DOI: 10.3886/icpsr38903.v1
title: Adaptation of the DNase I Procedure to the Biomek ® NXP Robotic Platform for More Efficient and Automated Sexual Assault Sample Processing, Virginia, 2019-2022
title: Version 1

description: The goal of the project was to adapt, optimize, validate and integrate DNase I differential extraction protocol into the current sexual assault casework workflow on the Beckman Coulter Biomek NXP automation workstations (Brea, CA) at the Virginia Department of Forensic Science. The end goal was to expedite, without compromising quality, the processing of sexual assault samples.
description: The project was broken up into three phases: 1. Evaluation and optimization of a manual DNase differential extraction protocol (DE) protocol by combining epithelial cell lysis and DNase I digestions of mock sexual assault sample conditions; 2. Programming, evaluating, and optimizing automated DNase I digestion conditions on the Beckman Coulter Biomek NXP Liquid Handling Automation Workstation (NXP); 3. Validating the optimized, semi-automated DNase DE protocol on the NXP.
Female donors S17, S27, S28, and S29 collected buccal, vaginal/cervical, and/or rectal cell samples with cotton tipped swabs, which were air dried and stored at room temperature. Semen was collected from male donor S11 and frozen at negative 20 degrees Celsius 250 microliter aliquots. To test the effects of contamination two approaches were taken. The first was for one donor to use Replens Vaginal Moisturizer one to seven days prior to collecting vaginal/cervical samples. In the second approach, 100 microliters of semen dilutions were pipetted directly into common substrates in sexual assault cases, resulting in a U.S. quarter-sized sample area, and dried prior to use.
Epithelial cell lysis was performed in the presence of Proteinase K (ProK) which degrades proteins. Following thawing at room temperature, ProK was added to epithelial cell lysis buffer. Pooled solution was gently mixed/inverted and added to tubes containing swab heads or to empty tubes to serve as reagent blanks. DNase I was then purchased from Worthington Biomedical Corporation in Lakewood, New Jersey for use in the DNase DE protocol.
Following manual or semi-automated DE, automated DNA purifications were performed with NXP. DNA was quantitated and samples were evaluated for Y-DNA concentration (Y-DNA), autosomal-DNA concentration (A-DNA), A-DNA to Y-DNA ratio (A/Y ratio), and the degradation index (DI). The A/Y ratio measures the relative amount of female to male DNA in a sample, with values of roughly one indicating the presence of only male DNA. Values greater than one indicate the presence of female DNA. The DI measures the level of DNA degradation in samples. Samples with DIs greater than two were designated as progressively more degraded the higher the value as recommended by the manufacturer.
description: Anonymized samples were collected under WCG (WIRB-Copernicus Group, Inc.) IRB protocols. WCG is a commercial IRB that provides review and oversight for industry-sponsored clinical trials and other research involving human subjects. Four female volunteers anonymized as S17, S27, S28, and S29 and one male volunteer anonymized as S11 were included in the sample.
description: Datasets: 
DS0: Study-Level Files
DS1: DNase RunSheet Dataset
DS2: Experimental Results Dataset
DS3: DNase Trough Method Dataset