Establishing a second-tier panel of 18 ancestry informative markers to improve ancestry distinctions among Asian populations |
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| Institution: | 1. Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China;2. Department of Forensic Medicine, Sichuan Police College, Luzhou 646000, Sichuan, China;3. Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China;4. Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China;5. Criminal Investigation Team of Liangshan Public Security Bureau, Liangshan, Sichuan, China;6. Department of Forensic Genetics, Chengdu Public Security Bureau, Institute of Forensic Science, Chengdu 610081, Sichuan, China;1. Núcleo de Genética Humana e Molecular (NGHM), Universidade Federal do Espírito Santo, Espírito Santo, Brazil;2. Laboratório de DNA Forense, Departamento de Laboratórios Forenses, Polícia Civil do Espírito Santo, Espírito Santo, Brazil;1. Forensic Science SA, GPO Box 2790, Adelaide, South Australia, 5001, Australia;2. College of Science and Engineering, Flinders University of South Australia, GPO Box 2100, Adelaide, South Australia, 5001, Australia;1. Forensic Science SA, GPO Box 2790, Adelaide, South Australia, 5001, Australia;2. College of Science and Engineering, Flinders University of South Australia, GPO Box 2100, Adelaide, South Australia, 5001, Australia;1. Laboratorio MANLAB, Área de Filiaciones, Buenos Aires, Argentina;2. Laboratorio de Diversidad Genética, Instituto Multidisciplinario de Biología Celular IMBICE, La Plata, Buenos Aires, Argentina;3. Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina;4. Colegio Oficial de Farmacéuticos y Bioquímicos, Buenos Aires, Argentina;5. Fundación INGEN, Monte Grande, Argentina;6. DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Brazil;7. Institute of Pathology and Molecular Immunology from University of Porto (IPATIMUP), Portugal;8. Instituto de Investigação e Inovação em Saúde, I3S, Universidade do Porto, Portugal;9. CMUP, Centro de Matemática da Universidade do Porto, Porto, Portugal;1. Institute of Forensic Medicine, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, China;2. Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, China;3. Institute of Criminal Science and Technology, Karamay City Public Security Bureau, Karamay, China;4. Institute of Criminal Investigation, Zhengzhou City Public Security Bureau, Zhengzhou, China;5. Institute of Criminal Science and Technology Research, Lanzhou City Public Security Bureau, Lanzhou, China;6. Department of Criminal Investigation Bureau of Shaanxi Provincial Public Security, Xi’an, China;7. Institute of Forensic Science, Kunming Public Security Bureau, Kunming, China;1. Defense Forensic Science Center, Forest Park, GA, USA;2. Georgia Institute of Technology, Atlanta, GA, USA |
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| Abstract: | At present, several mature ancestry informative SNP (AISNP) panels are used to distinguish between continental regions of the world, but a more accurate division within the continent requires a secondary panel to complete. However, many AISNPs for the subgroup ancestry inference are selected from the Kidd Lab panel of 55 AISNPs or other published papers. These panels inevitably lack valuable markers for subgroup ancestry inference. Therefore, instead of choosing from the published panels, we used the 1000 Genomes Project to screen potentially informational markers in Asian populations, including single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (InDels). The allele frequencies of all autosomal SNPs and InDels of the 1000 Genomes Project were compared between 10 populations in Asia to identify markers with the largest pairwise allele frequency differences. Finally, we established a second-tier panel of 18 AIMs in this study, which not only divided the 26 populations of the 1000 Genomes Project into six clusters, but also divided the Asia subgroup into four clusters: Gujarati, East Asia, Southeast Asia and South Asia. |
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| Keywords: | SNP Ancestry informative markers SNaPshot Asia East Asia Ancestry inference |
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