Genetic Structure Analysis and Kinship Inference in a Male Pedigree Based on Next-generation Sequencing

Yifei ZENG; Jiamei JIANG; Junwei RUAN; Yan XIANG; Linlin LIU; Shengjie NIE; Liping HU

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Article Navigation > Journal of Kunming Medical University > 2026 > Accepted Manuscript

Yifei ZENG, Jiamei JIANG, Junwei RUAN, Yan XIANG, Linlin LIU, Shengjie NIE, Liping HU. Genetic Structure Analysis and Kinship Inference in a Male Pedigree Based on Next-generation Sequencing[J]. Journal of Kunming Medical University.

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Genetic Structure Analysis and Kinship Inference in a Male Pedigree Based on Next-generation Sequencing

1.
College of Forensic Medicine，Kunming Medical University，Kunming Yunnan 650500
2.
Judicial Expertise Center，Qujing Public Security Bureau，Qujing Yunnan 655000，China

Received Date: 2026-04-10

Abstract

Abstract

Objective To explore a next-generation sequencing （NGS）-based strategy combining Y-chromosomal short tandem repeat （Y-STR） analysis for narrowing the paternal lineage with autosomal STR analysis for classifying kinship distance, thereby further improving the accuracy and efficiency of suspect screening in criminal cases involving male suspects. Methods Peripheral blood samples were collected from 42 male members of the same paternal pedigree in Qujing, Yunnan Province, in June 2024; 41 were included in the subsequent pedigree analysis. Four unrelated males outside the pedigree and 23 pairs of samples with genetically confirmed kinship relationships from routine casework were additionally included for validation. STR genotyping was performed on fifty-two autosomal STRs and 81 Y-STRs using the SET B-S138 NGS panel. Ratios of identity by state （RIBS） were calculated for each sample pair based on the autosomal STR profiles, and kinship degrees were assigned according to forensic genealogical relationship classification criteria. A Fisher linear discriminant model with equal prior probabilities was constructed using RIBS, and its performance was evaluated using samples with known kinship relationships. Results The number of alleles identified by autosomal STR sequence-based genotyping increased by 32.54% compared with length-based genotyping. The discriminant function was D = 21.599×RIBS−6.864, with D > 2.386 indicating close kinship whereas D≤2.386 indicating distant kinship. Under equal prior probabilities and equal misclassification costs, the corresponding RIBS classification threshold was 0.428292. The overall resubstitution accuracy was 98.78%. At this threshold, all 23 known close-kin pairs and all 164 unrelated pairs involving males outside the pedigree were correctly classified. Conclusion NGS reveals additional sequence-level variation and improves the allele-resolution capacity of autosomal STR typing. The RIBS-based discriminant model enables preliminary binary classification of close versus distant kinship among pedigree members. This combined autosomal STR and Y-STR strategy may further narrow the target range using autosomal STR information after pedigree-database matching has identified a candidate paternal lineage, thereby improving the efficiency of criminal investigations.
- Next-generation sequencing,
- Sequence polymorphism,
- Genetic relationship,
- Identity by state score

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References(23)

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