Using big data from probabilistic genotyping to solve crime

Forensic Science South Australia (FSSA) has been using STRmix™ software to deconvolute all reported DNA mixtures since 2012. Almost a decade of deconvolutions had led to a substantial repository of analysed profile data that can be interrogated to observe trends in case type, location or occurrence. In addition, deconvolutions can be compared in order to identify common DNA donors and reveal new intelligence information in cases where DNA profiling has previously provided no investigative information. As a proof of concept all samples deconvoluted as part of criminal casework (suspect or no-suspect) were interrogated and compared to each other using the mixture-to-mixture comparison feature in STRmix™. Within the Adelaide region there were 32 groups of cases that had evidence samples linked by a common DNA donor with LR > 1 million which was in addition to direct links and mixture searching links identified previously. These groups of cases can then be interrogated to reveal additional information to inform Police intelligence gathering. Our paper reports on the findings of this proof-of-concept study.     

Would the real allele please stand up? Compiling DNA artefacts for the GlobalFiler PCR amplification kit – a South Australian approach

ABSTRACT

This article presents a compendium of DNA artefacts observed using the GlobalFiler and GlobalFiler Express PCR kits (ThermoFisher Scientific) during DNA reference profile assessment at Forensic Science SA (FSSA). The data are currently used to assist with the interpretation of GlobalFiler DNA evidence profiles encountered in the course of routine case work at FSSA. Over 1000 reference profiles have passed observation by reference DNA run readers. An artefact was considered confirmed if it was observed in five or more individual reference samples and could be confirmed upon re-PCR. Artefacts were documented in the following two categories: (1) those with a location independent of true allelic products and (2) those with a location relative to a true allelic product. The artefacts observed were positioned within and outside of allelic designations and were typically less than 1% of the closest allelic product. Artefacts reported here are observed from reference samples only. Their causes are largely unknown and warrant further investigation. Post-developmental artefacts may be encountered due to storage and handling conditions. As such, continued monitoring of reference samples for low level artefacts is warranted.     

Searching mixed DNA profiles directly against profile databases

DNA databases have revolutionised forensic science. They are a powerful investigative tool as they have the potential to identify persons of interest in criminal investigations. Routinely, a DNA profile generated from a crime sample could only be searched for in a database of individuals if the stain was from single contributor (single source) or if a contributor could unambiguously be determined from a mixed DNA profile. This meant that a significant number of samples were unsuitable for database searching. The advent of continuous methods for the interpretation of DNA profiles offers an advanced way to draw inferential power from the considerable investment made in DNA databases. Using these methods, each profile on the database may be considered a possible contributor to a mixture and a likelihood ratio (LR) can be formed. Those profiles which produce a sufficiently large LR can serve as an investigative lead.In this paper empirical studies are described to determine what constitutes a large LR. We investigate the effect on a database search of complex mixed DNA profiles with contributors in equal proportions with dropout as a consideration, and also the effect of an incorrect assignment of the number of contributors to a profile. In addition, we give, as a demonstration of the method, the results using two crime samples that were previously unsuitable for database comparison. We show that effective management of the selection of samples for searching and the interpretation of the output can be highly informative.     

A law enforcement intelligence framework for use in predictive DNA phenotyping

ABSTRACT

Analysis of information about physical characteristics, biogeographical ancestry or common genetic ancestors from crime scene DNA is a technique aimed at informing an intelligence process, rather than obtaining evidence for a criminal trial. This intelligence supports tactical or operational decision-making. Like other forms of intelligence there is a risk for it to be misconstrued or for its investigative value to be misunderstood. The potential for intelligence derived from DNA to divert investigative resources or result in unnecessary intrusions into individual privacy can be mitigated by applying an appropriate intelligence doctrine. Establishing an appropriate framework could reduce the need for government regulation of these emerging capabilities in the context of law enforcement use.     

Relationship between interchange usage and risk of hamstring injuries in the Australian Football League

ObjectivesTo study risk factors for hamstring injury in the Australian Football League (AFL), in particular the effect of recent changes in match participation (increased use of the interchange bench) on hamstring injury.DesignAnalysis of hamstring match injury statistics extracted from an injury database combined with match participation statistics extracted from a player statistics database.Methods56,320 player matches in the AFL over the period 2003–2010 were analyzed, in which 416 hamstring injuries occurred.ResultsIn a Generalized Estimating Equation (GEE) analysis accounting for clustering of different teams, significant predictors of hamstring injuries were recent hamstring injury (RR 4.16, 95% CI 3.19–5.43), past history of ACL reconstruction (RR 1.69, 95% CI 1.09–2.60), past history of calf injury (RR 1.58, 95% CI 1.37–1.82), opposition team making 60 or more interchanges during the game (RR 1.38, 95% CI 1.12–1.68) and player having made 7 or more interchanges off the field in the last 3 weeks (protective RR 0.74, 95% CI 0.59–0.93).ConclusionsThese findings suggest that regular interchanges protect individual players against hamstring injuries, but increase the risk of hamstring injury for opposition players. These findings can be explained by a model in which both fatigue and average match running speed are risk factors for hamstring injury. A player who returns to the ground after a rest on the interchange bench may himself have some short-term protection against hamstring injury because of the reduced fatigue, but his rested state may contribute to increased average running speed for his direct opponent, increasing the risk of injury for players on the opposition team.     

Haplotype distribution in a forensic full mtDNA genome database of admixed Southern Brazilians and its association with self-declared ancestry and pigmentation traits

Background:The advent of massively parallel sequencing (MPS) applications focused on the generation of forensic-quality full mitochondrial genome sequences led to a popularization of the technique on a global scale. However, the lack of forensic-graded population databases has refrained a wider adoption of full genome sequences as the industry standard, despite its better discrimination capacity of individual maternal lineages.Purpose:This work describes a forensic-oriented full mtDNA genome database comprised of 480 samples from a Southern Brazilian population.Methods:A collection of mitochondrial sequences were obtained from low-pass, full genome DNA sequencing results. The complete sample set was evaluated regarding haplotype composition and distribution. Summary statistics and forensic parameters were calculated and are presented for the database, with detailed information concerning the impact of removing genetic information in the form of specific variants or increasingly larger genomic regions. Interpopulational analysis comparing haplotypical diversity in Brazilian and 26 worldwide populations was also performed. The association between mitochondrial genetic variability and phenotypic diversity was also evaluated in populations, with self-declared ancestry and three distinct phenotypic pigmentation traits (eyes, skin and hair colors) as parameters.Results:The presented database can be used to evaluate mitochondrial-related genetic evidence, providing LR values of up to 20,465 for unobserved haplotypes. Haplotype distribution in Southern Brazil seems to be different than the remaining of the country, with a larger contribution of maternal lines with European origin. Despite association can be found between lighter and darker phenotypes or self-declared ancestry and haplotype distribution, prediction models cannot be reliably proposed due to the admixed nature of the Brazilian population.Conclusions:The proposed database provides a basis for statistical calculation and frequency estimation of full mitochondrial genomes, and can be part of an integrated, representative, national database comprising most of the genetic diversity of maternal lineages in the country.     

Streamlining the decision-making process for international DNA kinship matching using Worldwide allele frequencies and tailored cutoff log10LR thresholds

The identification of human remains belonging to missing persons is one of the main challenges for forensic genetics. Although other means of identification can be applied to missing person investigations, DNA is often extremely valuable to further support or refute potential associations. When reference DNA samples cannot be collected from personal items belonging to a missing person, a direct DNA identification cannot be carried out. However, identifications can be made indirectly using DNA from the missing person’s relatives. The ranking of likelihood ratio (LR) values, which measure the fit of a missing person for any given pedigree, is often the first step in selecting candidates in a DNA database. Although implementing DNA kinship matching in a national environment is feasible, many challenges need to be resolved before applying this method to an international configuration. In this study, we present an innovative and intuitive method to perform international DNA kinship matching and facilitate the comparison of DNA profiles when the ancestry is unknown or unsure and/or when different marker sets are used. This straightforward method, which is based on calculations performed with the DNA matching software BONAPARTE, Worldwide allele frequencies and tailored cutoff log₁₀LR thresholds, allows for the classification of potential candidates according to the strength of the DNA evidence and the predicted proportion of adventitious matches. This is a powerful method for streamlining the decision-making process in missing person investigations and DVI processes, especially when there are low numbers of overlapping typed STRs. Intuitive interpretation tables and a decision tree will help strengthen international data comparison for the identification of reported missing individuals discovered outside their national borders.     

The first Australian conviction resulting from a familial search

ABSTRACT

Familial Searching has been used in numerous jurisdictions globally since the turn of the century and has provided successful investigative leads and prosecutions. We present a familial search performed at Forensic Science SA in conjunction with the South Australian Police that resulted in an intelligence lead, arrest and conviction of an individual, which we believe is the first such conviction in Australia. A DNA profile of male origin was obtained from exhibits collected from two different sexual assaults which did not match any individuals on the National DNA database. A familial search was conducted resulting in a candidate list of potential relatives. After further exclusionary DNA work using Y-STRs, a single individual gave strong support as a possible child or parent of the unknown male who left the crime stain. After further police investigation of this male, he was subsequently arrested and ultimately pleaded guilty to the two assaults. We briefly discuss the police and scientific work involved in this case and also some of the more general issues and processes around familial searching in Australia.     

The Patient Experience in Radiology: Observations From Over 3,500 Patient Feedback Reports in a Single Institution

PurposeTo identify factors associated with the patient experience in radiology based on patient feedback reports from a single institution.MethodsIn a departmental patient experience committee initiative, all imaging outpatients are provided names and roles of all departmental employees with whom they interact, along with contact information for providing feedback after their appointment. All resulting feedback was recorded in a web-based database. A total of 3,675 patient comments over a 3-year period were assessed in terms of major themes. Roles of employees recognized within the patient comments were also assessed.ResultsPatient feedback comments most commonly related to professional staff behavior (74.5%) and wait times (11.9%), and less commonly related to a spectrum of other issues (comfort during the exam, quality of the facilities, access to information regarding the exam, patient privacy, medical records, the radiology report, billing). The most common attributes relating to staff behavior involved patients’ perceptions of staff caring, professionalism, pleasantness, helpfulness, and efficiency. Employees most commonly recognized by the comments were the technologist (50.2%) and receptionist (31.6%) and much less often the radiologist (2.2%). No radiologist was in the top 10% of employees in terms of the number of comments received.ConclusionPatients' comments regarding their experiences in undergoing radiologic imaging were largely influenced by staff behavior and communication (particularly relating to technologists and receptionists), as well as wait times, with radiologists having a far lesser immediate impact. Radiologists are encouraged to engage in activities that promote direct visibility to their patients and thereby combat risks of the perceived “invisible” radiologist.     

Validation of SmartRank: A likelihood ratio software for searching national DNA databases with complex DNA profiles

Searching a national DNA database with complex and incomplete profiles usually yields very large numbers of possible matches that can present many candidate suspects to be further investigated by the forensic scientist and/or police. Current practice in most forensic laboratories consists of ordering these ‘hits’ based on the number of matching alleles with the searched profile. Thus, candidate profiles that share the same number of matching alleles are not differentiated and due to the lack of other ranking criteria for the candidate list it may be difficult to discern a true match from the false positives or notice that all candidates are in fact false positives. SmartRank was developed to put forward only relevant candidates and rank them accordingly. The SmartRank software computes a likelihood ratio (LR) for the searched profile and each profile in the DNA database and ranks database entries above a defined LR threshold according to the calculated LR. In this study, we examined for mixed DNA profiles of variable complexity whether the true donors are retrieved, what the number of false positives above an LR threshold is and the ranking position of the true donors. Using 343 mixed DNA profiles over 750 SmartRank searches were performed. In addition, the performance of SmartRank and CODIS were compared regarding DNA database searches and SmartRank was found complementary to CODIS. We also describe the applicable domain of SmartRank and provide guidelines. The SmartRank software is open-source and freely available. Using the best practice guidelines, SmartRank enables obtaining investigative leads in criminal cases lacking a suspect.     

Analysis of more than 20,000 injuries in European professional football by using a citizen science-based approach: An opportunity for epidemiological research?

ObjectivesIt has been claimed that analyses of large datasets from publicly accessible, open-collaborated (“citizen science-based”) online databases may provide additional insight into the epidemiology of injuries in professional football. However, this approach comes with major limitations, raising critical questions about the current trend of utilizing citizen science-based data. Therefore, we aimed to determine if citizen science-based health data from a popular online database on professional football players can be used for epidemiological research, i.e. in providing results comparable to other data sources used in previously published studies.DesignRetrospective database analysis.MethodsTransfermarkt.com (Transfermarkt; Hamburg; Germany) is a publicly accessible online database on various data of professional football players. All information provided in the section “injury history” of football players from the top five European leagues over a period of ten seasons (2009/10–2018/19) was analyzed. Frequency, characteristics, and incidence of injuries were reported according to seasons and countries, and results compared with three previously published databases (a scientific injury surveillance, a media-based study, and an insurance database).ResultsOverall, 21,598 injuries of 11,507 players were analyzed from the Transfermarkt.com database. Incidence was 0.63 injuries per player-season (95% confidence interval 0.62 to 0.64) but significant differences between subgroups (countries, years) were found. In comparison to other databases, citizen science-based data was associated with lower injury incidences and higher proportions of severe injuries.ConclusionsWith few exceptions (e.g., severe injuries), the use of citizen science-based health data on professional football players cannot be recommended at present for epidemiological research.     

Differences in local and national database recordings of deaths from suicide

A search was undertaken at Forensic Science South Australia (FSSA) for all cases of suicide registered in South Australia, Australia, over a 10-year period from January 2003 to December 2012. More recent data was not accessioned as not all contemporary cases may have been completed or formally registered. The data were compared to corresponding numbers on two national registers: the National Coronial Information System (FSSA, with a death rate of 13.3/100,000 population. NCIS data were available from 2003 to 2010, with 1542 suicides recorded (12.3/100,000 population). ABS data were available from 2003 to 2011, with 1366 deaths coded as suicides (12.4/100,000 population). Significant differences were found between local data on suicides and related data accrued nationally from the same population, with only 67.8% of local drug overdoses recorded on the NCIS. Although this represents an Australian-based study the conclusions have global applications. Thus, given the likely accuracy of local data, reliance on smaller, community-specific datasets in any country/jurisdiction may be of far greater use in analyzing and monitoring such complex cases.     

Development and validation of a fast and automated DNA identification line

The importance of DNA evidence for gaining investigative leads demands a fast workflow for forensic DNA profiling performed in large volumes. Therefore, we developed software solutions for automated DNA profile analysis, contamination check, major donor inference, DNA database (DDB) comparison and reporting of the conclusions. This represents the Fast DNA IDentification Line (FIDL) and this study describes its development, validation and implementation in criminal casework at the authors’ institute. This first implementation regards single donor profiles and major contributors to mixtures. The validation included testing of the software components on their own and examination of the performance of different DDB search strategies. Furthermore, end-to-end testing was performed under three conditions: (1) testing of scenarios that can occur in DNA casework practice, (2) tests using three months of previous casework data, and (3) testing in a casework production environment in parallel to standard casework practices. The same DNA database candidates were retrieved by this automated line as by the manual workflow. The data flow was correct, results were reproducible and robust, results requiring manual analysis were correctly flagged, and reported results were as expected. Overall, we found FIDL valid for use in casework practice in our institute. The results from FIDL are automatically reported within three working days from receiving the trace sample. This includes the time needed for registration of the case, DNA extraction, quantification, polymerase chain reaction and capillary electrophoresis. FIDL itself takes less than two hours from intake of the raw CE data to reporting. Reported conclusions are one of five options: (1) candidate retrieved from DDB, (2) no candidate retrieved from DDB, (3) high evidential value with regards to reference within the case, (4) results require examination of expert, or (5) insufficient amount of DNA obtained to generate a DNA profile. In our current process, the automated report is sent within three working days and a complete report, with confirmation of the FIDL results, and signed by a reporting officer is sent at a later time. The signed report may include additional analyses regarding e.g. minor contributors. The automated report with first case results is quickly available to the police enabling them to act upon the DNA results prior to receiving the full DNA report. This line enables a uniform and efficient manner of handling large numbers of traces and cases and provides high value investigative leads in the early stages of the investigation.     

Evaluation of salivary DNA obtained from dental prosthesis and its applicability in forensic investigations

AimThis study evaluated the salivary DNA obtained from dental prosthesis after a period of storage and its applicability in human identification.Material and methodsIn first phase, DNA was extracted after a span of 1 week and 1 month from the dental prosthesis dipped in whole saliva for 15 min. It was followed by PCR and electrophoresis.In second phase, from extracted DNA samples 15 STRs (short tandem repeats) of human genomic DNA were amplified via polymerase chain reaction.Results & conclusionDNA isolated from saliva stained dental prosthesis after a period of storage and the techniques employed are adequate for further forensic analysis.     

A national surveillance study of the current status of reirradiation using brachytherapy in Japan

PurposeThis study aimed to explore the current status and pattern of practice for reirradiation using brachytherapy (ReRT-BT) through a survey in Japan.Materials and MethodsWe distributed an e-mail-based questionnaire to 153 institutions equipped with high-dose-rate brachytherapy facilities.ResultsWe received responses from 76 institutions (49.7%). Forty-three of these institutions performed ReRT-BT and 42 institutions (55%) performed ReRT-BT during 2009–2018. However, 29 of the 42 institutions (69%) reported difficulty in obtaining ReRT-BT case information from their respective databases. Almost all the institutions encountered insufficient database system to extract details about the ReRT-BT cases. Responses from 33 institutions included the number of ReRT-BT cases; this increased from 90 in the period 2009–2013 (institution median = 0.5; 0–16) to 172 in the period 2014–2018 (institution median = 2; 0–26). Nine institutions had to perform ReRT-BT for more than one case per year. The major location for cancer treatment was the pelvis (94%), followed by the head and neck (5%) and others (1%). In six site-specific scenarios, barring uterine corpus cancer recurrence, more than 90% of radiation oncologists agreed to perform ReRT-BT, whereas other areas (head and neck, prostate, and rectal cancer) gained 16–37% agreement.ConclusionsThis decade saw an increase in the number of ReRT-BT cases in Japan and radiation oncologists’ interest in ReRT-BT as a viable therapeutic option. However, scarce availability, immature education system, and insufficient database system are barriers to further consensus building.     

Distribution of Reported StarClose SE Vascular Closure Device Complications in the Manufacturer and User Facility Device Experience Database

PurposeTo evaluate the type and frequency of complications associated with the StarClose SE vascular closure device reported to the U.S. Food and Drug Administration (FDA) Manufacturer and User Facility Device Experience (MAUDE) database for comparison with complications reported in clinical trials.Materials and MethodsComplications reported in the MAUDE database related to use of the StarClose SE vascular closure device were reviewed. Keyword searches by device and manufacturer were performed for a 16-month period from July 2009–October 2010. Reports were analyzed according to complication type, frequency, and resolution, if specified. These data were compared with data on StarClose SE device complications, which included three prospective randomized trials and five prospective nonrandomized trials.ResultsKeyword searches returned 1,107 total records and 1,118 categorizable StarClose SE device complications from the 16-month MAUDE database–reporting period. Complications in order of frequency (absolute number and relative frequency, respectively) included failure to achieve hemostasis (409, 36.6%), inability to complete the deployment sequence (268, 24.0%), entrapped deployment device (224, 20%), clip not deployed (151,13.5%), late bleeding or oozing from dermatotomy site (25, 2.2%), vessel occlusion (19, 1.7%), retroperitoneal hematoma (12, 1.1%), pseudoaneurysm formation (6, 0.5%) and death (4, 0.4%). The distribution of complications differed appreciably from the combined adverse events compiled from the published trials evaluating the StarClose SE device. There were no records describing inability to remove the deployment device in the published trials, whereas this represented the third most common complication reported to the MAUDE database. Bleeding or oozing from the dermatotomy site, the most frequent relative complication reported in the published literature (53.4%), represented 2.2% of the total complications reported to the MAUDE database.ConclusionsThe type and frequency of complications reported in the MAUDE database on the StarClose SE vascular closure device differ from those published in clinical trials both in relative distribution and in type. Although these differences may reflect in part reporting biases, the distribution of complications reported to the MAUDE database may represent useful information in the use of this device.     

Percutaneous Closure Devices Do Not Reduce the Risk of Major Access Site Complications in Patients Undergoing Elective Carotid Stent Placement

PurposeTo examine the risk of femoral access site complications in patients undergoing carotid stent placement who were treated with a closure device compared with patients who were not treated with a closure device.Materials and MethodsA national, multihospital patient database, the Premier Perspective database, was used to identify patients hospitalized for carotid stent placement from 2006–2011. To reduce potential selection bias, a propensity score was generated for each patient using relevant clinical variables. Propensity score adjustment via 1:1 matching was performed on patients who did and did not receive a closure device. Primary outcomes were minor femoral access site complications and major complications requiring procedural intervention. Secondary outcomes included in-hospital mortality, stroke, and blood transfusion.ResultsAmong 12,287 patients who underwent carotid stent placement at 217 hospitals, 6,398 (52%) received a closure device on the day of the procedure. After propensity score matching, patients who received a closure device had a lower likelihood of minor access site complications (4.2% vs 5.4%; odds ratio = 0.77; 95% confidence interval, 0.55–0.93; P = .0071) compared with patients who did not receive a closure device; however, this difference was small and likely not clinically relevant. Both groups had a similar risk of major access site complications (P = .32), in-hospital mortality (P = .0520), and stroke (P = .31).ConclusionsUse of a closure device was not associated with a substantially reduced risk of major adverse events after carotid stent placement and was associated with only a small improvement in minor access site complications.     

DNA profiles from matchsticks

ABSTRACT

Matchsticks may be found in forensic investigations, and here we report on a method to generate informative DNA profiles from a matchstick. Matchsticks were struck or held emulating striking, cellular material was removed using a tape-lift method and DNA profiles were generated from a small portion of the tape-lift using either direct PCR amplification or post-extraction PCR. Performing an extraction from the tape-lift prior to PCR resulted in 62% of profiles being informative, compared with 86% held and 97% struck matchsticks that underwent direct PCR. Incorporation of a tape-lift method into matchstick analysis allows effective collection of cellular material for the generation of genetic information from the striker of the matchstick.     

ProbRank: An efficient DNA database search method for complex mixtures per a quantitative likelihood ratio model

Searching a DNA Database with a DNA profile from an evidentiary trace can provide investigative leads in a forensic case. Various searching approaches exist such as conventional methods based on matching alleles or more advanced methods computing likelihood ratios (LR) while considering drop-in and drop-out. Here we examine the potential of using a quantitative LR model (EuroForMix model incorporated in ProbRank method) that takes peak heights into account in comparison to a qualitative LR model (LRmix model implemented in SmartRank method). Both methods present DNA database candidates in order of decreasing LR. Especially regarding minor contributors in complex mixtures, the method using the quantitative model outperforms the method using the qualitative model in terms of sensitivity and specificity as more true donors and less adventitious matches are retrieved. ProbRank is to be implemented in DNAStatistX and is sufficiently fast for daily use.