Internal validation of an improved system for forensic application: a 41-plex Y-STR panel

Siyu Chai; Min Li; Ruiyang Tao; Ruocheng Xia; Qianqian Kong; Yiling Qu; Liqin Chen; Shiquan Liu; Chengtao Li; Pengyu Chen; Suhua Zhang

doi:10.1093/fsr/owad012

Internal validation of an improved system for forensic application: a 41-plex Y-STR panel

Forensic Sci Res. 2023 Apr 11;8(1):70-78. doi: 10.1093/fsr/owad012. eCollection 2023 Mar.

Authors

Siyu Chai^{1

2}, Min Li^{2

3}, Ruiyang Tao², Ruocheng Xia², Qianqian Kong^{2

4}, Yiling Qu^{2

5}, Liqin Chen⁴, Shiquan Liu⁶, Chengtao Li², Pengyu Chen¹, Suhua Zhang^{2

7}

Affiliations

¹ Key Laboratory of Cell Engineering of Guizhou Province, Clinical Stem Cell Research Institute, Affiliated Hospital of Zunyi Medical University, Zunyi, China.
² Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, China, Shanghai, China.
³ School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
⁴ Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot, China.
⁵ Department of Forensic Science, Medical School of Soochow University, Suzhou, China.
⁶ Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China.
⁷ School of Basic Medical Sciences, Fudan University, Shanghai, China.

Abstract

Y-chromosome short tandem repeats (Y-STRs) have a unique role in forensic investigation. However, low-medium mutating Y-STRs cannot meet the requirements for male lineage differentiation in inbred populations, whereas rapidly mutating (RM) high-resolution Y-STRs might cause unexpected exclusion of paternal lineages. Thus, combining Y-STRs with low and high mutation rates helps to distinguish male individuals and lineages in family screening and analysis of genetic relationships. In this study, a novel 6-dye, 41-plex Y-STR panel was developed and validated, which included 17 loci from the Yfiler kit, nine RM Y-STR loci, 15 low-medium mutating Y-STR loci, and three Y-InDels. Developmental validation was performed for this panel, including size precision testing, stutter analysis, species specificity analysis, male specificity testing, sensitivity testing, concordance evaluation, polymerase chain reaction inhibitors analysis, and DNA mixture examination. The results demonstrated that the novel 41-plex Y-STR panel, developed in-house, was time efficient, accurate, and reliable. It showed good adaptability to directly amplify a variety of case-type samples. Furthermore, adding multiple Y-STR loci significantly improved the system's ability to distinguish related males, making it highly informative for forensic applications. In addition, the data obtained were compatible with the widely used Y-STR kits, facilitating the search and construction of population databases. Moreover, the addition of Y-Indels with short amplicons improves the analyses of degraded samples.

Key points: A novel multiplex comprising 41 Y-STR and 3 Y-InDel was developed for forensic application.The multiplex included rapidly mutating Y-STRs and low-medium mutating Y-STRs, which is compatible with many commonly used Y-STR kits.The multiplex is a powerful tool for distinguishing related males, familial searching, and constructing DNA databases.

Keywords: 41-plex Y-STR panel; familial searching; forensic genetics; male identification; validation.