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KinshipLR: software development and application for complex kinship testing in forensic genetics.

Xingru Zhang1, Yating Fang2, Yuxin Guo3

  • 1Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an 710004, China; School of Basic Medical Science, Anhui Medical University, Hefei 230031, China.

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|September 4, 2025
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Summary

Optimizing complex kinship testing, this study found that adding X-STRs to autosomal STRs significantly improves accuracy. The KinshipLR R package and IBS-SVM method enhance genetic marker selection for reliable forensic applications.

Keywords:
Complex kinship testingDNA markersFamily simulationLikelihood ratioNext generation sequencing

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Area of Science:

  • Forensic genetics
  • Population genetics
  • Bioinformatics

Background:

  • Complex kinship testing faces challenges due to intricate genetic data and unoptimized marker selection.
  • Systematic evaluation of genetic markers like autosomal STRs, SNPs, and X-STRs is lacking for complex relationships.

Purpose of the Study:

  • To develop an R package, KinshipLR, for optimizing genetic marker selection in complex kinship testing.
  • To evaluate the efficacy of autosomal STRs, SNPs, and X-STRs across diverse kinship scenarios and populations.
  • To compare the performance of different evaluation algorithms for kinship analysis.

Main Methods:

  • Developed the KinshipLR R package for biomarker selection.
  • Conducted 10,000 simulations using Chinese population allele frequency data for various scenarios.
  • Assessed factors influencing testing accuracy: relationship type, population, marker type, and algorithms (LR vs. IBS-SVM).

Main Results:

  • Genetic marker efficacy in kinship testing varies significantly across populations.
  • Integrating 27 X-STRs with 20 CODIS-STRs substantially boosts accuracy for relationships like siblings and aunt-niece.
  • The IBS with SVM method demonstrates superior performance over traditional LR-based methods in complex kinship testing.

Conclusions:

  • The study provides a tailored approach for selecting genetic markers to improve complex kinship testing efficiency and reliability.
  • Findings offer valuable insights for optimizing forensic genetic applications.
  • X-STRs play a crucial role in enhancing the power of kinship testing, especially in challenging scenarios.