Development of a SNP set for human identification: A set with high powers of discrimination which yields high genetic information from naturally degraded DNA samples in the Thai population |
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| Affiliation: | 1. Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;2. Medical Genetic Section, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand;3. Institute of Forensic Medicine, Police General Hospital, Royal Thai Police, Bangkok 10330, Thailand;4. Laboratory for Genotyping Development, Center for Genomic Medicine, RIKEN Yokohama Institute, Kanagawa 230-0045, Japan;1. Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;2. Medical Genetic Section, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand;3. Institute of Forensic Medicine, Police General Hospital, Royal Thai Police, Bangkok 10330, Thailand;4. Laboratory for Genotyping Development, Center for Genomic Medicine, RIKEN Yokohama Institute, Kanagawa 230-0045, Japan;1. Faculty of Pharmacy, Medical College, Jagiellonian University, Kraków, Poland;2. Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland;3. Faculty of Health Sciences, Medical College, Jagiellonian University, Kraków, Poland;1. Molecular Genetics Lab., Institute for Immunological Research, University of Cartagena, Cartagena, Colombia;2. DNA Forensic Laboratory, Argentinean Forensic Anthropology Team (EAAF), Córdoba, Argentina;3. Molecular Biology Research Laboratory, Lagos University Teaching Hospital (LUTH), Lagos, Nigeria;4. FCIID Annex, Nigeria Police Force, Lagos, Nigeria;5. DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Brazil;6. IPATIMUP, Institute of Pathology and Molecular Immunology from University of Porto, Portugal;1. The George Washington University, Department of Forensic Science, 2100 Foxhall Road, NW, Washington, DC, 20007, United States;2. Thermo Fisher Scientific, 180 Oyster Point Boulevard, South San Francisco, CA, 94080, United States;3. Yale University School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, CT, 06520, United States;1. Department of Forensic Medicine, National Police University of China, No. 83, Tawan Street, Huanggu District, Shenyang, Liaoning 110854, PR China;2. Criminal Science and Technology Institute of Liaoning Province, No. 2, Qishan Middle Road, Huanggu District, Shenyang, Liaoning 110032, PR China;3. China Medical University School of Forensic Medicine, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning 110122, PR China;1. Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA;2. Department of Chemistry Malaysia, Kuching Branch, Lot 3148, Block 14, Jalan Sultan Tengah, 93050 Petra Jaya, Kuching, Malaysia |
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| Abstract: | This study describes the development of a SNP typing system for human identification in the Thai population, in particular for extremely degraded DNA samples. A highly informative SNP marker set for forensic identification was identified, and a multiplex PCR-based Invader assay was developed. Fifty-one highly informative autosomal SNP markers and three sex determination SNP markers were amplified in two multiplex PCR reactions and then detected using Invader assay reactions. The average PCR product size was 71 base pairs. The match probability of the 54-SNP marker set in 124 Thai individuals was 1.48 × 10−21, higher than that of STR typing, suggesting that this 54-SNP marker set is beneficial for forensic identification in the Thai population. The selected SNP marker set was also evaluated in 90 artificially degraded samples, and in 128 naturally degraded DNA samples from real forensic casework which had shown no profiles or incomplete profiles when examined using a commercial STR typing system. A total of 56 degraded samples (44%) achieved the matching probability (PM) equivalent to STR gold standard analysis (successful genotyping of 44 SNP markers) for human identification. These data indicated that our novel 54-SNP marker set provides a very useful and valuable approach for forensic identification in the Thai population, especially in the case of highly to extremely degraded DNA.In summary, we have developed a set of 54 Thai-specific SNPs for human identification which have higher discrimination power than STR genotyping. The PCRs for these 54 SNP markers were successfully combined into two multiplex reactions and detected with an Invader assay. This novel SNP genotyping system also yields high levels of genetic information from naturally degraded samples, even though there are much more difficult to recover than artificially degraded samples. |
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| Keywords: | Human identification Degraded DNA Short tandem repeat (STR) Single nucleotide polymorphism (SNP) Invader assay |
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