The Effect of Sample and Sample Matrix on DNA Processing: Mechanisms for the Detection and Management of Inhibition in Forensic Samples

The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.

The effect of sample and sample matrix on DNA processing: Mechanisms for the detection and management of inhibition in forensic samples

The presence of inhibitory substances in biological forensic samples has, and continues to affect the quality of the data generated following DNA typing processes. Although the chemistries used during the procedures have been enhanced to mitigate the effects of these deleterious compounds, some challenges remain. Inhibitors can be components of the samples, the substrate where samples were deposited or chemical(s) associated to the DNA purification step. Therefore, a thorough understanding of the extraction processes and their ability to handle the various types of inhibitory substances can help define the best analytical processing for any given sample. A series of experiments were conducted to establish the inhibition tolerance of quantification and amplification kits using common inhibitory substances in order to determine if current laboratory practices are optimal for identifying potential problems associated with inhibition. DART mass spectrometry was used to determine the amount of inhibitor carryover after sample purification, its correlation to the initial inhibitor input in the sample and the overall effect in the results. Finally, a novel alternative at gathering investigative leads from samples that would otherwise be ineffective for DNA typing due to the large amounts of inhibitory substances and/or environmental degradation was tested. This included generating data associated with microbial peak signatures to identify locations of clandestine human graves. Results demonstrate that the current methods for assessing inhibition are not necessarily accurate, as samples that appear inhibited in the quantification process can yield full DNA profiles, while those that do not indicate inhibition may suffer from lowered amplification efficiency or PCR artifacts. The extraction methods tested were able to remove >90% of the inhibitors from all samples with the exception of phenol, which was present in variable amounts whenever the organic extraction approach was utilized. Although the results attained suggested that most inhibitors produce minimal effect on downstream applications, analysts should practice caution when selecting the best extraction method for particular samples, as casework DNA samples are often present in small quantities and can contain an overwhelming amount of inhibitory substances.^

Comparison of Common Field/Clinical Measures to Standard Laboratory Measures of Hydration Status

Context: Accurately determining hydration status is a preventative measure for exertional heat illnesses (EHI). Objective: To determine the validity of various field measures of urine specific gravity (Usg) compared to laboratory instruments. Design: Observational research design to compare measures of hydration status: urine reagent strips (URS) and a urine color (Ucol) chart to a refractometer. Setting: We utilized the athletic training room of a Division I-A collegiate American football team. Participants: Trial 1 involved urine samples of 69 veteran football players (age=20.1+1.2yr; body mass=229.7+44.4lb; height=72.2+2.1in). Trial 2 involved samples from 5 football players (age=20.4+0.5yr; body mass=261.4+39.2lb; height=72.3+2.3in). Interventions: We administered the Heat Illness Index Score (HIIS) Risk Assessment, to identify athletes at-risk for EHI (Trial 1). For individuals “at-risk” (Trial 2), we collected urine samples before and after 15 days of pre-season “two-a-day” practices in a hot, humid environment(mean on-field WBGT=28.84+2.36oC). Main Outcome Measures: Urine samples were immediately analyzed for Usg using a refractometer, Diascreen 7® (URS1), Multistix® (URS2), and Chemstrip10® (URS3). Ucol was measured using Ucol chart. We calculated descriptive statistics for all main measures; Pearson correlations to assess relationships between the refractometer, each URS, and Ucol, and transformed Ucol data to Z-scores for comparison to the refractometer. Results: In Trial 1, we found a moderate relationship (r=0.491, p<.01) between URS1 (1.020+0.006μg) and the refractometer (1.026+0.010μg). In Trial 2, we found marked relationships for Ucol (5.6+1.6shades, r=0.619, p<0.01), URS2 (1.019+0.008μg, r=0.712, p<0.01), and URS3 (1.022+0.007μg, r=0.689, p<0.01) compared to the refractometer (1.028+0.008μg). Conclusions: Our findings suggest that URS were inconsistent between manufacturers, suggesting practitioners use the clinical refractometer to accurately determine Usg and monitor hydration status.