Investigation of a Y-chromosome screening approach for sexual assault evidence using the QIAGEN Investigator Casework GO! kit

Following an alleged sexual assault, a victim may undergo a medical examination whereby internal or external bodily swabs may be collected and submitted to a forensic laboratory to be screened for the presence of semen. At Forensic Science SA (FSSA), this involves microscopic examination of a smear prepared from each swab for the presence of sperm. Microscopic detection of sperm is confirmatory for semen, but the process is very time-consuming, especially where very low levels are present. Moreover, microscopy results are not a reliable predictor of the amount of male DNA that might be recovered. SWGDAM recommends a direct-to-DNA approach as an efficient alternative. Therefore, we investigated the Qiagen Casework GO! kit (CWG), in conjunction with the Y-chromosome marker in the Quantifiler Trio DNA quantification kit, for the rapid screening of sexual assault swabs for the presence of male DNA (termed ‘Y-screen’). We initially investigated two swab types, the Copan cotton swab (currently used in Forensic Examination Collection Kits (FECK) submitted to FSSA) and the Sarstedt Forensic XL swab (a Forensic DNA grade alternative). The optimal size of the swab cutting and the volume of CWG lysis mix for the Y-screen was determined to be 1/8 and 100 μL, respectively, which ensured cost minimization and sample preservation. The performance of the optimized Y-screen method was compared with conventional microscopy using a series of simulated sexual assault swabs constructed by spiking female buccal swabs with serial dilutions of semen. For Copan cotton swabs, all samples with detectable sperm by microscopy had detectable levels of male DNA using the Y-screen. The Y-screen also showed greater sensitivity than microscopy for this swab type, detecting male DNA in 8% of samples where sperm was not observed. In contrast, 36% of Forensic XL swabs gave undetectable male DNA when sperm was observed by microscopy, which indicated that the Y-screen approach with CWG may not be compatible with all swab types. A casework trial of the Y-screen approach using 46 FECK swabs (Copan cotton swabs) submitted across 29 cases confirmed the higher sensitivity of the Y-screen approach as compared to conventional microscopy. Here, 44% of FECK swabs that had no observable sperm by microscopy had detectable male DNA using the Y-screen. There were no instances where the FECK swabs with observable sperm by microscopy had undetectable male DNA using the Y-screen. Our study confirmed the utility of the Y-screen approach using CWG to expedite the downstream DNA analysis of FECK swab samples in operational casework.