Objectives

Forensic investigative genetic genealogy (FIGG) has grown rapidly as an emerging field of forensic genetics in recent years. It generally refers to the technique of detecting identity-by-descent (IBD) segments between individuals using large-scale single nucleotide polymorphism (SNP) databases generated by whole-genome microarrays or sequencing, thereby inferring distant kinship. Currently, short tandem repeats (STR) analysis still faces challenges in distant relative identification. Therefore, taking advantage of the short processing time and high accuracy of SNP chip technology, our research innovatively utilizes the Illumina Infinium Asian Screening Array (ASA) to screen more SNPs suitable for kinship inference in the Chinese population from family samples, and realizes the forensic SNP pedigree depiction.

Material and methods

We collected 97 real samples from two families including relatives from 1st to 9th degree and unrelated individuals to obtain ASA chip sequencing data. The reference data of Chinese Han in Beijing China (CHB) and Southern Han Chinese (CHS) from the 1000 Genomes Project were used to simulate 10000 pairs of different relatives. Following rigorous quality control, we obtained 135,981 and 558,770 autosomal SNPs, forming two SNP datasets, and evaluated the performance of identity-by-state (IBS), ITO, IBD and kinship coefficient methods in pedigree inference.

Results and conclusions

The results indicated the mean combined IBS scores (CIBS) and ITO scores showed a gradual decrease from first to ninth degree for two SNP datasets. We calculated the IBD segment lengths at different levels of kinship and concluded that the closer the kinship, the greater the IBD. The average IBD lengths of 558,770 and 135,981 SNPs were 2,797.6 Mb and 2,719.27 Mb respectively at the first degree, while in the seventh to ninth degree, they were all lower than 50 Mb. Additionally, the study predicted kinship by kinship coefficients from two SNP datasets by clusIBD and PLINK, finding that the kinship coefficients and the accuarcy of kinship prediction for more distant relatives were lower. PLINK achieved prediction accuracies exceeding 90% for parent-child (96.7%), full-siblings (94.4%) and second degree (91.1%) in both datasets, with accuracy rates exceeding 60% for third and fourth degrees. ClusIBD achieved 96.7% and 97.2% for parent-child and full-siblings respectively. However, at 135,981 SNPs, its accuracy for predicting second degree (84.2%) was significantly lower than at 558,770 SNPs (95%). Consequently, higher-density SNPs in the ASA chip are beneficial for pedigree inference, particularly at third degree relationships and beyond.

Authors

• Chaoran Sun (Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, China)
• Qiang Zhu (Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, China)
• Hewen Yao (Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, China)
• Haibo Luo (Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, China)
• Feng Song (Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, China)