Massively parallel sequencing of sex-chromosomal STRs in Saudi Arabia reveals patrilineage-associated sequence variants

• Published in: Forensic science international : genetics 2020-11, Vol.49, p.102402-102402, Article 102402
• Main Authors: Khubrani, Yahya M., Jobling, Mark A., Wetton, Jon H.
• Format: Article
• Language: English
• Subjects: Haplogroup; HGDP; Massively parallel sequencing (MPS); Population structure; Saudi Arabia; X-STRs; Y-SNPs; Y-STRs
• ISSN: 1872-4973; 1878-0326
• DOI: 10.1016/j.fsigen.2020.102402

•Sequences of 24 Y-STRs and 6 X-STRs generated in 89 Saudi Arabian males.•SNPs and repeat array motifs in Y-STRs are associated with common Middle East haplogroups.•Discordances between CE and MPS linked to length vs sequencing-based genotyping of rare variants.•High heterozygosity but low regional differentiation at X-STRs. Massively parallel sequencing (MPS) of forensic STRs has the potential to reveal additional allele diversity compared to conventional capillary electrophoresis (CE) typing strategies, but population studies are currently relatively few in number. The Verogen ForenSeq™ DNA Signature Prep Kit includes both Y-STRs and X-STRs among its targeted loci, and here we report the sequences of these loci, analysed using Verogen’s ForenSeq™ Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0, in a representative sample of 89 Saudi Arabian males. We identified 56 length variants (equivalent to CE alleles) and 75 repeat sequence sub-variants across the six X-STRs analysed; equivalent figures for the set of 24 Y-STRs were 147 and 192 respectively. We also observed two flanking sequence variants for the X-, and six for the Y-STRs. Recovery of sequence data and concordance with CE data (where available) across the tested loci was good, though rare flanking variation affected interpretation and allele calling at DYF387S1 and DXS7132. Examination of flanking sequences of the Y-STRs revealed five SNPs (L255, M4790, BY7692, Z16708 and S17543) previously shown to define specific haplogroups by Y-chromosome sequencing. These define Y-haplogroups in 62 % of our sample, a proportion that increases to 91 % when haplogroup-associated repeat-sequence motifs are also considered. A population-level comparison of the Saudi Arabian X-STRs with a global sample showed our dataset to be part of a large cluster of populations of West Eurasian and Middle Eastern origin.