternity Testing with a Combination of Well-Established SNP and STR Markers Using Massively Parallel Sequencing |
| title_sort | noninvasive prenatal paternity testing with a combination of well established snp and str markers using massively parallel sequencing |
| topic | forensic genetics noninvasive prenatal paternity testing short tandem repeat single nucleotide polymorphism |
| url | https://www.mdpi.com/2073-4425/12/3/454 |
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