Development and validation of a capture sequencing panel containing 9000 SNPs for inferring distant relatives in East Asian populations

Inferring distant relatives has long presented a significant challenge in forensic science. Recently, forensic researchers have increasingly focused on single nucleotide polymorphisms (SNPs) as a potent tool for this purpose. In this study, we developed and validated a capture sequencing panel comprising 9000 SNPs specifically aimed at inferring distant relatives within East Asian populations. Initially, we screened the 9000 SNPs from four data sources: the Infinium Global Screening Array, the Infinium Chinese Genotyping Array, the Single-Nucleotide Polymorphism database, and the 1000 Genomes Project. Subsequently, we established a likelihood ratio (LR)-based algorithm utilizing pedigree genotyping data from Han Chinese populations. Next, we constructed a sequencing method for the 9000 SNPs employing hybridization capture sequencing technology. Finally, the 9000 SNP panel was evaluated following the validation guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), including studies on repeatability, concordance, sensitivity, species specificity, PCR inhibition, DNA degradation, DNA mixture and casework-type samples. The results demonstrated that the 9000 SNPs exhibited considerable genetic polymorphism within East Asian populations, with an average minor allele frequency of 0.4521. The panel of 9000 SNPs was demonstrated to reliably identify relatives up to the 5th degree and certain 6th degree using the GSA SNP array for pedigree genotyping. Furthermore, the 9000 SNP panel yielded robust and reliable genotyping results for trace DNA (1.953 ng), degraded DNA (50 bp), and mixed DNA (19:1 ratio), showing specific species specificity and resistance to PCR inhibition. In conclusion, this study highlights the significant potential of the 9000 SNP panel for inferring distant relatives in East Asian populations, providing a valuable tool for forensic applications. Further validation in a larger sample size is needed to confirm our observations.