Developmental validation of a 381 Y-chromosome SNP panel for haplogroup analysis in the Chinese populations |
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| Institution: | 1. Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China;2. School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China;3. Department of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, China;4. Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China;5. Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China;6. School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China;1. Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia;2. School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia;3. Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand;4. University of Auckland, Department of Statistics, Auckland, New Zealand;1. Centre for Forensic Science, University of Technology Sydney, Ultimo, NSW 2007, Australia;2. Australian Museum Research Institute, Australian Museum, Sydney, NSW 2001, Australia;1. University Ulm, Institute of Legal Medicine, Albert-Einstein-Allee 23, Ulm 89081, Germany;2. Ludwig-Maximilians University Munich, Geschwister-Scholl-Platz 1, München 80539, Germany;1. Institute of Forensic Medicine, University Basel, Pestalozzistrasse 22, 4056 Basel, Switzerland;2. Institute of Medical Informatics and Statistics, Kiel University and University-Hospital Schleswig-Holstein, Brunswiker Str. 10, 24105 Kiel, Germany;3. Institute of Forensic Medicine, Kantonsspital St. Gallen, Rorschacher Strasse 95, 9007 St. Gallen, Switzerland;4. Institute of Forensic Medicine, University Bern, Murtenstrasse 26, 3008 Bern, Switzerland |
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| Abstract: | Y-chromosome single nucleotide polymorphism (Y-SNP) shows great variation in geographical distribution and population heterogeneity and can be used to map population genetics around the world. Massive parallel sequencing (MPS) methodology enables high-resolution Y-SNP haplogrouping for a certain male and is widely used in forensic genetics and evolutionary studies. In this present study, we used MPS to develop a customized 381 Y-SNP panel (SifaMPS 381 Y-SNP panel) to investigate the basic structure and subbranches of the haplogroup tree of the Chinese populations. The SifaMPS 381 Y-SNP panel covers all the Y-SNPs from our previously designed 183 Y-SNP panel and additional SNPs under the predominant haplogroups in the Chinese populations based on certain criteria. We also evaluated the sequencing matrix, concordance, sensitivity, repeatability of this panel and the ability to analyze mixed and case-type samples based on the Illumina MiSeq System. The results demonstrated that the novel MPS Y-SNP panel possessed good sequencing performance and generated accurate Y-SNP genotyping results. Although the recommended DNA input was greater than 1.25 ng, we observed that a lower DNA amount could still be used to analyze haplogroups correctly. In addition, this panel could handle mixed samples and common case-type samples and had higher resolution among Chinese Han males than previously reported. In conclusion, the SifaMPS 381 Y-SNP panel showed an overall good performance and offers a better choice for Y-SNP haplogrouping of the Chinese population, thereby facilitating paternal lineage classification, familial searching and other forensic applications. |
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| Keywords: | Forensic genetics Massively parallel sequencing (MPS) Y chromosome Single nucleotide polymorphisms (SNPs) Haplogroup |
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