Forensic investigative genetic genealogy based on low-quality DNA whole genome sequencing data

Single nucleotide polymorphism (SNP) microarray technology is widely used for data acquisition in Forensic Investigative Genetic Genealogy (FIGG), but it requires high-quality DNA. Previous studies have demonstrated that whole-genome sequencing (WGS) outperforms SNP microarray technology in genotyping forensic trace and degraded DNA, improving both SNP call rates and genotyping concordance. This study evaluates the accuracy of FIGG using WGS data from low-quality DNA. We performed WGS on DNA samples with varying input amounts (1.0-0.05 ng) and different degrees of fragmentation (500-50 bp). We extracted 645,199 autosomal SNPs corresponding to a SNP microarray and conducted kinship analysis using identity-by-descent via identical-by-state. Results indicated that FIGG accuracy for 0.5 ng DNA input matched that of 200 ng DNA. Likewise, samples with an average fragment length of 200 bp demonstrated accuracy comparable to non-degraded DNA. However, when DNA input quantities fell below 0.2 ng or average fragment length was shorter than 100 bp, genealogy inference accuracy significantly decreased (P < 0.05). We further confirmed that genotype imputation technology could significantly improve genealogy inference accuracy of low-quality DNA sequencing data. All imputed samples (0.2 ng, 0.1 ng, 0.05 ng, 100 bp, 50 bp) showed no significant differences in genealogy inference accuracy compared to standard samples (200 ng DNA and non-degraded DNA) (P > 0.05). These research findings have important implications for forensic practice, providing methodological guidance for kinship inference of low-quality DNA samples.