Forensic DNA laboratory automation – Principles and guidelines

There is a lack of clear guidelines for project managers, laboratory managers and forensic scientists on strategies for the automation of forensic DNA laboratory processes and operational implementation of new technologies. This is reflected in the failure rate of projects in the forensic DNA testing environment. We present a set of guidelines and concepts important for forensic laboratory automation. Some case studies from past projects are presented. These consist of partial (or modular) automation (n = 2) and full automated robotically integrated systems (n = 2).Technology Management principles and concepts are crucial to prevent failure of projects, e.g. early adoption of untried technologies, and organizational factors. The future of laboratory automation is modular until such time as new discontinuous technologies will replace the need of the traditional manual laboratory configuration in totality.     

3D GPR in forensics: Finding a clandestine grave in a mountainous environment

In the present work we show a forensic case study carried out in a mountainous environment. Main objective was to locate a clandestine grave which is around 10–20 years old and contains human remains of one individual and a metallic tool, probably a pick. Survey design started with an experimental burial of a pick at the expected depth (1 m) as well as the calculation of synthetic radargrams in order to know if the 250 MHz antenna was suitable for its detection and to have a record of the reflection of the pick. Conclusions extracted from the experiments together with rough terrain conditions suggested the use of the 250 MHz antenna which allowed a good compromise between target detection and dense grid acquisition of an extensive survey area.     

Soil sample metagenome NGS data management for forensic investigation

Soil analysis is a valuable resource in forensic investigation. Classical forensic soil analysis involves examination of its physical characteristics and chemical composition, such as soil type, colour, particle size, shape, pH, elemental, mineral and organic content. However the limited variability of these parameters is not always allowing adequate discrimination between soil samples. As soil supports extreme diversity of microorganisms and eukaryotic communities, microbiological approaches have been proposed. Several molecular approaches for microbial DNA profiling are available; however there is a lack of published data of implementation of the next generation sequencing (NGS) approaches for forensic soil analysis.The aim of the current study was elaboration of criteria for soil metagenome data management and database searching. We used our previously sequenced collection of 11 samples collected from different environments (forests, fields, grasslands, urban park) with different flora. The single sample collection includes 9 soil samples per one sampling area (30 m × 30 m) spaced by 15 m. In the current study we concentrated mainly on 18S rRNA gene V2-V3 region for fungi however SSU rRNA region for arbuscular mycorrhizal (AMF) fungi and V2-V3 hypervariable region of 16S rRNA gene for bacterial communities were taken into account. The sequencing was performed by Roche/454 platform. For data analysis OTU based approach on mothur software and NCBI BLASTN search were used. NCBI BLASTN analysis revealed altogether 2983 AMF matches and 8997 18S matches as well as 25477 OTUs (16S) were determined. Several data filtration approaches were used for data management. We found that 18S marker results could be used to create and run a filtered database that is computationally much more efficient and flexible. Our results have broad impact; however more samples have to be analysed, additional studies performed and cooperation between soil scientists and forensic scientists is required to be able to implement these novel techniques into the routine forensic practice.     

Assessing the potential application of X-chromosomal haploblocks in population genetics and forensic studies

Haploblocks are segments of the genome with little recombination that may be of interest in forensic and population genetics. Criteria to select autosomal haploblocks have been previously described, leading to the identification of candidate regions that, a priori, met the conditions to be used as forensic genetic markers. Still, the potential of X-chromosomal haploblocks remains unexplored.The present work aimed to provide basis for designing strategies for selection of X-haploblocks defined by single nucleotide polymorphisms (SNPs) using next generation sequencing approach. The potential application in population genetics and forensic studies was addressed. One of the conditions considered in the haploblock selection was the simultaneous inclusion of short tandem repeats (STRs) currently used in forensic casework to allow the distinction between SNP-defined haplotypes and increase the resolution for fine-scale studies. Given the size of the X chromosome (∼150 Mbps), only four haploblocks could be selected in order to guarantee their independence.     

SNP genotyping of forensic casework samples using the 52 SNPforID markers

The analysis of degraded DNA is one of the biggest challenges in forensic casework. SNPs, which can be amplified using small amplicons, have previously been successfully applied to the profiling of forensic evidence that could not be analyzed using conventional STRs. Here we selected the 52 SNPforID SNP markers, with amplicons that ranged in size from 59 bp to 115 bp, and used them to profile a range of casework samples from Malaysia. DNA degradation is a common problem in Malaysia due to the high temperatures and humidity. To carry out the study we modified the 52 SNPforID markers into four 13-plex SNaPshot assays to enable easier interpretation of profiles on the ABI PRISM^® 310 and 3500.Fifty-one crime samples comprising bloodstains on cloth, swabs, and a mat and 2 swabs of trace DNA from 10 crime scenes in Malaysia were profiled after DNA extraction using a phenol–chloroform method. The samples were also subjected to STR analysis using the Powerplex^® 16 system (Promega), which resulted in only 17 full profiles and 9 partial profiles; using SNPs, 36 full profiles and 5 partial profiles could be generated.     

Freezing skeletal muscle tissue does not affect its decomposition in soil: Evidence from temporal changes in tissue mass,microbial activity and soil chemistry based on excised samples

The study of decaying organisms and death assemblages is referred to as forensic taphonomy, or more simply the study of graves. This field is dominated by the fields of entomology, anthropology and archaeology. Forensic taphonomy also includes the study of the ecology and chemistry of the burial environment. Studies in forensic taphonomy often require the use of analogues for human cadavers or their component parts. These might include animal cadavers or skeletal muscle tissue. However, sufficient supplies of cadavers or analogues may require periodic freezing of test material prior to experimental inhumation in the soil. This study was carried out to ascertain the effect of freezing on skeletal muscle tissue prior to inhumation and decomposition in a soil environment under controlled laboratory conditions. Changes in soil chemistry were also measured. In order to test the impact of freezing, skeletal muscle tissue (Sus scrofa) was frozen (?20 °C) or refrigerated (4 °C). Portions of skeletal muscle tissue (～1.5 g) were interred in microcosms (72 mm diameter × 120 mm height) containing sieved (2 mm) soil (sand) adjusted to 50% water holding capacity. The experiment had three treatments: control with no skeletal muscle tissue, microcosms containing frozen skeletal muscle tissue and those containing refrigerated tissue. The microcosms were destructively harvested at sequential periods of 2, 4, 6, 8, 12, 16, 23, 30 and 37 days after interment of skeletal muscle tissue. These harvests were replicated 6 times for each treatment. Microbial activity (carbon dioxide respiration) was monitored throughout the experiment. At harvest the skeletal muscle tissue was removed and the detritosphere soil was sampled for chemical analysis. Freezing was found to have no significant impact on decomposition or soil chemistry compared to unfrozen samples in the current study using skeletal muscle tissue. However, the interment of skeletal muscle tissue had a significant impact on the microbial activity (carbon dioxide respiration) and chemistry of the surrounding soil including: pH, electroconductivity, ammonium, nitrate, phosphate and potassium. This is the first laboratory controlled study to measure changes in inorganic chemistry in soil associated with the decomposition of skeletal muscle tissue in combination with microbial activity.     

Age estimation by pulp/tooth area ratio in canines: Cameriere's method assessed in an Indian sample using radiovisiography

Age estimation of an individual whether living or dead is an intimidating task in forensic investigations. Since teeth are more resistant to most peri- and post-mortem changes, they are frequently used for identification and age estimation when skeletal remains are in poor condition. However, most methods are destructive and warrant extraction of teeth which is not feasible in living individuals. Cameriere's et al. put forth a radiographic method of age estimation by pulp to tooth area ratio (AR) in canines and revealed a linear regression between age and the AR. In the present study, we estimated the AR in 456 canines (upper, lower and both) in an Indian sample (114 males and 114 females) using radiovisiography technique. Linear regression equations were derived for upper canine, lower canine and both using the AR to estimate chronological age. Additionally, the efficacy of these equations was also evaluated in younger age group (<45 years). The formulas derived, i.e., age = 96.795 ? 513.561x₁ (Eq. (1)) for upper canine, age = 88.308 ? 458.137x₂ (Eq. (2)) for lower canine and age = 99.190 ? 283.537x₁ ? 306.902x₂ + 400.873x₁x₂ (Eq. (3)) for both the canines were applied to predict the chronological age. The mean value of residuals using these regression equations ranged from 4.28 to 6.39 years with upper canine equation generally giving a precise result. When these equations were applied for younger ages (<45 years), the regression equation derived from both canines gave a better result (mean residual 2.70 years). Overall these equations were better able to predict the age in younger ages, i.e., up to 45 years.     

Validation studies in forensic odontology – Part 1: Accuracy of radiographic matching

As part of a series of studies aimed at validating techniques in forensic odontology, this study aimed to validate the accuracy of ante-mortem (AM)/postmortem (PM) radiographic matching by dentists and forensic odontologists. This study used a web-based interface with 50 pairs of AM and PM radiographs from real casework, at varying degrees of difficulty. Participants were shown both radiographs as a pair and initially asked to decide if they represented the same individual using a yes/no binary choice forced-decision. Participants were asked to assess their level of confidence in their decision, and to make a conclusion using one of the ABFO (American Board of Forensic Odontology), INTERPOL (International Criminal Police Organisation) and DVISys? (DVI System International, Plass Data Software) identification scale degrees. The mean false-positive rate using the binary choice scale was 12%. Overall accuracy was 89% using this model, however, 13% of participants scored below 80%. Only 25% of participants accurately answered yes or no > 90% of the time, with no individual making the correct yes/no decision for all 50 pairs of radiographs. Non-odontologists (lay participants) scored poorly, with a mean accuracy of only 60%. Use of the graded ABFO, DVISYS and INTERPOL scales resulted in general improvements in performance, with the false-positive and false-negative rates falling to approximately 2% overall. Inter-examiner agreement in assigning scale degrees was good (ICC = 0.64), however there was little correlation between confidence and both accuracy or agreement among practitioners. These results suggest that use of a non-binary scale is supported over a match/non-match call as it reduces the frequency of false positives and negatives. The use of the terms “possible” and “insufficient information” in the same scale appears to create confusion, reducing inter-examiner agreement. The lack of agreement between higher-performing and lower-performing groups suggests that there is an inconsistency in the cognitive processes used to determine similarity between radiographs.     

Bloodstain age estimation through infrared spectroscopy and Chemometric models

The chemical profiling of bloodstains is essential to link the suspect with the crime. The current study proposed a proof-of-concept methodology for the investigation of bloodstains by utilizing advanced ATR-FTIR spectroscopy coupled with new generation chemometric methods. Current study provides encouraging data to allow discrimination between human and animal blood though with small sample size. In this study, different models for the age estimation of human bloodstains are developed from the trained data sets of 1–175 days old bloodstains. The models such as curve estimation (CE), multiple linear regression (MLR), and partial least squares regressions (PLSR) are developed to determine the best prediction model for aged human bloodstains. The obtained results on the dating of bloodstains are very encouraging and also tested for unknown samples. The maximum dating errors are observed in the curve estimation models whereas, the other models MLR, PLSR show excellent age estimation of unknown bloodstains. These models represent an error of ~3 ± 1 days and ~4 ± 1 days in actual and estimated date, respectively, which is lowest ever reported so far. The present methodology is expected to provide a valuable insight into forensic society and hence, to the law enforcement community. The present methodology can further be explored for an ideal model by including all other external variables/factors and for more longer aging time.     

Experimental results of fingerprint comparison validity and reliability: A review and critical analysis

Our purpose in this article is to determine whether the results of the published experiments on the accuracy and reliability of fingerprint comparison can be generalized to fingerprint laboratory casework, and/or to document the error rate of the Analysis–Comparison–Evaluation (ACE) method. We review the existing 13 published experiments on fingerprint comparison accuracy and reliability. These studies comprise the entire corpus of experimental research published on the accuracy of fingerprint comparisons since criminal courts first admitted forensic fingerprint evidence about 120 years ago. We start with the two studies by Ulery, Hicklin, Buscaglia and Roberts (2011, 2012), because they are recent, large, designed specifically to provide estimates of the accuracy and reliability of fingerprint comparisons, and to respond to the criticisms cited in the National Academy of Sciences Report (2009).Following the two Ulery et al. studies, we review and evaluate the other eleven experiments, considering problems that are unique to each. We then evaluate the 13 experiments for the problems common to all or most of them, especially with respect to the generalizability of their results to laboratory casework.Overall, we conclude that the experimental designs employed deviated from casework procedures in critical ways that preclude generalization of the results to casework. The experiments asked examiner-subjects to carry out their comparisons using different responses from those employed in casework; the experiments presented the comparisons in formats that differed from casework; the experiments enlisted highly trained examiners as experimental subjects rather than subjects drawn randomly from among all fingerprint examiners; the experiments did not use fingerprint test items known to be comparable in type and especially in difficulty to those encountered in casework; and the experiments did not require examiners to use the ACE method, nor was that method defined, controlled, or tested in these experiments.Until there is significant progress in defining and measuring the difficulty of fingerprint test materials, and until the steps to be followed in the ACE method are defined and measurable, we conclude that new experiments patterned on these existing experiments cannot inform the fingerprint profession or the courts about casework accuracy and errors.     

Genetic variation in a Japanese population,using the multiplex 24 STRs analysis system

Allele frequency distributions for 24 short tandem repeat (STR) loci were determined using the PowerPlex^R Fusion System (Promega) in 407 Japanese samples. The most informative locus among the 22 STR loci, excluding Amelogenin and DYS391, was Penta E (power of discrimination (PD) = 0.98), while the least informative was TPOX(PD = 0.831). The 22 loci combined matching probability (MP) was calculated to be 4.13 × 10⁻²⁶. These parameters indicated the usefulness of this 24 STR analysis in forensic personal identification and parentage testing among Japanese population.     

Estimation of legal age using calcification stages of third molars in living individuals

The increased number of adolescents and young adults with unknown or inaccurately given date of birth is a current issue in justice and legal medicine. The objective of this study was to determine the extent to which third molar calcification stages assessed on panoramic X-rays could be useful as additional criteria for forensic age estimation in living individuals, focusing on the legally important ages 17 and 18.In a retrospective multi-center study, the developmental stage of each individual's third molar was analyzed using Demirjian's scale in 2360 cases. Additionally, sex, age and ancestry were assessed.Individuals with the lowest calcification stage of all present molars in stage H were ≥ 18 years with a likelihood of ≥ 99.05% in the female (n = 388), and ≥ 99.24% in the male (n = 482) population.The lowest calcification stage of all present third molars proved to be useful as an additional reliable criterion for the determination of an age ≥ 18 years.     

Recovery of human DNA profiles from poached deer remains part 2: Improved recovery protocol without the need for LCN analysis

Although poaching is a common wildlife crime, the high and prohibitive cost of specialised animal testing means that many cases are left un-investigated. We previously described a novel approach to wildlife crime investigation that looked at the identification of human DNA on poached animal remains (Tobe, Govan and Welch, 2011). Human DNA was successfully isolated and amplified from simulated poaching incidents, however a low template protocol was required which made this method unsuitable for use in many laboratories. We now report on an optimised recovery and amplification protocol which removes the need for low template analysis.Samples from 10 deer (40 samples total — one from each leg) analysed in the original study were re-analysed in the current study with an additional 11 deer samples. Four samples analysed using Chelex did not show any results and a new method was devised whereby the available DNA was concentrated. By combining the DNA extracts from all tapings of the same deer remains followed by concentration, the recovered quantity of human DNA was found to be 29.5 pg ± 43.2 pg, 31 × greater than the previous study. The use of the Investigator Decaplex SE (QIAGEN) STR kit provided better results in the form of more complete profiles than did the AmpF?STR® SGM Plus® kit at 30 cycles (Applied Biosystems). Re-analysis of the samples from the initial study using the new, optimised protocol resulted in an average increase of 18% of recovered alleles. Over 17 samples, 71% of the samples analysed using the optimised protocol showed sufficient amplification for comparison to a reference profile and gave match probabilities ranging from 7.7690 × 10^? 05 to 2.2706 × 10^? 14.The removal of low template analysis means this optimised method provides evidence of high probative value and is suitable for immediate use in forensic laboratories. All methods and techniques used are standard and are compatible with current SOPs. As no high cost non-human DNA analysis is required the overall process is no more expensive than the investigation of other volume crime samples. The technique is suitable for immediate use in poaching incidents.     

Touch DNA collection from improvised explosive devices: A comprehensive study of swabs and moistening agents

Improvised explosive devices (IEDs) are used in devastating terrorist attacks worldwide and daily in Thailand. Touch DNA deposited during IED assembly are subjected to intense heat and pressure, resulting in rare events of usable DNA profiles obtained from real casework. No study has simultaneously evaluated both swab brands and moistening agents for touch DNA collection from substrates encountered in IED evidence. In this study, we investigated the effects of swab brands and moistening agents on DNA collection from adhesive tape, a common IED substrate. A full factorial design using four cotton swab brands (two forensic and two medical cotton swabs) and six moistening agents (DNA-free water, phosphate-buffered saline, ethanol, sodium dodecyl sulfate, isopropanol, and lysis buffer) was employed (24 total combinations). Using buffy coats, we found that DNA recovery depended on both swab brands and moistening agents (p < 0.05). The optimal method recovered significantly higher DNA amount from real IED cases compared to the standard Royal Thai Police method. Percentages of high partial profiles also increased. Our results changed the standard operating protocol of the Thai police. Other commonly found substrates from IED cases are being investigated to maximize the evidential value obtained from touch DNA.     

Experimental forensic studies of the preservation of pollen in vehicle fires

The implications of the recent recommendations of the Law Commission regarding the use of admissibility tests have the potential to be far reaching for forensic disciplines that rely on the expertise of highly qualified expert witnesses. These disciplines will need a concomitant body of peer-reviewed experiments that provides a basis for the interpretations of such evidence presented in court. This paper therefore, presents such results from two experiments which were undertaken to address specific issues that were raised in cases presented in the British courtroom. These studies demonstrate that there is a variability in the persistence of Lily, Daffodil and Tulip pollen when exposed to high temperatures between 0.5 min and 1440 min (24 h). It was possible to identify all three pollen types after 30 min of exposure to 400 °C, and after shorter time frames the threshold for successful identification was 700 °C after 0.5 min for all pollen types tested and 500 °C for Daffodil and Lily after 5 min of heat exposure. Over longer time periods (18 h (1080 min)) the different pollen types were found to persist in a viable form for identification at 300 °C (Lily), 200 °C (Daffodil) and 50 °C (Tulip). These findings, albeit from a small sample of pollen types, provide empirical contextual information that would contribute to such evidence having sufficient scientific weight to meet admissibility criteria and be viable evidence for a court. These studies demonstrate the value in seeking pollen evidence from even such extreme crime scenes as encountered in vehicular fires.     

Population genetic data of 38 autosomal InDels in San Basilio de Palenque,the first free town in America

In order to increase the information about Indels, we report allele frequencies and statistical parameters of forensic efficiency obtained typing a sample of 114 unrelated healthy individuals living in San Basilio de Palenque – Colombia using a panel of 38 autosomal InDels. No significant deviations from Hardy–Weinberg expectations were found except in the marker rs10629077 (p = 0.0002). The present database will be useful for forensic and paternity purposes for the region studied. Moreover, these additional markers can help forensic laboratories to solve parentage testing as well as to improve the analysis of degraded DNA samples.     

Two-dimensional metric comparisons between dynamic bare footprints and insole foot impressions-forensic implications

Footwear may be found at crime scenes as physical evidence. Such footwear often has impression features of the wearer’s foot on the insole of the shoe. Scientific research and literature have established that footprints are distinct. This study compares two-dimensional measurements on bare footprints to foot impressions on insoles to determine if significant differences or similarities exist. Dynamic footprints were collected from 51 donors using the Identicator® Inkless Shoe Print Model LE 25P system. Seven foot length and width measurements were taken based on the Reel linear measurement method. Footprint measurements between bare footprints and foot impressions on the insoles were compared. Only two differences (p > 0.05) were observed between the various bare footprint and insole foot impression measurements on the right and left side for most of the measurements, CALC (p < 0.001) and A1 (p = 0.04). Bare footprint and insole A5 measurements on the left side were also significantly different (p = 0.015). The results of the study have implications in the forensic analysis of foot impression evidence on insoles in footwear in assisting with identifying the wearer of said footwear. Situations may arise in the forensic context when comparing the foot impression on the insole of footwear to a suspect’s bare footprint or a footprint from post-mortem remains. This study contributes to the scant literature available on the topic and to understanding the similarities and differences observed in the various linear measurements that may be utilized in the comparison process of footprint impressions on shoe insoles to bare footprints.     

Development and validation of highly selective screening and confirmatory methods for the qualitative forensic analysis of organic explosive compounds with high performance liquid chromatography coupled with (photodiode array and) LTQ ion trap/Orbitrap mass spectrometric detections (HPLC-(PDA)-LTQOrbitrap)

An LTQ-Orbitrap FTMS is a new (hybrid) mass spectrometric (MS) analyzer. It allows for the acquisition of full scan MSⁿ (n-stage fragmentations, n = 1 − n) spectra with the linear ion trap detector (LTQ) at high speed and/or with the Fourier Transform-detector (Orbitrap) with ultra high mass resolution (> 60,000 at m/z < 400 amu) and high mass accuracy (≤ 1 ppm with internal calibration). In addition it may be coupled with liquid chromatography (LC) with photo diode array (PDA) detection.Two methods for the forensic screening and confirmation of all common trace explosives in post-blast residues have been developed on this instrument using atmospheric pressure chemical ionization (APCI). In one run, the nitrogen-containing explosives are analyzed with the combination of “LC-(PDA)-APCI(−)-LTQ MS²/Orbitrap FTMS” (Method 1). In another run, peroxide explosives are analyzed with “LC-APCI(+)-LTQ MS²/Orbitrap FTMS” (Method 2).The performance of both methods has been validated according to procedures defined in the EU COMMISSION DECISION implementing Council Directive 96/23/EC concerning the performance of analytical methods and the interpretation of results (DC 2002/657/EC) and other standards (NEN 17025 and NEN 7777). The methods are highly selective due to the simultaneous utilization of the Orbitrap FTMS and LTQ MS², both of which are highly selective detectors Tested explosive compounds can be detected in the molecular ion form by the Orbitrap analyzer with minimal mass interference in different matrices when using an extremely narrow mass tolerance detection window (≤ 2 ppm). The identification of a detected compound follows an identification point system. Experimental results show that almost all explosive compounds meet the confirmation criteria (minimum 4 points) required for the positive identification by the DC 2002/657/EC.     

Characterisation of forward stutter in the AmpFlSTR® SGM Plus® PCR

PCR amplification of tetrameric short tandem repeats (STRs) can lead to Taq enzyme slippage and artefact products typically one repeat unit less in size than the parent STR. These back stutter or n ? 4 amplification products are low-level relative to the amplification of the parent STR but are widely seen in the forensic community where tetrameric STRs are employed in the generation of DNA profiles. To aid the interpretation of DNA mixtures where minor contributor(s) might be present in comparable amounts to the back stutter products, the typical amounts of back stutter generated have been well characterised and guidelines for interpretation are in place. However, further artefacts thought to be Taq enzyme slippage leading to products with one repeat unit greater than the parent sequence (n + 4 or forward stutter) or two repeats less (n ? 8 or double back stutter) also occur, but these have not been well characterised despite their potential influence in mixture interpretations. Here we present findings with respect to these additional artefacts from a study of 10,000 alleles and include guidelines for interpretation.