Analysis and application of sequence polymorphism features of 41 forensic Y-chromosome short tandem repeat loci

Y chromosome short tandem repeat (Y-STR) is an important genetic marker in forensic practices. Length-based Y-STR genotyping method has been used to screen paternal lineages and successfully solved many serious cases. However, it is hard to discriminate paternal lineages with similar or identical length-based Y-STR genotypes. Next-generation sequencing-based Y-STR genotyping method could be used to solve the problem, and already be applied to criminal scene investigations. Nevertheless, previously studied data were inadequate and scattered, and sequence features of Y-STR loci were insufficiently summarized, which hindered the deep forensic application of Y-STR loci. Here, we review the sequence features of repeat and flanking regions on 41 widely used forensic Y-STR loci based on public literature data. Furthermore, we identify haplogroup-associated Y chromosome single nucleotide polymorphisms within these regions and explore potential applications of sequence-based polymorphisms. This review is expected to serve as a valuable reference for paternal lineage discrimination and paternal biogeographic ancestry inference using Y-STR sequence features.