The Qiagen Investigator ® Quantiplex HYres as an alternative kit for DNA quantification

Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics

The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.

Validation of the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B for phenotypic and biogeographical ancestry predictions using the Micro MiSeq® Flow Cells

In anticipation of offering phenotypic and biogeographical ancestry predictions to help resolve cases, the Verogen ForenSeq™ DNA Signature Prep kit/Primer Mix B was evaluated in the context of Micro MiSeq® Flow Cells. These flow cells were determined as the best format for a quick turnaround time response and cost effective approach compared to standard flow cells. The phenotype informative SNPs (piSNPs) and ancestry informative SNPs (aiSNPs) were thoroughly examined through sensitivity, reproducibility and repeatability, concordance, robustness (mock casework) and low level DNA mixture studies purposely selecting individuals with different phenotypes (hair and eye color) when possible and different biogeographical ancestry. SNP locus-specific interpretation thresholds were established for the Universal Analysis Software (UAS) based on surviving alleles and SNP predictor rank to minimize false homozygous genotypes and maximize the information that can be derived from an unknown sample. Dropin alleles' intensity determined an appropriate threshold to minimize false heterozygous SNP genotypes. The selection of inappropriate interpretation thresholds was shown to have major consequences on phenotypic predictions. A 3.2% and 4.8% minor DNA component contribution to a DNA mixture had no impact on ancestry predictions whereas a 9.1% contribution did. The multi-locus SNP genotypes generated using the ForenSeq™ DNA Signature Prep kit/Primer Mix B were shown to be reliable, reproducible, concordant and resulted in predictions that were also reliable, reproducible and concordant based on the limited number of donors (N = 19) used in this study.

The recovery of touch DNA from RDX-C4 evidences

RDX (Royal Demolition Explosive) is the organic compound with the formula (O2NNCH2)3. It is a white solid material without smell or taste, widely used as an explosive. It is more energetic explosive than TNT, and it was used widely in World War II. The estimated number of RDX-C4 cases in Bahrain ranged between the years 2015–2018 (May) with a total quantity of 370.72 KG in a total number of 38 cases. The effect of explosive RDX-C4 is very massive and can cause many causalities and fatalities among civilians and policemen. These cases consisted of adhesive film with tapes wrapped around RDX-C4 substance (Demolition Charge M112), black batteries, pipes, black bag contained RDX-C4, and in magnetic improvised explosive device (IED). Touch DNA recovery utilized different collection methods, such as nylon swabbing, tape lifting, and direct cutting of certain parts of the samples that were positive of RDX-C4 through DXR Raman Spectrometer. Samples were extracted and purified with magnetic beads chemistry and quantified. Low copy DNA extracts were subjected to a concentration step. DNA extracts were amplified and processed for detection to obtain reliable results using GlobalFiler Amplification PCR kit and run through ABI 3500xL Genetic Analyzer for fragment length determination. We have discovered that RDX-C4 cannot bind to the DNA nor to the solutions used in DNA typing. Thus, it does not cause DNA inhibition or degradation. From this point of view, we were successful in obtaining acceptable and fit results using advanced techniques. This study will be very useful and informative to assist the forensic community in terrorism case applications worldwide as terrorists do not respect geographical boundaries nor ethnicities of the victims, and the use of DNA profiling technology is the most suitable way to identify the terrorists and keep an end to their violence.

Assessment of autosomal and male DNA extracted from casework samples using Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit for autosomal-STR and Y-STR profiling

Short repetitive regions in autosomal and Y chromosomes known as short tandem repeats (STRs) are currently used for DNA profiling in crime investigations. However, DNA profiling requires a sufficient quality and quantity of DNA template, which is often not obtained from trace evidence or degraded biological samples collected at the scene of a crime. Here, we assessed autosomal and male DNA components extracted from crime scene and mock casework samples using the Casework Direct Kit, Custom and compared the results against those obtained by extraction of matching samples using well-established Maxwell 16 System DNA IQ Casework Pro Kit. The quantity and quality of extracted DNA obtained using both Casework Direct Kit, Custom and Maxwell 16 System DNA IQ Casework Pro Kit were analyzed using PowerQuant Systems followed by autosomal and Y-chromosome STR profiling using GlobalFiler Express PCR Amplification Kit and PowerPlex Y23 System, respectively. Our results showed that the Casework Direct Kit and Maxwell 16 DNA IQ Casework Pro Kit have more or less equal capacity to extract inhibitor free DNA, but that the latter produces slightly better quality and more DNA template and subsequently higher numbers of STR allele calls for autosomal and Y-STR analyses. Nonetheless, the Casework Direct Kit, Custom is the quicker and cheaper option for extraction of good, clean DNA from high content material and might best be used for extraction of reference samples. Such reference DNA samples typically come from buccal swabs or freshly drawn blood. So, in general, they can confidently be expected to have a high nucleic acid content and to be inhibitor-free.

Improved resolution of mixed STR profiles using a fully automated differential cell lysis/DNA extraction method

Sexual assault evidence often contains sperm cells, which are typically separated from nonsperm cells using manual differential lysis procedures. The goal of this study was to evaluate the automated QIAGEN QIAcube for this purpose and to compare it to manual QIAGEN and manual organic differential methods using DNA yields and STR profile data for assessment. DNA yields were determined by qPCR, followed by multiplex STR amplification, CE analysis, and mixture interpretation. The automated method was capable of effective cell separation, producing DNA yields sufficient for STR amplification. Further, sperm fraction human:male DNA ratios from the QIAcube samples were consistently closer to the desired 1:1 and STR profiles were less likely to result in mixtures, with 6-8× fewer female alleles detected (median 1.5 alleles). Ultimately, using the QIAcube for automated differential processing of semen-containing mixtures reduces the need for downstream mixture interpretation and improves STR profile quality with substantially less hands-on time.

Human DNA degradation assessment and male DNA detection by quantitative-PCR followed by high-resolution melting analysis

We developed a q-PCR technique that simultaneously evaluates the extent of degradation and determines the gender of a human DNA donor. QYDEG HRM is a triplex real-time PCR whose products are analysed by high-resolution melting (HRM). The system produces three amplicons: (1) transducin (beta)-like 1, Y-linked (TBL1Y) (84bp); (2) large-target sequence (DGlt) (244bp); and (3) small-target sequence (DGst) (152bp). After HRM analysis, three melting peaks are detected in male DNA samples and two in female DNA samples. An imbalance between the DGst and DGlt melting peak heights allows for the estimation of the extent of DNA degradation. For sensitivity assessment, triplicate aliquots of 0.0032 to 50ng/μL DNA were tested, denoting good linearity and reproducibility. The results also showed the analysis to be precise and accurate in the DNA range of 0.04-5ng/μL. Diverse types of DNA samples were tested: experimentally heat-degraded DNA; crime scene samples derived from casework and highly degraded samples with partial STR profiles from corpse material and mass disaster events. The results were compared with those obtained from the Plexor^® and PowerQuant^® commercial kits. Additionally, the quantification results of the QYDEG HRM triplex correlate well with the STR amplification that was subsequently obtained. The method is simple, cost-effective and helpful for determining the DNA integrity and the sex of a sample donor in any field where human DNA quantification is required.