The battle of the titans: Comparative performance of Kintelligence, microarray, and shotgun sequencing in ten Estonian cases with unidentified human remains.

To conduct forensic investigative genetic genealogy (FIGG), reliable true-positive matches in genetic genealogy databases are required, which in turn depend on the generation of high-quality SNP profiles. This is particularly challenging for unidentified human remains (UHRs) originating from populations underrepresented in such databases. In this pilot study, ten Estonian UHR cases with available blood or skeletal remains were analysed using three SNP-typing technologies: the ForenSeq Kintelligence Kit, a customised microarray (EstGSA), and shotgun sequencing (SGS). The performance of each technology was assessed based on profile quality, database upload success, and match informativeness in GEDmatch PRO™. The ForenSeq Kintelligence Kit generated uploadable profiles for all samples, with quality metrics indicating high-quality genotypes. However, sufficiently close relatives were not identified in the database, which illustrated the limitations of the kit in this underrepresented population. EstGSA produced uploadable profiles for all six blood samples and one skeletal sample, whereas uploads failed for the three more degraded skeletal remains. SGS generated uploadable profiles for nine of ten remains, and outperformed the microarray-based genotyping for challenging samples. Both EstGSA and SGS enabled identification of distant and possibly true-positive matches in GEDmatch PRO™, demonstrating their value for FIGG in underrepresented populations. However, the results underscored the critical importance of profile quality, as distant associations often depend on single shared DNA segments that may be disrupted by genotyping errors.