Tetra-allelic SNPs: Informative forensic markers compiled from public whole-genome sequence data |
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| Affiliation: | 1. Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain;2. Grupo de Medicina Xenómica (GMX), Faculty of Medicine, University of Santiago de Compostela, Spain;3. Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia;1. DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines;2. Philippine Genome Center, University of the Philippines, Philippines;3. Balik Scientist, Philippine Council for Industry, Energy and Emerging Technology Research and Development – Department of Science and Technology, Philippines;1. State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Room 109, 2nd Biology Building, Shanghai 200433, PR China;2. Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, PR China, Shanghai 200063, PR China;3. PEOPLESPOTINC R&D, PR China, Beijing 102206, PR China;4. Department of Forensic Medicine, Medical College of Soochow University, Suzhou 215123, PR China;1. Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University, 3-17 Renmin South Road, Chengdu, 610041 Sichuan, China;2. Department of Forensic Genetics, Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu 610081 Sichuan, China;3. College of life Sciences, Sichuan University, Chengdu, 610041 Sichuan, China;4. Bio-resources Key Laboratory of Minister of Education, Sichuan University, Chengdu, 610041 Sichuan, China;1. Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;2. Forensic Biology Laboratory, Israel Police, Israel Police National HQ, Jerusalem 91906, Israel;3. Cellmark Forensics, Dallas, TX, USA;1. Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands;2. National Institute of Public Health, Department of Forensic Biology, P.O. Box 4404 Nydalen, 0403 Oslo, Norway;3. National Institute of Public Health, Department of Forensic Medicine, P.O. Box 4950 Nydalen, 0424 Oslo, Norway |
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| Abstract: | ![]()
Multiple-allele single nucleotide polymorphisms (SNPs) are potentially useful for forensic DNA analysis as they can provide more discrimination power than normal binary SNPs. In addition, the presence in a profile of more than two alleles per marker provides a clearer indication of mixed DNA than assessments of imbalanced signals in the peak pairs of binary SNPs. Using the 1000 Genomes Phase III human variant data release of 2014 as the starting point, this study collated 961 tetra-allelic SNPs that pass minimum sequence quality thresholds and where four separate nucleotide substitution alleles were detected. Although most of these loci had three of the four alleles in combined frequencies of 2% or less, 160 had high heterozygosities with 50 exceeding those of ‘ideal’ 0.5:0.5 binary SNPs. From this set of most polymorphic tetra-allelic SNPs, we identified markers most informative for forensic purposes and explored these loci in detail. Subsets of the most polymorphic tetra-allelic SNPs will make useful additions to current panels of forensic identification SNPs and ancestry-informative SNPs. The 24 most discriminatory tetra-allelic SNPs were estimated to detect more than two alleles in at least one marker per profile in 99.9% of mixtures of African contributors. In European contributor mixtures 99.4% of profiles would show multiple allele patterns, but this drops to 92.6% of East Asian contributor mixtures due to reduced levels of polymorphism for the 24 SNPs in this population group. |
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| Keywords: | Single nucleotide polymorphisms (SNPs) Multiple-allele SNPs Tetra-allelic SNPs 1000 Genomes Ancestry informative markers Mixed DNA |
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