Forensic investigative genetic genealogy (FIGG) is an innovative approach to identifying perpetrators and unidentified human remains. However, the accuracy of genotyping is often compromised in cases involving severely damaged remains with highly degraded DNA, which can lead to the underestimation or missed detection of genetic relatedness. To address this challenge, we have developed a method called clusIBD that detects identity-by-descent (IBD) segments by identifying clusters of regions characterized by low rates of opposite homozygosity or mismatches between samples. In this study, we systematically evaluated the efficacy of clusIBD for kinship inference using authentic ancient and degraded human remains.

First, we analyzed a well-characterized Late Neolithic family dataset (~5,700 years old), followed by genotype imputation using GLIMPSE2. The results showed that clusIBD detected IBD segments with mean lengths of 2,707 ± 1,332 cM, 1,522 ± 555 cM, 708 ± 364 cM, 354 ± 230 cM, 174 ± 111 cM, 66 ± 52 cM, and 20 ± 19 cM for first- to seventh-degree relatives, respectively. This performance consistently outperformed that of ancIBD, TRUFFLE, and IBIS. In terms of relationship classification, clusIBD achieved an overall accuracy of 66.09%, substantially higher than ancIBD (10.5%), TRUFFLE (2.54%), and IBIS (0%). Notably, clusIBD identified several pairs of individuals who had been classified as unrelated in the original study as sixth- to seventh-degree relationships.

In a separate real-world case involving remains buried for approximately 70 years and characterized by highly fragmented DNA and typical post-mortem damage patterns, clusIBD detected around 640 cM of shared IBD segments between the unidentified individual and one of five putative relatives. Although the inferred relationship differed somewhat from the anticipated grandparent–grandchild relationship, this outcome demonstrates the practical applicability of the method in forensic contexts involving severely degraded samples.

In conclusion, our study shows that clusIBD substantially improves IBD detection and kinship inference from highly degraded DNA compared with the other methods mentioned above. The method successfully recovers cryptic relatedness that was overlooked in previous studies and shows promise for real-world forensic applications involving aged and damaged remains. Collectively, these results establish clusIBD as a robust and promising tool for forensic genetic investigations, particularly in scenarios where traditional approaches are constrained by suboptimal DNA quality.

Authors

• Ran Li (Sun Yat-sen University, China)
• Hongyu Sun (Sun Yat-sen University, China)