Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise |
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| Affiliation: | 1. Department of Public Health Sciences and Pediatrics, University of Turin, Italy;2. Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, The Netherlands;3. Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, Australia;4. Department of Forensic Genetics, Studio Indagini Mediche e Forensi (SIMEF), Reggio Calabria, Italy;5. Department of Medical and Surgical Sciences, Institute of Legal Medicine, University of Bologna, Italy;6. Department of Biomedical and Surgical Sciences, Section of Legal Medicine and Forensic Science, University of Perugia, Italy;7. Dipartimento di Medicina Legale, del Lavoro, Psicologia Medica e Criminologia, Università di Genova, Italy;8. Department of Medical Sciences, University of Turin, Italy;9. HuGeF, Human Genetics Foundation, Turin, Italy;10. Department of Public Health, UOL of Legal Medicine, University of Ferrara, Italy;11. SC Medicina Legale, Università di Modena, Italy;12. Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Italy;13. ANDROS Day Surgery Clinic, Forensic Genetics Unit, Palermo, Italy;14. SOD Genetics Diagnostics, Forensic Genetics, Azienda Ospedaliera Universitaria Careggi, Florence, Italy;15. Section of Legal Medicine, Università Politecnica Delle Marche, Ancona, Italy;p. Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Italy;q. Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy;r. Department of Molecular Medicine, University of Padova, Italy;s. Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Italy;t. Department of Biomedical Sciences and Human Oncology, Medical Genetics Unit, “Aldo Moro” University of Bari, Italy;u. Istituto di Medicina Legale, Università Cattolica del Sacro Cuore, Roma, Italy;v. Department of Biopathology, Medical and Forensic Biotechnologies, University of Palermo, Italy;w. Department of Medicine, Surgery and Health, University of Trieste, Italy;x. Dipartimento di Sanità Pubblica e Medicina di Comunità, Università degli Studi di Verona, Italy;y. Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Italy;1. Department of Forensic Biology, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China;2. Department of Forensic Analytical Toxicology, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China;3. The Center for Material Evidence, Tibet Autonomous Region Public Security, Lhasa 850000, Tibet Autonomous Region, China;1. Forensic Science Service of the Beijing Public Security Bureau, 100192, Beijing, China;2. Taiyuan Public Security Bureau, 030001, Taiyuan, China;3. Beijing Microread Genetics Co., Ltd., 100045, Beijing, China;4. Suzhou Microread Genetics Co., Ltd., 215002, Suzhou, China;1. UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium;2. KU Leuven, Department of Imaging & Pathology, Biomedical Forensic Sciences, Leuven, Belgium;3. KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, Leuven, Belgium;4. KU Leuven, Laboratory of Socioecology and Social Evolution, Department of Biology, Leuven, Belgium;1. Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands;2. Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Postzone S-05-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands;3. Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands;1. University of Central Lancashire, School of Forensic and Investigative Sciences, Preston, UK;2. General Department of Forensic Sciences and Criminology, Dubai Police General Head Quarters, Dubai, United Arab Emirates;3. Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands |
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| Abstract: | Recently introduced rapidly mutating Y-chromosomal short tandem repeat (RM Y-STR) loci, displaying a multiple-fold higher mutation rate relative to any other Y-STRs, including those conventionally used in forensic casework, have been demonstrated to improve the resolution of male lineage differentiation and to allow male relative separation usually impossible with standard Y-STRs. However, large and geographically-detailed frequency haplotype databases are required to estimate the statistical weight of RM Y-STR haplotype matches if observed in forensic casework. With this in mind, the Italian Working Group (GEFI) of the International Society for Forensic Genetics launched a collaborative exercise aimed at generating an Italian quality controlled forensic RM Y-STR haplotype database. Overall 1509 male individuals from 13 regional populations covering northern, central and southern areas of the Italian peninsula plus Sicily were collected, including both “rural” and “urban” samples classified according to population density in the sampling area. A subset of individuals was additionally genotyped for Y-STR loci included in the Yfiler and PowerPlex Y23 (PPY23) systems (75% and 62%, respectively), allowing the comparison of RM and conventional Y-STRs. Considering the whole set of 13 RM Y-STRs, 1501 unique haplotypes were observed among the 1509 sampled Italian men with a haplotype diversity of 0.999996, largely superior to Yfiler and PPY23 with 0.999914 and 0.999950, respectively. AMOVA indicated that 99.996% of the haplotype variation was within populations, confirming that genetic-geographic structure is almost undetected by RM Y-STRs. Haplotype sharing among regional Italian populations was not observed at all with the complete set of 13 RM Y-STRs. Haplotype sharing within Italian populations was very rare (0.27% non-unique haplotypes), and lower in urban (0.22%) than rural (0.29%) areas. Additionally, 422 father-son pairs were investigated, and 20.1% of them could be discriminated by the whole set of 13 RM Y-STRs, which was very close to the theoretically expected estimate of 19.5% given the mutation rates of the markers used. Results obtained from a high-coverage Italian haplotype dataset confirm on the regional scale the exceptional ability of RM Y-STRs to resolve male lineages previously observed globally, and attest the unsurpassed value of RM Y-STRs for male-relative differentiation purposes. |
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| Keywords: | Y-chromosome Rapidly mutating Y-STRs (RM Y-STRs) Haplotype Lineage differentiation Relative differentiation Italy |
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