Developmental validation of a 381 Y-chromosome SNP panel for haplogroup analysis in the Chinese populations

Ruiyang Tao; Min Li; Siyu Chai; Ruocheng Xia; Yiling Qu; Chunyan Yuan; Guangyuan Yang; Xinyu Dong; Yingnan Bian; Suhua Zhang; Chengtao Li

doi:10.1016/j.fsigen.2022.102803

Developmental validation of a 381 Y-chromosome SNP panel for haplogroup analysis in the Chinese populations

Forensic Sci Int Genet. 2023 Jan:62:102803. doi: 10.1016/j.fsigen.2022.102803. Epub 2022 Oct 29.

Authors

Ruiyang Tao¹, Min Li², Siyu Chai³, Ruocheng Xia¹, Yiling Qu⁴, Chunyan Yuan⁵, Guangyuan Yang⁵, Xinyu Dong⁶, Yingnan Bian¹, Suhua Zhang⁷, Chengtao Li⁸

Affiliations

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 Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, China.
⁴ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China.
⁵ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China.
⁶ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China.
⁷ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China. Electronic address: zhang_suhua@fudan.edu.cn.
⁸ Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China. Electronic address: lichengtaohla@163.com.

PMID: 36368220
DOI: 10.1016/j.fsigen.2022.102803

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.

Keywords: Forensic genetics; Haplogroup; Massively parallel sequencing (MPS); Single nucleotide polymorphisms (SNPs); Y chromosome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosomes, Human, Y*
DNA
East Asian People
Genetics, Population
Haplotypes
High-Throughput Nucleotide Sequencing / methods
Humans
Male
Polymorphism, Single Nucleotide*

Substances

DNA