Sex-specific marker abnormalities in a phenotypic male involved in a sexual assault case

Sex determination is critical in criminal investigations, particularly when male and female DNA is mixed. In this case, although semen indicators were detected, human identification protocols revealed extremely low male DNA concentrations and incomplete Y-chromosomal short tandem repeat (Y-STR) profiles. Autosomal short tandem repeat (A-STR) results from the used tissues and pubic hairs showed an A-STR pattern consistent with a female genotype, lacking Y-chromosome loci (DYS391, Y-indel, and AMELY (Amelogenin gene located on the Y chromosome), whereas the same reduced Y-STR profile was observed across some samples. Despite the low male contribution, the suspect's A-STR profile was still detectable within the mixed DNA. Additional sex-marker analyses, including SRY (Sex-determining region of the Y chromosome) and X-chromosomal short tandem repeat (X-STR) profiling, confirmed the presence of SRY and revealed heterozygous X-STR patterns, suggesting an atypical male genotype involving possible azoospermia or partial Y-chromosomal loss. These findings align with several potential genetic explanations, including Y-to-X translocation, XXY syndrome, major Y-chromosome deletions, or XX-male syndrome. This case underscores the importance of carefully interpreting reduced Y-STR patterns in sexual assault investigations and highlights the value of incorporating SRY testing when conventional sex-determination markers are inconclusive.