Assessing sequence variation and genetic diversity of currently untapped Y-STR loci

Abstract

With the advent of massively parallel sequencing (MPS) the full genetic variation of short tandem repeat (STR) markers can be assessed. Most MPS efforts of forensic interest to date have focused on autosomal STRs, with far less attention to the potential genetic variation contained within Y-STR loci. Many of the non-commercialized Y-STR loci described previously have not been reassessed with MPS to determine the full level of genetic diversity of these markers at the sequence level. In this study, genomic data were mined from the Phase 3 1000 Genomes Project to identify forensically relevant STRs using lobSTR, HipSTR, and an in-house pipeline. These loci then were typed in a dual-phase approach with an Illumina Custom Amplicon (281 markers; ≤ 425 bp) panel followed by an AmpliSeq Custom Amplicon (83 markers; ≤ 275 bp) panel using four populations (African American, US Caucasian, US East Asian, and US Southwest Hispanic). STRs also were assayed with the ForenSeq Signature Prep Kit. The genetic diversity of the loci was assessed and ranked for a final set of 81 loci. When ranking all loci with respect to genetic diversity highest-to-lowest, seven of the top ten loci are not utilized in a current commercial assay.