Exploring the sources of peak height reduction during low-template, compromised DNA data analysis
Taranow, Lauren Mikal
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The genetic profiles of evidentiary samples found at crime scenes are generated in order to determine the likelihood that a person contributed to DNA to the sample. One of the most challenging aspects of forensic deoxyribonucleic acid (DNA) analysis is that samples collected from crime scenes often contain only trace amounts of DNA; these samples are often referred to as low template DNA (LTDNA). Due to the low initial concentration of genetic material in LTDNA samples, substantive environmental insults will likely result in compromised DNA profiles that exhibit lower allele peak heights than expected, or in some cases, complete allele drop-out. The research detailed in this study investigates the impact various sources of compromise have on relative fluorescent unit (RFU) signal obtained from LTDNA samples. The potential for stochastic allele loss during a silica extraction of DNA prior to downstream processing is first considered using a dynamic systems model simulating the probability for allelic loss at each step in the procedure. Next, the impacts of damaging or degrading the DNA on the electropherogram signal are explored. Trends in RFU signal of LTDNA samples subjected to sonication by a sonic dismembrator probe, ultraviolet (UV) irradiation, and enzymatic digestion by two different enzymes are assessed, with the aim of creating a reference for typical behaviors in RFU signal data in compromised LTDNA. The distributions of electropherogram profile data from compromised LTDNA are then compared against one another in order to determine if the compromising methods explored in the study act on the samples in similar ways. The RFU signal data from the compromised LTDNA are then evaluated alongside the provided degradation index (DI) value resulting from quantification using the Quantifiler® Trio quantification kit (Thermo Fisher Scientific, Oyster Point, CA). The DI value acts as an early assessment of the quality of DNA samples and can be used to optimize downstream processing. Its ability to accurately predict behavior in compromised LTDNA samples is assessed through comparison of the DI value to the decrease in RFU signal as the samples are subjected to higher levels of simulated environmental insults.