Optimization and validation of a novel direct-lysis differential extraction procedure
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Forensic analysis of DNA from sexual assault kits is a laborious process. These samples may be a mixture of sperm and male or female epithelial cells (E-cells). Generally, it is the sperm cells that are of greatest forensic value. Since its introduction in 1985 by Gill, Jefferys and Warrett, differential extraction has remained an essential pre-PCR extraction procedure adopted by most forensic laboratories for the preferential lysis of E-cells and isolation of sperm cells/male fraction prior to DNA profiling. The differential extraction procedure operates based on the packaging of DNA in these two types of cells. The E cells are first lysed by sodium dodecyl sulfate (SDS) and Proteinase K which leaves the sperm cells intact. The mixture is centrifuged leaving E-cell DNA in the supernatant and sperm cells in the pellet. After several wash steps to remove residual E cell DNA, the sperm fraction is then subjected to lysis using SDS, proteinase K, and dithiothreitol (DTT). DTT reduces the disulfide bonds present in the sperm nucleus, thereby releasing sperm cell DNA. The traditional Gill method of differential extraction, while proven to be highly effective in providing two separate fractions for a simplified interpretation of profiles, is a labor intensive and time-consuming process, requiring approximately six hours of an analyst’s concentration. In a casework scenario where an evidence sample is of a higher E cell concentration compared to sperm cells, it is inevitable to obtain mixture profiles that becomes more difficult to interpret. To mitigate carryover from the female fraction, the sperm cell fraction is usually subjected to multiple wash steps. Furthermore, the resulting fractions must be subjected to additional pre-PCR DNA purification procedures to remove PCR inhibitors such as SDS and Proteinase K which result in varying degrees on DNA loss. Progress has been made over the years to introduce methods that allow for PCR-ready lysates without additional purification steps, often referred to as direct lysis methods. However, none have been proven to be viable options for use in sexual assault samples. Our laboratory has developed a novel differential extraction procedure that is not only time-efficient and less laborious but also utilizes a direct-lysis procedure requiring no further pre-PCR purification for most samples. The novel procedure uses ZyGEM, which contains the thermophilic EA1 protease proven to effectively digest biological samples and produce PCR-ready lysates suitable for downstream nucleic acid amplification, thereby minimizing DNA loss. The procedure uses a multi-enzymatic approach and utilizes the different optimal activity temperatures of the enzymes to perform most of the process in a DNA extraction lab thermocycler, requiring only a single centrifugation for the usual separation of the E-cell fraction and no subsequent washing steps for the sperm cell fraction. It has the potential to be a rapid, robust procedure that can be easily implemented in any forensic laboratory. This thesis will describe the procedure and report progress in the procedure optimization.