Extended Kinship Inference Part 1: Evaluation of Short Tandem Repeats and Single Nucleotide Polymorphisms Using Likelihood Ratios and Haplotype Matching

Medium- and long-range kinship analysis using single nucleotide polymorphism (SNP) genotyping allows law enforcement to generate investigative leads by identifying an unknown individual through their close and distant genetic relatives. Short-range kinship inference can be conducted through calculation of likelihood ratios (LRs) using population allele frequency data and the degree of similarity between two DNA profiles but has historically been limited to short tandem repeat (STR) profiles. Alternatively, identical by descent (IBD) segment matching algorithms can be used to detect shared DNA haplotypes between two genetically related individuals that have been inherited from a common ancestor. The ForenSeq® Kintelligence Kit enables law enforcement and forensic laboratories to utilize medium-density SNP sequencing technology for extended kinship inference by analyzing 10,230 SNPs. In this study, DNA from two pedigrees was used to compare the ability of STR profiles, identity-informative SNP (iiSNP) profiles, Kintelligence profiles and Kintelligence and direct-to-consumer profiles available on public genetic genealogy databases to detect and classify genetic relationships. The DNA profiles were analyzed using DBLR™ software to calculate kinship LRs or uploaded to GEDmatch PRO™ for IBD segment matching with either database searching or one-to-one comparisons. The LRs calculated for STR and iiSNP profiles were able to correctly infer first degree relationships (i.e., parent, offspring, and full sibling), with the combined discrimination power able to distinguish between second degree relationships. LRs calculated for the Kintelligence profiles exceeded one million for 93% of full sibling to fifth degree relationships tested. IBD segment matching was effective for detecting first to fifth degree relatives when Kintelligence profiles were searched on the GEDmatch PRO™ database. The results of this study demonstrate that the Kintelligence Kit is a valuable tool for law enforcement and forensic investigators, offering an advanced method for medium-range kinship testing using either LRs or IBD segment matching.