Comparison of results using temperature controlled differential extraction and differential extraction using the QIAGEN EZ1 advanced

The sexual assault kit backlog in the United States has become an increasing problem over the years. Combined with the number of kits laboratories receive with how it takes to extract the deoxyribonucleic acid (DNA) from the cells, it is hard for labs to keep up with the demand. The extraction method used is called differential extraction, where the epithelial cells from the victim are separated from the sperm cells from the perpetrator into different fractions. The Temperature Controlled Differential Extraction (TCDE) method is a novel procedure developed by the Cotton Lab at the Boston University School of Medicine and designed to decrease the extraction time while performing just as well, if not better, than traditional differential extraction methods. The TCDE method uses a series of temperature-controlled enzymes to lyse cells and purify the DNA extract. The purpose of this study is to compare this TCDE method to a method implemented by QIAGEN using the EZ1® Advanced biorobot for purification, which is used in many forensic laboratories. Ten female donors each received ten cotton swabs for vaginal cell collection; cotton swabs are typically found in sexual assault kits. Each swab then received either 5ng, 25ng, or 50ng of male DNA in the form of sperm cells. One half of the swab was processed using the TCDE procedure while the other half was processed using the EZ1® method. The TCDE method results in three fractions: the Epithelial Fraction (EF), the Material Fraction (MF), and the Sperm Fraction (SF). The EZ1® protocol was modified to include the additional MF. Results of both the quantitation data as well as the electropherograms (EPGs) produced are compared between the two methods. The quantitation data for the EF shows a variable amount of female DNA recovered due to the uncontrolled amount of female epithelial cells added to the swabs from the donors. The MF shows that large amounts of female epithelial DNA remain in the fraction for the EZ1® protocol and not the TCDE protocol because of the nuclease activity of one of the enzymes. The remaining male DNA on the MF can be used to compare to a known male profile, showing that there is valuable data potentially left behind. Regarding the SF, the EZ1® protocol resulted in a higher yield of DNA than the TCDE, however, the TCDE SF electropherograms are still able to be used for comparisons against known male profiles. The TCDE protocol cuts extraction time by almost half, and the quantitation results and EPGs prove that this method has the potential to become the new standard method of differential extraction