Performance of ancestry-informative SNP and microhaplotype markers |
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| Affiliation: | 1. National Centre for Forensic Studies, Faculty of Science and Technology, University of Canberra, Canberra, Australia;2. Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain;3. Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria;4. Centre for Forensic Science, School of Mathematical and Physical Sciences (MaPS), Faculty of Science, University of Technology Sydney, Sydney, Australia;1. Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, China;2. Department of Forensic Biology, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 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. Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain;2. Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia;1. Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain;2. Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Victoria, Australia;3. University of California San Francisco, San Francisco, California, USA;4. Department of Forensic Science, George Washington University, Mount Vernon College Campus, Washington, USA;5. Department of Biology, University of Aveiro, Aveiro, Portugal;6. Fiji Police Forensic Biology and DNA Laboratory, Nasova, Suva, Fiji;7. Universitat de Barcelona, Barcelona, Spain;8. Galician Foundation of Genomic Medicine (SERGAS), CIBERER (University of Santiago de Compostela), Sanatiago de Compostela, Spain;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 |
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| Abstract: | The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg’s informativeness for (ancestry) assignment (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by In. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations. |
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| Keywords: | Biogeographical ancestry Single nucleotide polymorphism (SNP) Microhaplotype Allele frequency Ancestry-informative markers Population differentiation potential |
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