THE effect of different levels of degradation and DNA concentrations on the quality of genetic profiles

The Usefulness of qPCR Data for Sample Pre-Assessment and Interpretation of Genetic Typing Results

DNA quantification is a crucial step in the STR typing workflow for human identification purposes. Given the reaction's nature, qPCR assays may be subjected to the same stochastic effects of traditional PCR for low-input concentrations. The study aims to evaluate the precision of the PowerQuant® (Promega) kit assay measurements and the degree of variability for DNA templates falling below the optimal threshold of the PowerPlex® ESX-17 Fast STR typing kit (Promega). Five three-fold dilutions of the 2800 M control DNA (Promega) were set up. Each dilution (concentrations: 0.05, 0.0167, 0.0055, 0.00185, and 0.000617 ng/µL) was quantified and amplified in four replicates. Variability for qPCR results, STR profile completeness, and EPGs' peak height were evaluated. The qPCR-estimated concentration of casework samples was correlated with profile completeness and peak intensity, to assess the predictive value of qPCR results for the successful STR typing of scarce samples. qPCR was subjected to stochastic effects, of which the degree was inversely proportional to the initial input template. Quantitation results and the STR profile's characteristics were strongly correlated. Due to the intrinsic nature of real casework samples, a qPCR-derived DNA concentration threshold for correctly identifying probative STR profiles may be difficult to establish. Quantitation data may be useful in interpreting and corroborating STR typing results and for clearly illustrating them to the stakeholders.

Which tissue to take? A retrospective study of the identification success of altered human remains

In forensic medicine, deceased are usually identified by comparing ante- and post-mortem dental or radiological features. However, in severe putrefaction, burning or absent reference data, the remaining tool for identifying human remains is DNA genotyping. But even a DNA-based identification can be challenging when confronted with a high post-mortem interval or heat impacts because it can lead to undesirable degradation of the DNA that varies among tissue types. This retrospective study investigated the identification success in 402 altered human corpses over seven years by comparing the examined tissue types from decomposed, skeletonised and burnt corpses as well as bodies found in water. For each tissue, the STR genotyping results and the number of additional or parallel genetic analyses were evaluated. By comparing the amplification success in samples from altered and unaltered remains, condition-based and tissue-specific differences were observed. With a mean number of 1.6 additional amplifications in cases with well-preserved corpses and 4.5 in altered corpses, the results showed significantly more DNA analyses for altered remains. In 83% of the cases, extra amplifications were performed to identify the corpse. The tissue-specific differences revealed an uncertainty in choosing suitable material from altered corpses for a successful DNA profile. Especially for bone and muscle samples, the genotyping success was the most unpredictable. Furthermore, comparing the retrospective outcome with other research findings, a remarkable variety of recommendations for the "best tissue choice" exists in the forensic community. Thus, our survey highlights the advantages of a broader and systematic approach on hard and soft tissues for successful DNA-based identification of altered human remains at first attempt.

Development of a quantitative PCR-based method for studying temporal DNA degradation in waterlogged bone

While several studies have examined temporal DNA degradation in bones collected from terrestrial environments, studies on temporal DNA degradation in bones collected from aquatic environments are limited and mostly based on case studies. The objective of this study was to assess the impact of long-term submersion, aquatic environment, bone type and DNA extraction method on DNA quality and quantity. Bone samples (scapulae and ribs), collected every ~1000 ADD from a freshwater lake and river, underwent DNA extraction via ChargeSwitch^® gDNA Plant Kit and organic phenol-chloroform methods, and DNA quantitation using both TaqMan and SYBR Green-based quantitative PCR (qPCR) methods. Results suggest that in both bone types, quality of recovered DNA (i.e., degradation index) declined significantly with increase in submersion time. Among two bone types, quality of recovered DNA from scapulae declined faster than rib samples. There was no significant difference in recovered DNA quantity between bone types, DNA extraction methods, or locations but various interactions between these variables showed significant difference. Overall, it can be concluded that DNA can be extracted from waterlogged bone in sufficient quantity to generate an STR profile up to 4000 ADD.

Assessing the performance of quantity and quality metrics using the QIAGEN Investigator® Quantiplex® pro RGQ kit

The Quantiplex® Pro RGQ kit quantifies DNA in a sample, supports the detection of mixtures and assesses the extent of DNA degradation based on relative ratios of amplified autosomal and male markers. Data show no significant difference in the accuracy and sensitivity of quantification between this and the Promega PowerQuant® System, both detecting the lowest amount of DNA tested, 4 pg. Laboratory controlled mixed male:female DNA samples together with mock sexual assault samples were quantified across a range of mixture ratios. Analysis software detected mixed DNA samples across all ratios for both quantification kits. Subsequent STR analysis using the Investigator® 24Plex QS Kit was able to corroborate mixture detection down to 1:25 male:female DNA ratios, past which point mixtures appeared identical to single-source female samples. Analysis software also detected laboratory degraded DNA samples, with data showing a positive trend between the Degradation Index (DI) and length of time of sonication. When used on ancient remains the assay was able to triage samples for further analysis, and STR profiles were concordant with DNA quantification results in all instances. STR analyses of laboratory-controlled sensitivity, mixture, and degradation studies supports the quality metric obtained from quantification. These data support the use of the Quantiplex® Pro RGQ kit for sample screening and quantification in forensic casework and ancient DNA studies.