Forensic validation of the SNPforID 52-plex assay |
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| Institution: | 1. Centre for Haematology, ICMS, Barts & the London, Queen Mary''s School of Medicine & Dentistry, London, United Kingdom;2. Institute of Legal Medicine, Johannes Gutenberg University, Mainz, Germany;3. Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria;4. Department of Forensic Genetics, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark;5. Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain;6. Institute of Legal Medicine, University of Cologne, Cologne, Germany;1. Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China;2. Department of Internal Medicine, Affiliated Hospital of Inner Mongolia University for Nationalities, Tongliao, China;1. Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China;2. Department of Fetal Medicine and Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 2699 West Gaoke Rd, Shanghai 201204, China;3. Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China;4. West China School of Basic Medical Science and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China;5. Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China;6. Department of Biochemistry and Molecular Biology, Shanghai Medical College of Fudan University, Shanghai 200032, China;1. Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark;2. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark;1. Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Immunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina;2. National Research Council, CONICET, Buenos Aires, Argentina;1. State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil;2. IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Portugal;3. Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal;1. Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria;2. Forensic Science Program, The Pennsylvania State University, University Park, PA, USA;1. Forensic Science South Australia, Adelaide, Australia;2. Flinders University, Adelaide, Australia;1. Institute for Molecular Medicine, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA;2. Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA;3. Molecular Anthropology Laboratory, Department of Anthropology, University of California, One Shields Avenue, Davis, CA 95616, USA;4. Graduate Group in Forensic Science, University of California,One Shields Avenue, Davis, CA 95616, USA;5. Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia;1. Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland;2. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;3. Institute of Forensic Medicine, Forensic Molecular Biology Dpt., University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland |
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| Abstract: | The advantages of single nucleotide polymorphism (SNP) typing in forensic genetics are well known and include a wider choice of high-throughput typing platforms, lower mutation rates, and improved analysis of degraded samples. However, if SNPs are to become a realistic supplement to current short tandem repeat (STR) typing methods, they must be shown to successfully and reliably analyse the challenging samples commonly encountered in casework situations.The European SNPforID consortium, supported by the EU GROWTH programme, has developed a multiplex of 52 SNPs for forensic analysis, with the amplification of all 52 loci in a single reaction followed by two single base extension (SBE) reactions which are detected with capillary electrophoresis.In order to validate this assay, a variety of DNA extracts were chosen to represent problems such as low copy number and degradation that are commonly seen in forensic casework. A total of 40 extracts were used in the study, each of which was sent to two of the five participating laboratories for typing in duplicate or triplicate. Laboratories were instructed to carry out their analyses as if they were dealing with normal casework samples. Results were reported back to the coordinating laboratory and compared with those obtained from traditional STR typing of the same extracts using Powerplex® 16 (Promega). These results indicate that, although the ability to successfully type good quality, low copy number extracts is lower, the 52-plex SNP assay performed better than STR typing on degraded samples, and also on samples that were both degraded and of limited quantity, suggesting that SNP analysis can provide advantages over STR analysis in forensically relevant circumstances. However, there were also additional problems arising from contamination and primer quality issues and these are discussed. |
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