When autosomal short tandem repeats fail: optimized primer and reaction design for Y-chromosome short tandem repeat analysis in forensic casework.

Y-chromosomal short tandem repeats (Y-STRs) are useful forensic DNA markers in investigation of sexual assault cases when a mixture of male and female DNA (e.g., in vaginal swabs) is present in a sample, especially when DNA of the male contributor is present only in very small amount compared to the DNA of the female victim. With autosomal STR analysis of male and female DNA, male DNA in mixtures can usually be detected and correctly interpreted only when it exceeds 5%. However, the amplification of some Y-STRs is known to result in polymerase chain reaction (PCR) products that are not associated with the Y-chromosome, but derive from the X-chromosome and/or autosomal regions. This can cause problems in the interpretation of results, particularly when female DNA is present in excess. Consequently, more specific and sensitive Y-STR primers and PCR conditions are needed. This paper presents two casework examples in which sensitive Y-STR multiplexes (with the addition of PCR enhancer) were successfully used in the analysis of mixtures of male and female DNA, the male component not interpretable by standard autosomal STR typing.