Polymorphisms and microvariant sequences in the Japanese population for 25 Y-STR markers and their relationships to Y-chromosome haplogroups |
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| Affiliation: | 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. 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. 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. Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu 610041, China;2. Hainan Provincial Blood Center, Haikou 570311, China;1. Carabinieri, Reparto Investigazioni Scientifiche di Roma, Sezione di Biologia, Rome, Italy;2. Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy;3. Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy;4. Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy;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 |
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| Abstract: | Y-chromosomal short tandem repeat (Y-STR) markers have been used for forensic purposes such as kinship analysis of male-linage and detection of a male DNA component in a mixture of male and female DNA. Recently, rapidly mutating Y-STR (RM Y-STR) markers were reported that are expected to help distinguish close male relatives. This study provides data of Y-chromosomal haplotypes for 25 Y-STR markers, including six RM Y-STR markers (DYS576, DYS627, DYS518, DYS570, DYS449 and DYF387S1) typed with the Yfiler™ Plus kit in 1299 males of the Japanese population. Discrimination capacity increased from 87.2% for 16 Y-STR markers with the Yfiler™ kit to 99.6% for 25 Y-STR markers with the Yfiler™ Plus kit. We characterized sequences of observed microvariant alleles of eight Y-STR markers and a low-amplified allele of DYS390 by Sanger sequencing. DYF387S1, a multi-locus Y-STR marker that is located at two positions on the human Y-chromosome, was observed in tri-allelic patterns in 51 of 1299 samples (3.9%) and we found an extremely high frequency of the tri-allelic pattern of DYF387S1 in haplogroup C-M131. We also analyzed Y-STR gene diversity in each haplogroup and its relevance to mutation rates. |
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| Keywords: | Y-STR Yfiler™ Plus Rapidly mutating Y-STR Microvariant sequence Y-chromosome haplogroup |
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