Construction of A Novel 5-Dye Fluorescent Multiplex System With 30 Y-STRs for Patrilineal Relationship Prediction.

Journal: Electrophoresis
Published Date: Aug 20, 2025

Abstract

Nowadays, Y chromosome short tandem repeats (Y-STRs) are widely used in forensic medicine practice, which has great significance for ancestry tracing, male lineage evolution, and male paternal relatives. Rapidly mutating Y-STRs (RM Y-STRs) have been shown to have greater potential to distinguish males from males in the patrilineal line. Therefore, a novel 5-dye fluorescent multiplex system with 30 Y-STRs was developed and optimized to screen out more RM Y-STRs and fasting mutating Y-STRs (FM Y-STRs). New primers were designed, and composite system construction was carried out. A series of experiments were conducted following the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), including polymerase chain reaction (PCR) amplification conditions, sensitivity, stability, species specificity, mixture and degraded sample studies, mutation analysis, and population studies. The results suggested that changing PCR amplification conditions in a reasonable range hardly affected the genotyping. The system showed excellent sensitivity and stability in sensitivity and stability studies. Even with UV-C exposure for up to 96 h, the system performed well in male blood samples and semen-vaginal secretion mixtures. Mutation analysis was performed on 582 father-son pairs, and 4 RM Y-STRs and 7 FM Y-STRs were identified, with mutation rates ranging from 1.72 × 10 to 20.62 × 10. Furthermore, on the basis of mutation rate analysis, eight machine learning methods were used to construct and compare patrilineal relationship prediction models, inferring the relationship by predicting the number of meiosis. Overall, the multiplex system displays favorable performance and has a greater potential for application in forensic science practice.

Authors

  • Chaoran Sun
    Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China.
  • Zhirui Zhang
    Department of Hydraulic Engineering, Tongji University, Shanghai, 200092, China.
  • Xindi Wang
    Montreal Neurological Institute, McGill University, Montreal, Québec, Canada. Electronic address: sandywang.rest@gmail.com.
  • Bo Liu
    Wuhan United Imaging Healthcare Surgical Technology Co., Ltd., Wuhan, China.
  • Chengye Zhou
    College of Automation (Artificial Intelligence), Hangzhou Dianzi University, Hangzhou 310018, P. R. China.
  • Yufei Yang
  • Chuanxu Wang
    Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China.
  • Sunxi Xu
    Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan Province, China.
  • Chang Wang
    Key Laboratory of the plateau of environmental damage control, Lanzhou General Hospital of Lanzhou Military Command, Lanzhou, China.
  • Lagabaiyila Zha
    Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China.
  • Jienan Li
    Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China.
  • Haibo Luo
    Key Laboratory of Opto-Electronic Information Processing, Chinese Academy of Sciences, Shenyang, 110016, China; Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China; Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China. Electronic address: luohb@sia.cn.
  • Feng Song
    Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China.

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