A comparison of likelihood ratios calculated from surface DNA mixtures using MPS and CE Technologies.

This study evaluates the performance of analysing surface DNA samples using massively parallel sequencing (MPS) compared to traditional capillary electrophoresis (CE). A total of 30 samples were collected from various surfaces in an office environment and were analysed with CE and MPS. These were compared against 60 reference samples (office inhabitants). To identify contributors, likelihood ratios (LRs) were calculated for MPS and CE data using the probabilistic genotyping software MPSproto and EuroForMix respectively. Although a higher number of sequences/peaks were observed per DNA profile in MPS compared to CE, LR values were found to be lower for MPS data formats. This might be the result of the increased complexity of MPS data, along with a possible elevation of unknown alleles and/or artefacts. The study highlights avenues for improving MPS data quality and analysis to facilitate more robust interpretation of challenging casework-like samples.

Self-Supervised Learning for Improved Calibrationless Radial MRI with NLINV-Net.

PURPOSE: To develop a neural network architecture for improved calibrationless reconstruction of radial data when no ground truth is available for training. METHODS: NLINV-Net is a model-based neural network architecture that directly estimates images and coil sensitivities from (radial) k-space data via non-linear inversion (NLINV). Combined with a training strategy using self-supervision via data undersampling (SSDU), it can be used for imaging problems where no ground truth reconstructions are available. We validated the method for (1) real-time cardiac imaging and (2) single-shot subspace-based quantitative T1 mapping. Furthermore, region-optimized virtual (ROVir) coils were used to suppress artifacts stemming from outside the FoV and to focus the k-space based SSDU loss on the region of interest. NLINV-Net based reconstructions were compared with conventional NLINV and PI-CS (parallel imaging + compressed sensing) reconstruction and the effect of the region-optimized virtual coils and the type of training loss was evaluated qualitatively. RESULTS: NLINV-Net based reconstructions contain significantly less noise than the NLINV-based counterpart. ROVir coils effectively suppress streakings which are not suppressed by the neural networks while the ROVir-based focussed loss leads to visually sharper time series for the movement of the myocardial wall in cardiac real-time imaging. For quantitative imaging, T1-maps reconstructed using NLINV-Net show similar quality as PI-CS reconstructions, but NLINV-Net does not require slice-specific tuning of the regularization parameter. CONCLUSION: NLINV-Net is a versatile tool for calibrationless imaging which can be used in challenging imaging scenarios where a ground truth is not available.

Self-supervised learning for improved calibrationless radial MRI with NLINV-Net.

PURPOSE: To develop a neural network architecture for improved calibrationless reconstruction of radial data when no ground truth is available for training. METHODS: NLINV-Net is a model-based neural network architecture that directly estimates images and coil sensitivities from (radial) k-space data via nonlinear inversion (NLINV). Combined with a training strategy using self-supervision via data undersampling (SSDU), it can be used for imaging problems where no ground truth reconstructions are available. We validated the method for (1) real-time cardiac imaging and (2) single-shot subspace-based quantitative T1 mapping. Furthermore, region-optimized virtual (ROVir) coils were used to suppress artifacts stemming from outside the field of view and to focus the k-space-based SSDU loss on the region of interest. NLINV-Net-based reconstructions were compared with conventional NLINV and PI-CS (parallel imaging + compressed sensing) reconstruction and the effect of the region-optimized virtual coils and the type of training loss was evaluated qualitatively. RESULTS: NLINV-Net-based reconstructions contain significantly less noise than the NLINV-based counterpart. ROVir coils effectively suppress streakings which are not suppressed by the neural networks while the ROVir-based focused loss leads to visually sharper time series for the movement of the myocardial wall in cardiac real-time imaging. For quantitative imaging, T1-maps reconstructed using NLINV-Net show similar quality as PI-CS reconstructions, but NLINV-Net does not require slice-specific tuning of the regularization parameter. CONCLUSION: NLINV-Net is a versatile tool for calibrationless imaging which can be used in challenging imaging scenarios where a ground truth is not available.

Emerging use of air eDNA and its application to forensic investigations - A review.

Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Improvements in DNA technologies allow collection and profiling of trace samples, comprised of few cells, significantly expanding the types of exhibits targeted for DNA analysis to include touched surfaces. However, success rates from trace and touch DNA samples tend to be poorer compared to other biological materials such as blood. Simultaneously, there have been recent advances in the utility of environmental DNA collection (eDNA) in identification and tracking of different biological organisms and species from bacteria to naked mole rats in different environments, including, soil, ice, snow, air and aquatic. This paper examines the emerging methods and research into eDNA collection, with a special emphasis on the potential forensic applications of human DNA collection from air including challenges and further studies required to progress implementation.

Up in the air: Presence and collection of DNA from air and air conditioner units.

Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Touch or trace DNA samples from surfaces and objects deemed to have been contacted are frequently collected. However, a person of interest may not leave any traces on contacted surfaces, for example, if wearing gloves. A novel means of sampling human DNA from air offers additional avenues for DNA collection. In the present study, we report on the results of a pilot study into the prevalence and persistence of human DNA in the air. The first aspect of the pilot study investigates air conditioner units that circulate air around a room, by sampling units located in four offices and four houses at different time frames post-cleaning. The second aspect investigates the ability to collect human DNA from the air in rooms, with and without people, for different periods of time and with different types of collection filters. Results of this pilot study show that human DNA can be collected on air conditioner unit surfaces and from the air, with air samples representing the more recent occupation while air conditioner units showing historic use of the room.

Investigative use of human environmental DNA in forensic genetics.

Individuals leave behind traces of their DNA wherever they go. DNA can be transferred to surfaces and items upon touch, can be released into the air, and may be deposited in indoor dust. The mere presence of individuals in a location is sufficient to facilitate either direct or indirect DNA transfer into the surrounding environment. In this study, we analyzed samples recovered from commonly touched surfaces such as light switches and door handles in an office environment. We evaluated two different methods to isolate DNA and co-extract DNA and RNA from the samples. DNA profiles were compared to the references of the inhabitants of the different locations and were analyzed taking into consideration the type of sampled surface, sampling location and information about the activities in a room during the sampling day. Results from DNA samples collected from surfaces were also compared to those from air and dust samples collected in parallel from the same areas. We characterized the amount and composition of DNA found on various surfaces and showed that surface DNA sampling can be used to detect occupants of a location. The results also indicate that combining information from environmental samples collected from different DNA sources can improve our understanding of DNA transfer events in an indoor setting. This study further demonstrates the potential of human environmental DNA as an investigative tool in forensic genetics.

The invisible witness: air and dust as DNA evidence of human occupancy in indoor premises.

Humans constantly shed deoxyribonucleic acid (DNA) into the surrounding environment. This DNA may either remain suspended in the air or it settles onto surfaces as indoor dust. In this study, we explored the potential use of human DNA recovered from air and dust to investigate crimes where there are no visible traces available-for example, from a recently vacated drugs factory where multiple workers had been present. Samples were collected from three indoor locations (offices, meeting rooms and laboratories) characterized by different occupancy types and cleaning regimes. The resultant DNA profiles were compared with the reference profiles of 55 occupants of the premises. Our findings showed that indoor dust samples are rich sources of DNA and provide an historical record of occupants within the specific locality of collection. Detectable levels of DNA were also observed in air and dust samples from ultra-clean forensic laboratories which can potentially contaminate casework samples. We provide a Bayesian statistical model to estimate the minimum number of dust samples needed to detect all inhabitants of a location. The results of this study suggest that air and dust could become novel sources of DNA evidence to identify current and past occupants of a crime scene.

Non-self DNA on the neck: a 24 hours time-course study.

Non-self DNA is normally present on skin due to DNA transfer occurring during daily activities. The understanding of persistence and accumulation of foreign DNA on the neck can assist in the interpretation of DNA evidence collected from an assaulted victim. Establishing the composition and level of non-self DNA present is relevant, especially in cases where the victim cohabits with other individuals, such as partner and children. This study investigated the persistence and accumulation of non-self DNA on the neck, over the course of 24 h. DNA samples were collected from the neck of 20 adult volunteers at three time-points, on two days. The detection of a partner's DNA and DNA from unknown sources was studied in relation to the living arrangement and to the activities performed by each individual. An increased number of non-self alleles were detected over time. Partner's DNA was observed to accumulate during the day and to persist when an individual was absent from the shared home environment. DNA from unknown contributors was found on the neck of individuals that used public transport, attended public spaces and had social interactions. The data acquired from this study will help to increase knowledge on the composition of DNA present on an individual's neck in a daily situation.

A sequence-based 74plex microhaplotype assay for analysis of forensic DNA mixtures.

Microhaplotypes are emerging biomarkers for forensic applications. In this study, a sequence-based multiplex assay of 74 microhaplotypes (230 SNPs) was developed on the Ion Torrent S5™ (Thermo Fisher Scientific) system and the potential for its application to mixture deconvolution was explored. The 74 loci are distributed across the autosomal human genome and have Ae (i.e., effective number of alleles) values ranging from 1.307 to 6.010 (median = 2.706) and In (i.e., informativeness) values ranging from 0.096 to 0.660 (median = 0.251); the amplicon sizes range between 157 and 325 bp. The typing performance of the panel was evaluated on a series of in-silico two to five-person DNA mixtures and results were compared to fragment and sequence-based STRs. The 74plex-locus assay was found sensitive down to 0.05 ng of input DNA and effective for the analysis of mixtures at different contributor ratios and input DNA amounts. As expected, none or very partial minor CE-STR profile(s) were reported for highly imbalanced two-person and high-order DNA mixtures while sequencing of STRs enabled the detection of more individual minor alleles. For microhaplotypes, a full minor profile was detected down to a 20:1 ratio at 10 ng and minimal allele dropout at 1 ng of input DNA. A higher rate of allele dropout from the minor donor(s) was reported at 1 ng than 10 ng for three-person mixtures while for four- and five-person mixtures, the same number of dropouts was observed for almost all minor donors. Overall this microhaplotype panel is a powerful tool that can complement and enhance size- and sequence-based STR analysis of forensic DNA mixtures.