Completion of a worldwide reference panel of samples for an ancestry informative Indel assay |
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| Institution: | 1. Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain;2. Galician Foundation of Genomic Medicine (SERGAS), CIBERER (University of Santiago de Compostela), Sanatiago de Compostela, Spain;3. IPATIMUP – Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal;1. Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad Tecnológica Equinoccial, Mariscal Sucre Avenue, Quito 170129, Ecuador;2. Laboratorio de Genética Molecular, Centros Médicos Especializados Cruz Roja Ecuatoriana, Papallacta oe1-66, Quito 170512, Ecuador;3. Laboratorio de Genética Molecular, OMNI Hospital, Av. Juan Tanca Marengo, Guayaquil 090513, Ecuador;1. Forensic Genetics Unit, Institute of Legal Medicine, Faculty of Medicine, University of Santiago de Compostela, ES-15705 Santiago de Compostela, Galicia, Spain;2. Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, A-6020 Innsbruck, Austria;3. Penn State Eberly College of Science, University Park, PA, USA;4. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V‘s Vej 11, DK-2100 Copenhagen, Denmark;5. Grupo de Medicina Xenómica (GMX), Faculty of Medicine, University of Santiago de Compostela, Spain;6. Institute of Legal Medicine, University Hospital Cologne, D-50823 Cologne, Germany;7. Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia;1. Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy;2. Department of Chemistry, University of Turin, Turin, Italy;1. Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea;2. Institute of Forensic Medicine, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany;3. Institute of Legal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany;4. Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain;5. Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland;6. Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland;7. Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA;8. Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Rotterdam, The Netherlands;9. Department of Forensic Sciences, The George Washington University, Washington, D.C., USA;10. Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China;11. Defense Institute of Forensic Science, Ministry of National Defense, Seoul, South Korea;12. Institute of Forensic Science, Ministry of Public Security, Beijing, China;13. Laboratory of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland;1. Department of Mathematical Sciences, Aalborg University, Denmark;2. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark;1. Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA;2. Life Technologies, 1149 Chess Drive, Foster City, CA 94404, USA;3. Bioinformatics Research, National Marrow Donor Program, 3001 Broadway Street NE, Suite 100, Minneapolis, MN 55413, USA;4. 23 Hunting Ridge Road, Sharon, CT 06069, USA |
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| Abstract: | The use of ancestry informative markers (AIMs) in forensic analysis is of considerable utility since ancestry inference can progress an investigation when no identification has been made of DNA from the crime-scene. Short-amplicon markers, including insertion deletion polymorphisms, are particularly useful in forensic analysis due to their mutational stability, capacity to amplify degraded samples and straightforward amplification technique. In this study we report the completion of H952 HGDP–CEPH panel genotyping with a set of 46 AIM-Indels. The study adds Central South Asian and Middle Eastern population data, allowing a comparison of patterns of variation in Eurasia for these markers, in order to enhance their use in forensic analyses, particularly when combined with sets of ancestry informative SNPs. Ancestry analysis using principal component analysis and Bayesian methods indicates that a proportion of classification error occurs with European–Middle East population comparisons, but the 46 AIM-Indels have the capability to differentiate six major population groups when European–Central South Asian comparisons are made. These findings have relevance for forensic ancestry analyses in countries where South Asians form much of the demographic profile, including the UK, USA and South Africa. A novel third allele detected in MID-548 was characterized – despite a low frequency in the HGDP–CEPH panel samples, it appears confined to Central South Asian populations, increasing the ability to differentiate this population group. The H952 data set was implemented in a new open access SPSmart frequency browser – forInDel: Forensic Indel browser. |
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| Keywords: | AIM-Indels Central South Asia Middle East HGDP–CEPH |
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