An in-field evaluation of rapid DNA instruments for disaster victim identification

Disaster victim identification: the co-utilisation of applied biosystems RapidHIT ID system and DJI Matrice 300 drone for onsite DNA analysis

Disaster Victim Identification (DVI) following mass fatality events is critical in bringing closure to the victims' family members and their loved ones. However, post-disaster environments are typically unfavourable and pose difficulties for the execution of DVI procedures. Delays in collecting, transporting, and processing the samples may cause DNA to degrade, adversely impacting the identification process. Therefore, this study aimed to demonstrate the co-utilisation of RapidHIT ID (RHID) and DJI Matrice 300 (M300) for onsite DNA analysis using buccal swab samples. 40 samples (two replicates) were collected from 20 "victims" and another 40 (two replicates) from 20 corresponding "relatives". The first replicates were processed using RHID (n = 40) and the second replicates were analysed via conventional technologies (n = 40). This paper observed the genotyping success rate, kinship matching, concordance, comparing different sample collectors, storage interval, and time taken for both procedures. Results of this study showed that RHID could generate DNA profiles for all the samples (n = 40) with 90% of them showing full profiles, and managed to process samples that have been stored for up to six months. The drone-assisted procedure exhibits less time to obtain and analyse the samples but can still produce DNA profiles concordant with the conventional method (p > 0.05). In conclusion, RHID is sufficient to generate interpretable DNA profiles in harsh environments, and transporting samples by M300 drone can reduce the exposure time to process more quality DNA for DVI.

Improving the forensic genetic workflow for countries with small geographical areas: What are the options and how cost effective are they?

Forensic services worldwide often encounter considerable challenges relating to funding and infrastructure. Smaller jurisdictions or areas where forensic resources are scarce are faced with complicated choices in how they approach criminal casework, with a number of options available. Often these involve trade-offs between cost, time and data quality. Faced with such decisions it becomes important for the field to acknowledge the realities facing such jurisdictions, discuss the pros and cons of each approach, and identify a framework for making such decisions. This novel paper, reviews the available literature and identifies three main solutions for consideration: 1) the use of satellite laboratories for sample triage, 2) the use of a main regional laboratory for full forensic analysis and 3) the use of rapid DNA by police for reducing backlogs. Alongside these strategies, the impacts of cost and quality in regard to each of the stated options are considered. While the literature supports the assertion that some methods can reduce downstream costs via the reduction in turnaround times, there is limited data highlighting the business case used to support decision making when considering these options including the use of cost:benefit analyses or case studies, emphasizing the novelty of this paper. This is likely due to the commercialized nature of the forensic sector preventing the publication of a private laboratory's business approach. The lack of emphasis on the 'business case' in forensic literature has the potential to mislead R&D scientists who may consequently fail to consider such factors when performing their own research.

Preliminary study on mitochondrial DNA analysis from different sports items

Criminals often attempt to conceal blood-stained weapons used in violent crimes, making forensic evidence crucial in solving cases. This study explores the recovery and extraction of trace DNA from sports equipment, including cricket bats, table tennis racquets, and hockey sticks, which are frequently implicated in such incidents. Our research evaluates various double swab collection methods for retrieving trace DNA from these sports items, emphasizing those associated with blunt force trauma. We also compare presumptive and confirmatory tests to establish a direct correlation. This research consistently demonstrated robust DNA recovery, surpassing a 50 % threshold across all tests. Specifically, DNA recovery from buried samples reached an impressive 87 %, while washed samples still yielded a substantial 80 % efficiency. We conducted a comparative analysis between presumptive and confirmatory testing methods, establishing a direct correlation between the two. Variability in DNA recovery efficiency was observed and attributed to factors like the type of surface the items contacted, and ambient humidity levels. In addition to presenting robust DNA recovery rates, statistical analyses were employed to compare methods, establishing correlations and highlighting the influence of environmental factors on DNA recovery efficiency. These findings have significant implications for forensic investigations involving silent weapons crafted from sports equipment, emphasizing the need for standardized protocols and consideration of environmental factors in DNA analysis.

Pilot validation of on-field STR typing and human identity testing by MinION nanopore sequencing

Nanopore sequencing technology has broad application prospects in forensic medicine due to its small size, portability, fast speed, real-time result analysis capabilities, single-molecule sequencing abilities, and simple operation. Here, we demonstrate for the first time that nanopore sequencing platforms can be used to identify individuals in the field. Through scientific and reasonable design, a nanopore MinION MK1B device and other auxiliary devices are integrated into a portable detection box conducive to individual identification at the accident site. Individual identification of 12 samples could be completed within approximately 24 h by jointly detecting 23 short tandem repeat (STR) loci. Through double-blinded experiments, the genotypes of 49 samples were successfully determined, and the accuracy of the STR genotyping was verified by the gold standard. Specifically, the typing success rate for 1150 genotypes was 95.3%, and the accuracy rate was 86.87%. Although this study focused primarily on demonstrating the feasibility of full-process testing, it can be optimistically predicted that further improvements in bioinformatics workflows and nanopore sequencing technology will help enhance the feasibility of Oxford Nanopore Technologies equipment for real-time individual identification at accident sites.

An evaluation of the RapidHIT™ ID system for hair roots stained with Diamond™ Nucleic Acid Dye

The RapidHIT™ ID (RHID) system was evaluated for its suitability in processing a single hair root to obtain informative DNA profiles. Hair samples were assessed for nuclear DNA prior to DNA analysis using Diamond™ Nucleic Acid Dye (DD) and real-time Extended Depth of Field (EDF) imaging to visualise and count nuclei if present. Hairs were viewed under an Optico N300F LED Fluorescent Microscope and imaged using a MIchrome 5 Pro camera. Hair roots were processed through both the ACE GlobalFiler™ Express sample cartridge and the RapidINTEL™ sample cartridge. A total of 44 hairs including shed hairs (9) and plucked hairs (35) from 8 donors were evaluated in this study. The processing of hairs using the RHID system required the modification of a standard swab that allowed for hairs to be easily collected and placed into the cartridge but also allowed for the re-collection of hair roots post RHID analysis (for potential standard DNA workflow). 90% of plucked hairs with a high nuclei count (>100) resulted in a high partial or full DNA profile, with the remaining 10% resulting in a low partial profile. 44% of shed hairs resulted in a low partial profile, with the remaining hairs resulting in a null profile. This study demonstrated that the RHID system could successfully obtain a DNA profile from a single hair root with nuclei present post-DD staining. According to these results, it is suggested that when dealing with hairs containing fewer than 50 nuclei, using the RapidINTEL™ cartridge can enhance allele recovery.

Processing biological samples from simulated radiological terrorist events using Rapid DNA instruments

Two commercially available portable Rapid DNA instruments were evaluated for their ability to process 1 µL and 10 µL saliva samples deposited on metal and plastic surfaces and contaminated with surrogates of cesium (Cs)-137, strontium (Sr)-90 and cobalt (Co)-60; radioactive materials potentially released during a nuclear weapon accident or a radiological dispersal device detonation. A comparable success rate was noted for both Rapid DNA instruments when considering the number of complete and balanced DNA profiles, the number of profiles with a minimum of 10 autosomal STR loci (out of 23 [FlexPlex™ 27] or 21 [GlobalFiler™ Express]), and the possibility to search a national DNA database in Canada and the United States. Cobalt had an adverse impact on the quality of the megaplex short tandem repeat (STR) DNA profiles derived on each instrument for two of the three contamination levels tested in this study, i.e., 0.05 M and 0.1 M as reflected by a reduced number of detected alleles and decreased profile peak heights. Strontium exhibited some adverse effect on the Rapid DNA results when used at the highest contamination level (0.1 M) whereas cesium had none. No new artifacts were observed in the Rapid DNA profiles of samples spiked with the non-radiogenic surrogates. Importantly, in the context of a radiological/nuclear (RN) event, the ANDE™ 6C offers the possibility to dispose of all radioactive materials associated with contaminated samples quickly using a chip on which all steps of the Rapid DNA process are performed whereas the RapidHIT™ ID accumulates radioactive materials for many days before disposal. An individual handling 25 samples in a week (5 per day) on the RapidHIT™ ID at a 30.5 cm distance with a 5 min exposure to the radioactive source estimated at every run would exceed the 0.042 µSv/5 min limit with gamma dose rates for Cs at 0.13 mSv and for Co at 3.8 mSv. Beta dose rates calculated for the surrogate isotopes at the three concentrations tested were also above the recommended radiation exposure limit of 1 mSv/yr (0.042 µSv/5 min). Various potential mechanisms of action behind the interference noted for Sr and Co at high concentrations are presented. These elements may play a role in the steps prior to PCR (at the DNA molecule by binding to bases or to phosphate groups), during PCR (at the DNA polymerase as cofactors for catalytic sites), or even during amplified DNA fragment detection (as fluorescence quenchers).

Comparative analysis of two Rapid DNA technologies for the processing of blood and saliva-based samples

Rapid DNA technologies recently gained significant momentum as a means to generate DNA profiles faster than with standard laboratory workflows. Initially developed for the analysis of buccal reference samples, applications are being considered for other types of forensic samples. In this study, an identical set of 150 blood and saliva-based samples was processed using two different Rapid DNA technologies, the Applied BioSystems™ RapidHIT™ ID System using the RapidINTEL™ sample cartridge and the ANDE™ 6C Rapid DNA Analysis™ System using the I-Chip. A subset of samples were subjected to alternative collection methods or sample pre-treatments to determine the optimal strategy for each instrument. An equivalent sample set was also processed using a conventional DNA analysis workflow. The sensitivity range of the two Rapid DNA technologies was comparable based on blood and saliva dilution series, with both technologies able to generate full profiles from samples typically yielding 5-10 ng of DNA when processed using conventional DNA analysis. The brand of cotton swabs used for Rapid DNA analysis had an impact on the results for both systems. Differences were observed in success rate between the two systems when processing blood (on fabrics, FTA paper or hard surfaces) and saliva-based samples (drink containers, FTA paper, chewing gum, cigarette butt filter paper) and depended on the sample type. Importantly, deviating from the manufacturer's instructions for sample collection and pre-treatment was more detrimental to the ANDE 6C results. The quality of DNA profiles, as assessed using heterozygote peak height ratios, interloci balance and artifact presence, confirmed the results to be reliable and acceptable for single source samples. Profiling results were obtained when samples were reprocessed using the same Rapid DNA technology or conventional DNA analysis. Secondary analysis using a substitute software (GeneMapper ID-X v1.5) to recover additional genetic information was shown to be feasible. Finally, a comparison between the Applied Biosystems™ RapidHIT™ ID System Software v1.3.1 and v1.3.2 was also performed. Findings of this study could assist those interested in using Rapid DNA technology for blood or saliva-based samples, in various settings and for different applications.

A Systematic Review on Commercially Available Integrated Systems for Forensic DNA Analysis

This systematic review describes and discusses three commercially available integrated systems for forensic DNA analysis, i.e., ParaDNA, RapidHIT, and ANDE. A variety of aspects, such as performance, time-to-result, ease-of-use, portability, and costs (per analysis run) of these three (modified) rapid DNA analysis systems, are considered. Despite their advantages and developmental progress, major steps still have to be made before rapid systems can be broadly applied at crime scenes for full DNA profiling. Aspects in particular that need (further) improvement are portability, performance, the possibility to analyze a (wider) variety of (complex) forensic samples, and (cartridge) costs. Moreover, steps forward regarding ease-of-use and time-to-result will benefit the broader use of commercial rapid DNA systems. In fact, it would be a profit if rapid DNA systems could be used for full DNA profile generation as well as indicative analyses that can give direction to forensic investigators which will speed up investigations.

Rapid DNA Profile Development with Applied Biosystems RapidHIT™ ID System

The RapidHIT™ ID System by Applied Biosystems allows the generation of a CODIS compatible STR profile in 90 min. The preloaded cartridges, fully automated workflow, and user-friendly computer interface allow for quick and simple single sample processing both in the laboratory and outside by non-laboratory personnel, like law enforcement officers. DNA processing utilizes a direct amplification workflow to generate an STR profile targeting the CODIS or ESS core loci. In conjunction with the RapidLINK™ Software, the system performs an initial analysis, flagging any profiles that do not meet single-source full profile parameters. Additionally, the RapidLINK™ allows for users to manage a multi-instrument/multi-location Rapid DNA system and view results in real-time. This gives users off-site the ability to track and even analyze results. The system allows for rapid reference sample analysis in locations like booking stations and national or border security agencies to obtain quick feedback of database hits for investigative leads while the subject is still in custody. RapidHIT™ ID DNA systems can also be set up at sites to aid in victim identification during mass disasters. The following chapter describes the process of generating a forensic DNA profile using the RapidHIT™ ID instrumentation from start to finish. Additionally, basic use and analysis using the RapidLINK™ and GeneMarker™ HID software is included.

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019-2022

This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.