Development of a coding SNP panel for tracking the origin of whole-exome sequencing samples

Yong Huang; Yuanyuan Xiao; Shengqiu Qu; Jiaming Xue; Lin Zhang; Li Wang; Weibo Liang

doi:10.1186/s12864-024-10052-4

Development of a coding SNP panel for tracking the origin of whole-exome sequencing samples

BMC Genomics. 2024 Feb 5;25(1):142. doi: 10.1186/s12864-024-10052-4.

Authors

Yong Huang^#^{1

2}, Yuanyuan Xiao^#³, Shengqiu Qu³, Jiaming Xue³, Lin Zhang^{2

3}, Li Wang^{4

5}, Weibo Liang⁶

Affiliations

¹ West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China.
² Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, 610041, P.R. China.
³ Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, P.R. China.
⁴ Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, 610041, P.R. China. wicky.wangli@qq.com.
⁵ Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China. wicky.wangli@qq.com.
⁶ Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, P.R. China. liangweibo@scu.edu.cn.

^# Contributed equally.

Abstract

Whole-exome sequencing (WES) is widely used to diagnose complex genetic diseases and rare conditions. The implementation of a robust and effective quality control system for sample identification and tracking throughout the WES process is essential. We established a multiplex panel that included 22 coding single-nucleotide polymorphism (cSNP) loci. The personal identification and paternity identification abilities of the panel were evaluated, and a preliminary validation of the practical feasibility of the panel was conducted in a clinical WES case. These results indicate that the cSNP panel could be a useful tool for sample tracking in WES.

Keywords: Coding single-nucleotide polymorphisms; Parentage test; Personal identification; Sample tracking; Whole-exome sequencing.

MeSH terms

Exome Sequencing
Exome*
Genetic Testing / methods
High-Throughput Nucleotide Sequencing / methods
Humans
Polymorphism, Single Nucleotide*