Whole-genome sequencing of human remains to enable genealogy DNA database searches - A case report

Recently a number of high profile crime cases (e.g. the Golden State Killer) have successfully been solved or given new leads with the use of genome wide DNA data in combination with pairwise matching from individuals present in genealogy DNA databases. Such databases will primarily involve distant relatives which in turn require a large amount of genetic information, in the range of several hundred thousand to millions of SNPs, to be genotyped. While it nowadays is fairly straightforward to obtain such as data from high quality and high quantity DNA, it is still a challenge for degraded DNA of low quantity such in the case of forensic samples. Here we present a successful effort in obtaining genome-wide genotype data from human remains. The goal was to get investigative leads in order to identify the remains of an unknown male (the Ekeby man) that was found murdered in the south of Sweden in 2003. Whole-genome sequencing was performed on DNA originating from a bone sample. Three replicates of libraries were prepared using ThruPLEX DNA-seq Kit (Takara) which were sequenced on a HiSeq X instrument (Illumina). A mean coverage of 30X was obtained when the sequencing reads were mapped to a human reference genome. Following further bioinformatic processing, allele calling, quality checks and filtering to match the genealogy DNA database SNPs, genotypes for approximately one million SNPs were established. The resulting SNP genotypes were then used to search for relatives in the genealogy DNA database GEDmatch (www.gedmatch.com). A candidate list of relatives was obtained which was further processed using traditional genealogy methods in order to get leads about the identity of the unknown. In summary, this report shows how whole-genome sequencing successfully can be applied on forensic samples to create the SNP genotypes required for searches in genealogy DNA databases for the purpose of generating leads to identify missing or unknown persons, including perpetrators and victims.