The Identification of a 1916 Irish Rebel: New Approach for Estimating Relatedness From Low Coverage Homozygous Genomes

Abstract

Thomas Kent was an Irish rebel who was executed by the British forces in the aftermath of the Rising armed insurrection of 1916 and buried in a shallow grave on Cork prison's grounds. In 2015, ninety-nine years after his death, a state funeral was offered to his living family to honor his role in the struggle for Irish independence. However, due to inaccuracies in record keeping, the bodily remains from Cork prison that supposedly belonged to Kent could not be identified with absolute certainty. At the request of the Irish National Police (An Garda Siochana), we identified the remains presumed to be those of Kent using a novel method that compared homozygous single nucleotide polymorphisms obtained from next-generation shotgun sequencing with genetic data from two of Kent's known living relatives who share with him a third degree relationship. DNA degradation resulted in low sequence depth of Thomas Kent's DNA and only a few loci appeared as heterozygous, rendering traditional methods of relatedness estimation unusable. To remove potential bias, all loci were therefore analysed as homozygous, leading to a process we refer to as \"forced homozygote approach\". This procedure reduces the expected degree of relatedness to half of what is expected when heterozygotes are included; thus, Kent had a relationship coefficient (Queller and Goodnight's Rxy) of 12.5% with his third-degree relatives instead of the expected 25%. The results were confirmed using simulated data for different relatedness classes (2000 simulated individuals per class), also confirming Thomas Kent's identity. We argue that this method provides a necessary alternative for relatedness estimations, not only in forensic analysis, but also in ancient DNA studies, where reduced amounts of genetic information can limit the application of traditional methods.