Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection |
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| Institution: | 1. Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China;2. School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China;3. School of Life Sciences, Jilin University, Changchun 130012, China;4. Anhui Hopegenerich Biotechnology, Hefei 230031, China;5. Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China;6. Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China;7. Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China;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. Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, PR China, Shanghai 200063, China;2. Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China;1. Beijing institute of radiation medicine, 27 Taiping road, Beijing 100850, PR China;2. College of Life Science, Henan Normal University, No 46, East Jianshe Road, Xinxiang, Henan 453007, PR China;1. Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain;2. Life Sciences Dpt, Barcelona Supercomputing Center (BSC), Barcelona, Spain;3. ICREA, Barcelona, Spain;4. Genomes for Life-GCAT lab. Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain;5. In behalf of Genomes for Life GCAT Project, Spain;1. Beijing Institute of Microbiology and Epidemiology, 27 Taiping Road, Beijing 100850, PR China;2. Department of Pathology and Forensic Medicine, College of Medicine, Yanbian University, No. 977 Park Road, Jilin 133002, PR China |
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| Abstract: | Y-chromosomal haplogroups determined by Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal biogeographic ancestry inference, which has attracted a lot of interest in the forensic community. Recently, a comprehensive Y-SNP tool with dominant markers targeting haplogroups in R, E and I branches has been reported, which allows the inference of 640 Y haplogroups. It had a very good performance and could provide a high level of Y haplogroup resolution in most populations. However, the predominant haplogroups in the Chinese populations are O, C and N, suggesting that more Y-SNPs under these clades are needed to achieve the population-specific high resolution. Herein, aiming at the Chinese population, we presented a largely improved custom Y-SNP MPS panel that contains 256 carefully ascertained Y-SNPs based on our previous studies, and evaluated this panel via a series of tests, including the tests for concordance, repeatability, sensitivity, specificity, and stability, as well as the mixture, degraded and case-type sample analysis. The preliminary developmental validation demonstrated that this panel was highly reliable, sensitive, specific, and robust. In the sensitivity test, even when the DNA input was reduced to as low as 0.5 ng, the sample could still be assigned to the correct Y haplogroup. For mixture analysis, even the 1:99 (Male: Female) mixtures had no effects on the assignation of the Y haplogroup of the male contributor. In summary, this assay has provided a high-resolution Y-chromosomal haplogrouping workflow to determine a male’s paternal lineage and/or paternal biogeographic ancestry and could be widely used for Chinese Y-chromosomal haplogroups dissection. |
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| Keywords: | Forensic genetics Paternal lineage identification Y-chromosomal haplogroup Y-SNP Massively parallel sequencing (MPS) |
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