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

Daniel Fernandes, Kendra Sirak, Mario Novak, John A. Finarelli, John Byrne, Edward Connolly, Jeanette E. L. Carlsson, Edmondo Ferretti, Ron Pinhasi, Jens Carlsson
2017 Scientific Reports  
Thomas Kent was an Irish rebel who was executed by British forces in the aftermath of the Easter 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, inaccuracies in record keeping did not allow the bodily remains that supposedly belonged to Kent to be identified with absolute certainty. Using a novel
more » ... approach based on homozygous single nucleotide polymorphisms, we identified these remains to be those of Kent by comparing his genetic data to that of two known living relatives. As the DNA degradation found on Kent's DNA, characteristic of ancient DNA, rendered traditional methods of relatedness estimation unusable, we forced all loci homozygous, in a process we refer to as "forced homozygote approach". The results were confirmed using simulated data for different relatedness classes. 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. Estimating the genetic relatedness of modern individuals is routinely achieved by employing the use of microsatellites (synonymous with short tandem repeats (STRs)) or other genomic markers that estimate kinship coefficients based on probabilities of identity-by-descent (IBD) 1,2 . These methods, however, cannot be applied to cases where the DNA presents high levels of fragmentation and damage, as is common in ancient DNA (aDNA). Upon an organism's death, its genetic material starts to degrade and accumulate damage as repair enzymes no longer maintain the integrity of the molecular structure of DNA 3,4 . Among the many factors that contribute to the rate and severity of this phenomenon are temperature, the acidity of the surrounding depositional environment, ambient level of humidity, and the eventual invasion of environmental microbes into the organism's cells. As a result, DNA fragments extracted from preserved tissue (in most cases bone and teeth) that is recovered from either ancient or semi-ancient (e.g. many forensic cases) human remains are short in length, ranging from 30 to 70 base pairs (bp). The degradation process has a major impact on the success rates and authenticity of many PCR-based aDNA identification techniques 3-6 ; however, analysis of these short and damaged DNA molecules was revolutionised with the onset of Next Generation Sequencing (NGS) just over one decade ago. Next-generation shotgun sequencing has enabled aDNA studies to progress at a much faster rate than before, and when applied in
doi:10.1038/srep41529 pmid:28134350 pmcid:PMC5278401 fatcat:dtm3vpgr3rd3dfzncehenj3cvq