Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Haoliang Fan; Yiran Xu; Yutao Zhao; Kai Feng; Liuxi Hong; Qiancheng Zhao; Xiaoyu Lu; Meisen Shi; Haiyan Li; Lingxiang Wang; Shaoqing Wen

doi:10.1016/j.fsigen.2024.103029

Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Forensic Sci Int Genet. 2024 Mar 5:71:103029. doi: 10.1016/j.fsigen.2024.103029. Online ahead of print.

Authors

Haoliang Fan¹, Yiran Xu², Yutao Zhao³, Kai Feng⁴, Liuxi Hong⁵, Qiancheng Zhao⁶, Xiaoyu Lu⁷, Meisen Shi⁸, Haiyan Li⁹, Lingxiang Wang¹⁰, Shaoqing Wen¹¹

Affiliations

¹ MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China. Electronic address: fanhaoliang198931@163.com.
² Institute of Archaeological Science, Fudan University, Shanghai 200433, China. Electronic address: 1055217919@qq.com.
³ Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China. Electronic address: zhaoyutao007@163.com.
⁴ Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China. Electronic address: fengkaify@163.com.
⁵ Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China. Electronic address: 34905687@qq.com.
⁶ Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China. Electronic address: 271546314@qq.com.
⁷ Deepreads Biotech Company Limited, Guangzhou 510663, China. Electronic address: snowind67@pku.edu.cn.
⁸ Criminal Justice College of China University of Political Science and Law, Beijing 100088, China. Electronic address: shimeisen2000@163.com.
⁹ Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China. Electronic address: stfydna@163.com.
¹⁰ MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China. Electronic address: wlx.wang@foxmail.com.
¹¹ MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China. Electronic address: wenshaoqing@fudan.edu.cn.

PMID: 38518712
DOI: 10.1016/j.fsigen.2024.103029

Abstract

Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.

Keywords: Chinese surname; Geographical locations; Massive parallel sequencing; Paternal lineage; Validation study; Y-SNPs; Y-STRs; Y-haplogroups.