In silico detection of phylogenetic informative Y-chromosomal single nucleotide polymorphisms from whole genome sequencing data

A state‐of‐the‐art phylogeny of the human Y‐chromosome is an essential tool for forensic genetics. The explosion of whole genome sequencing (WGS) data due to the rapid progress of next‐generation sequencing facilities is useful to optimize and to increase the resolution of the phylogenetic Y‐chromosomal tree. The most interesting Y‐chromosomal variants to increase the phylogeny are SNPs (Y‐SNPs) especially since the software to call them in WGS data and to genotype them in forensic assays has been optimized over the past years. The PENNY software presented here detects potentially phylogenetic interesting Y‐SNPs in silico based on SNP calling data files and classifies them into different types according to their position in the currently used Y‐chromosomal tree. The software utilized 790 available male WGS samples of which 172 had a high SNP calling quality. In total, 1269 Y‐SNPs potentially capable of increasing the resolution of the Y‐chromosomal phylogenetic tree were detected based on a first run with PENNY. Based on a test panel of 57 high‐quality and 618 low‐quality WGS samples, we could prove that these newly added Y‐SNPs indeed increased the resolution of the phylogenetic Y‐chromosomal analysis substantially. Finally, we performed a second run with PENNY whereby all samples including those of the test panel are used and this resulted in 509 additional phylogenetic promising Y‐SNPs. By including these additional Y‐SNPs, a final update of the present phylogenetic Y‐chromosomal tree which is useful for forensic applications was generated. In order to find more convincing forensic interesting Y‐SNPs with this PENNY software, the number of samples and variety of the haplogroups to which these samples belong needs to increase. The PENNY software (inclusive the user manual) is freely available on the website http://bio.kuleuven.be/eeb/lbeg/software.