Inconsistent genotyping call at DYS389 locus and implications for interpretation

The male-specific Y chromosome short tandem repeat (STR) locus is used widely in forensic case, which are useful molecular tool to providing the biological evidence for male/female mixture and paternal lineage cases. The Y-STR analysis has been greatly facilitated by advent of commercial multiplex kit. However, even with well-designed robust multiplex kit, abnormal genotyping profile may be observed when encountering with mutations, such as deletion/duplication within the target region or mutation at the primer binding site. In this study, a single-allele shift by five nucleotides for the DYS389I marker between the AmpFlSTR(A (R)) Yfiler(A (R)) and Yfiler(A (R)) Plus PCR amplification kits while the same allele count for DYS389II was observed in eight unrelated Chinese male individuals. After further investigations by re-amplified with three additional multiplex kits, sanger, and next-generation sequencing, the discordance was finally proven caused by existing rare mutation in those sample, which contained two adjacent SNPs only one base apart in the sequence. This paper describes the molecular basis of the discordance at DYS389I genotyping between different commercial multiplex kits and could provide available information for enhancing of interpretation of abnormal Y-STR genotyping in forensic practice.