Forensic SNP genealogy inference identifies kinship by analyzing identity-by-descent (IBD) segments in high-density SNP data and has become a key technique for solving cold cases. However, current methods face two major challenges: (1) SNP microarrays require high-quality DNA, making it difficult to analyze trace or degraded DNA commonly found at crime scenes; (2) existing IBD algorithm parameters are mainly calibrated on European populations, lacking systematic validation in East Asian populations. To address these issues, we introduced the 1240K single nucleotide polymorphism (SNP) panel originally developed for ancient DNA research and established a long-range kinship inference pipeline based on the IBD algorithm. We evaluated the genetic polymorphism of the 1240K SNP panel using 504 East Asian individuals from the 1000 Genomes Project, assessed the performance of the IBD algorithm on 1,321 pairwise relationships (1st to 9th degree) derived from 161 real Chinese Han pedigrees, and systematically optimized three key parameters: IBD length threshold (cM), mismatch tolerance (het/hom), and linkage disequilibrium coefficient (R²). The results showed that the 1240K SNPs exhibited favorable genetic diversity and population discrimination power in East Asians. Optimizing the IBD length threshold to 2 cM and mismatch parameters to het13hom12 significantly improved kinship inference accuracy (7th degree confidence interval accuracy reached 83.70%, and Macro-F1 increased by 2.9% compared with default settings), whereas R²-based filtering did not substantially enhance performance. Under the optimized parameters, the 7th and 8th degree confidence interval accuracies were 83.70% and 74.19%, respectively. This study confirms that the 1240K SNP panel can be used not only for population genetic structure analysis but also for reliable kinship inference up to the 8th degree, demonstrating clear application potential in forensic genetics. It provides a feasible solution for genealogical analysis of trace and degraded DNA.
Zichen Tang, Zhen Jia, Zhixiao Fang, Pengchao Ji, Li Jiang, Wenting Zhao, Jing Liu, Yiliang Wei, Caixia Li
. Forensic investigative genetic genealogy research based on the 1240K SNPs panel[J]. Hereditas(Beijing), 0
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DOI: 10.16288/j.yczz.26-035
