Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing
Unbalanced and degraded mixtures (UDM) are very common in forensic DNA analysis. For example, DNA signals from criminal suspects are masked by a large amount of DNA from victims, or cell-free fetal DNA (cffDNA) in maternal plasma is masked by a high background of maternal DNA. Currently, detecting m...
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Frontiers Media S.A.
2022-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.800598/full |
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| author | Ranran Zhang Yu Tan Li Wang Hui Jian Jing Zhu Yuanyuan Xiao Mengyu Tan Jiaming Xue Fan Yang Fan Yang Weibo Liang |
| author_facet | Ranran Zhang Yu Tan Li Wang Hui Jian Jing Zhu Yuanyuan Xiao Mengyu Tan Jiaming Xue Fan Yang Fan Yang Weibo Liang |
| author_sort | Ranran Zhang |
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| description | Unbalanced and degraded mixtures (UDM) are very common in forensic DNA analysis. For example, DNA signals from criminal suspects are masked by a large amount of DNA from victims, or cell-free fetal DNA (cffDNA) in maternal plasma is masked by a high background of maternal DNA. Currently, detecting minor DNA in these mixtures is complex and challenging. We developed a new set of SNP-SNP microhaplotypes with short amplicons, and we successfully genotyped them using the new method of amplification-refractory mutation system PCR (ARMS-PCR) combined with SNaPshot technology based on a capillary electrophoresis (CE) platform. This panel reflects a high polymorphism in the Southwest Chinese Han population and thus has excellent potential for mixture studies. We evaluated the feasibility of this panel for UDM detection and noninvasive prenatal paternity testing (NIPPT). Fifteen SNP-SNPs detected minor DNA of homemade DNA mixtures, with a sensitivity of 0.025–0.05 ng and a specificity of 1:1,000. In addition, the panel successfully genotyped degraded DNA from single and mixed samples. Finally, 15 SNP-SNPs were applied to 26 trios. All samples displayed positive results with at least one marker to detect cffDNA. Besides, all fetal alleles in maternal plasma were confirmed by genotyping fetal genomic DNA from amniocentesis and paternal genomic DNA from peripheral blood. The results indicated that the SNP-SNP strategy based on the CE platform was useful for UDM detection and NIPPT. |
| format | Article |
| id | doaj-art-7451d43bb3a24ea8b023c31ee68e16d2 |
| institution | Kabale University |
| issn | 1664-8021 |
| language | English |
| publishDate | 2022-02-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj-art-7451d43bb3a24ea8b023c31ee68e16d22025-01-21T09:31:48ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-02-011210.3389/fgene.2021.800598800598Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity TestingRanran Zhang0Yu Tan1Li Wang2Hui Jian3Jing Zhu4Yuanyuan Xiao5Mengyu Tan6Jiaming Xue7Fan Yang8Fan Yang9Weibo Liang10Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, ChinaDepartment of Obstetrics and Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University, Chengdu, ChinaDepartment of Obstetrics and Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University, Chengdu, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, ChinaDepartment of Forensic Science and Technology, Sichuan Police College, Luzhou, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, ChinaDepartment of Obstetrics and Gynecology, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan University, Chengdu, ChinaDepartment of Ultrasonography, West China Second University Hospital Sichuan University, Chengdu, ChinaDepartment of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, ChinaUnbalanced and degraded mixtures (UDM) are very common in forensic DNA analysis. For example, DNA signals from criminal suspects are masked by a large amount of DNA from victims, or cell-free fetal DNA (cffDNA) in maternal plasma is masked by a high background of maternal DNA. Currently, detecting minor DNA in these mixtures is complex and challenging. We developed a new set of SNP-SNP microhaplotypes with short amplicons, and we successfully genotyped them using the new method of amplification-refractory mutation system PCR (ARMS-PCR) combined with SNaPshot technology based on a capillary electrophoresis (CE) platform. This panel reflects a high polymorphism in the Southwest Chinese Han population and thus has excellent potential for mixture studies. We evaluated the feasibility of this panel for UDM detection and noninvasive prenatal paternity testing (NIPPT). Fifteen SNP-SNPs detected minor DNA of homemade DNA mixtures, with a sensitivity of 0.025–0.05 ng and a specificity of 1:1,000. In addition, the panel successfully genotyped degraded DNA from single and mixed samples. Finally, 15 SNP-SNPs were applied to 26 trios. All samples displayed positive results with at least one marker to detect cffDNA. Besides, all fetal alleles in maternal plasma were confirmed by genotyping fetal genomic DNA from amniocentesis and paternal genomic DNA from peripheral blood. The results indicated that the SNP-SNP strategy based on the CE platform was useful for UDM detection and NIPPT.https://www.frontiersin.org/articles/10.3389/fgene.2021.800598/fullSNP-SNP microhaplotypeamplification-refractory mutation system PCRSNaPshotunbalanced and degraded mixturecell-free fetal DNAnoninvasive prenatal paternity testing |
| spellingShingle | Ranran Zhang Yu Tan Li Wang Hui Jian Jing Zhu Yuanyuan Xiao Mengyu Tan Jiaming Xue Fan Yang Fan Yang Weibo Liang Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing Frontiers in Genetics SNP-SNP microhaplotype amplification-refractory mutation system PCR SNaPshot unbalanced and degraded mixture cell-free fetal DNA noninvasive prenatal paternity testing |
| title | Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing |
| title_full | Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing |
| title_fullStr | Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing |
| title_full_unstemmed | Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing |
| title_short | Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing |
| title_sort | set of 15 snp snp markers for detection of unbalanced degraded dna mixtures and noninvasive prenatal paternity testing |
| topic | SNP-SNP microhaplotype amplification-refractory mutation system PCR SNaPshot unbalanced and degraded mixture cell-free fetal DNA noninvasive prenatal paternity testing |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.800598/full |
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