Category Archives: Forensic DNA

Journal articles relating to forensic DNA including disaster victim identification.

New book in the library collection: The murder of Allison Baden-Clay

The Murder of Allison Baden-Clay (2014) / David Murray
The Murder of Allison Baden-Clay is written by the investigative journalist who covered the case from the start. It weaves together exclusive interviews and police and court records to explain how a father with no criminal history came to be on trial for a brutal murder. It’s also a story about everyday choices and their consequences.

If you would like to borrow this item, click on the book title (make sure your details are correct) and click SEND.  If the book is currently on loan, we will add your details to the reservations list.

Forensic Science International: Genetics – recent online articles

Developing a DNA methylation assay for human age prediction in blood and bloodstain Available online 8 May 2015

Age prediction of an individual based on biological traces remained in a crime scene is of ultimate importance for criminal investigation. Growing evidence indicates that some CpG sites may have age-related methylation changes and thus may be a promising tool for age prediction. In this study, we utilized the pyrosequencing approach to screen age-related CpG (AR-CpG) sites for age prediction. Five AR-CpGs were identified as age-related markers from thirty-eight candidates, among which three CpG sites, ITGA2B_1, NPTX2_3, and NPTX2_4 were never reported in previous studies. We fit a linear regression model for age prediction based on methylation assay for 89 blood samples from donors aged 9-75 years old. The model included four AR-CpG markers in three gene fragments ASPA, ITGA2B and NPTX2 and enabled the age prediction with R2=0.819. The mean absolute deviation (MAD) from chronological age of the model was 7.870. We validated the linear regression model with a validation set of 40 blood samples, and the prediction MAD was 7.986. There was no statistically significant difference in age prediction between 20 pairs of blood samples and bloodstains. Six pairs of fresh and old bloodstains were analyzed using our assay. The obtained results showed the assay still performed an effective prediction on bloodstains after four-month storage in room conditions. This study indicates that our DNA methylation assay is a reliable and effective method for age prediction for forensic purposes.
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Evaluation of the RapidHIT™ 200 System: A comparative study of its performance with Maxwell® DNA IQTM/Identifiler® Plus/ABI 3500xL Workflow  Available online 8 May 2015

RapidHITTM System is a rapid DNA instrument that is capable of processing forensic samples from extraction through to capillary electrophoresis and profile generation within two hours. Evaluation of the RapidHITTM 200 System was conducted to examine several key performance indicators of the instrument, including reproducibility, contamination, sensitivity, versatility and the possibility of sample re-extraction. Results indicated that the RapidHITTM 200 System was capable of generating high quality DNA profiles which were comparable to those from the standard protocol comprising of Maxwell® 16 DNA IQTM System, Identifiler® Plus and ABI 3500xL. No contamination was detected during the studies. Results also showed that the instrument was able to generate DNA profiles from samples containing lower amounts of DNA (0.5 μl of blood) albeit with more allele and locus dropouts when compared to the standard protocol. The ability to process blood swabs, blood-stained FTA punches, semen swabs, buccal swabs, product of conception (POC), bone marrow, fingernail clippings and cigarette butts at a good success rate indicated the robustness and versatility of the RapidHITTM 200 System. Furthermore, additional alleles could be recovered via re-analysis of the failed samples using the standard protocol. In summary, our results showed that the RapidHITTM 200 System was able to process casework samples for the purpose of providing rapid intelligence through DNA database searches and reference matching. Confirmative DNA results can be obtained through either concurrent processing of duplicate samples via standard protocol or re-extraction of samples retrieved from the RapidHITTM sample cartridge.
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Allele frequencies of 20 autosomal STR in the population from Rio Grande do Sul Southern Brazil  Available online 7 May 2015

One of the solutions applied by most of the forensic experts – when faced
with unsolved cases of genetic reconstruction of deceased or missing persons
using only recommended loci by CODIS or by any other genetic databases system
– is to include a larger number of DNA regions [1]. When genetic mutations occur
between parents and progeny, by addition or deletion of repeating units in the
regions of occurrence of STR, the occurrence of null alleles or even single-parent
paternity cases, increasing the number of genetic markers, can also assist in
solving cases of paternity/maternity or any genetic link type[2].
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Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing Available online 6 May 2015
Long an important and useful tool in forensic genetic investigations, mitochondrial DNA (mtDNA) typing continues to mature. Research in the last few years has demonstrated both that data from the entire molecule will have practical benefits in forensic DNA casework, and that massively parallel sequencing (MPS) methods will make full mitochondrial genome (mtGenome) sequencing of forensic specimens feasible and cost-effective. A spate of recent studies has employed these new technologies to assess intraindividual mtDNA variation. However, in several instances, contamination and other sources of mixed mtDNA data have been erroneously identified as heteroplasmy. Wellvetted mtGenome datasets based on both Sanger and MPS sequences have found authentic point heteroplasmy in approximately 25% of individuals when minor component detection thresholds are in the range of 10-20%, along with positional distribution patterns in the coding region that differ from patterns of point heteroplasmy in the well-studied control region. A few recent studies that examined very low-level heteroplasmy are concordant with these observations when the data are examined at a common level of resolution. In this review we provide an overview of considerations related to the use of MPS technologies to detect mtDNA heteroplasmy. In addition, we examine published reports on point heteroplasmy to characterize features of the data that will assist in the evaluation of future mtGenome data developed by any typing method.
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Developmental Validation of the ParaDNA® Intelligence System—A novel approach to DNA profiling  Available online 6 May 2015

DNA profiling through the analysis of STRs remains one of the most widely used tools inhuman identification across the world. Current laboratory STR analysis is slow, costly and requiresexpert users and interpretation which can lead to instances of delayed investigations or non-testing of evidence on budget grounds. The ParaDNA® Intelligence System has been designed to provide asimple, fast and robust way to profile DNA samples in a lab or field-deployable manner. The System analyses 5-STRs plus amelogenin to deliver a DNA profile that enables users to gain rapid investigative leads and intelligent prioritisation of samples in human identity testing applications. Utilising an innovative sample collector, minimal training is required to enable both DNA analysts and nonspecialist personnel to analyse biological samples directly, without prior processing, in approximately 75 minutes. The test uses direct PCR with fluorescent HyBeacon® detection of STR allele lengths to provide a DNA profile. The developmental validation study described here followed the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines and tested the sensitivity, reproducibility, accuracy, inhibitor tolerance, and performance of the ParaDNA Intelligence System on a range of mock evidence items. The data collected demonstrate that the ParaDNA Intelligence System displays useful DNA profiles when sampling a variety of evidence items including blood, saliva, semen and touch DNA items indicating the potential to benefit a number of applications in fields such as forensic, military and disaster victim identification (DVI).
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Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application

Routine use of massively parallel sequencing (MPS) for forensic genomics is on the horizon. The last few years, several algorithms and workflows have been developed to analyze forensic MPS data. However, none have yet been tailored to the needs of the forensic analyst who does not possess an extensive bioinformatics background.

We developed our previously published forensic MPS data analysis framework MyFLq (My-Forensic-Loci-queries) into an open-source, user-friendly, web-based application. It can be installed as a standalone web application, or run directly from the Illumina BaseSpace environment. In the former, laboratories can keep their data on-site, while in the latter, data from forensic samples that are sequenced on an Illumina sequencer can be uploaded to Basespace during acquisition, and can subsequently be analyzed using the published MyFLq BaseSpace application. Additional features were implemented such as an interactive graphical report of the results, an interactive threshold selection bar, and an allele length-based analysis in addition to the sequenced-based analysis.
Practical use of the application is demonstrated through the analysis of four 16-plex short tandem repeat (STR) samples, showing the complementarity between the sequence- and length-based analysis of the same MPS data.
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Development of a forensically useful age prediction method based on DNA methylation analysis Available online 5 May 2015
Forensic DNA phenotyping needs to be supplemented with age prediction to become a relevant source of information on human appearance. Recent progress in analysis of the human methylome has enabled selection of multiple candidate loci showing linear correlation with chronological age. Practical application in forensic science depends on successful validation of these potential age predictors. In this study, eight DNA methylation candidate loci were analysed using convenient and reliable pyrosequencing technology. A total number of 41CpG sites was investigated in 420 samples collected from men and women aged from 2 to 75 years. The study confirmed correlation of all the investigated markers with human age. The five most significantly correlated CpG sites in ELOVL2 on 6p24.2, C1orf132 on 1q32.2, TRIM59 on 3q25.33, KLF14 on 7q32.3 and FHL2 on 2q12.2 were chosen to build a prediction model. This restriction allowed the technical analysis to be simplified without lowering the prediction accuracy significantly. Model parameters for a discovery set of 300 samples were R2 = 0.94 and the standard error of the estimate = 4.5 years. An independent set of 120 samples was used to test the model performance. Mean absolute deviation for this testing set was 3.9 years. The number of correct predictions ±5 years achieved a very high level of 86.7% in the age category 2-19 and gradually decreased to 50% in the age category 60-75. The prediction model was deterministic for individuals belonging to these two extreme age categories. The developed method was implemented in a freely available online age prediction calculator.
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Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™  Volume 17, July 2015, Pages 110–121
Next generation sequencing (NGS) offers the opportunity to analyse forensic DNA samples and obtain massively parallel coverage of targeted short sequences with the variants they carry. We evaluated the levels of sequence coverage, genotyping precision, sensitivity and mixed DNA patterns of a prototype version of the first commercial forensic NGS kit: the HID-Ion AmpliSeq™ Identity Panel with 169-markers designed for the Ion PGM™ system. Evaluations were made between three laboratories following closely matched Ion PGM™ protocols and a simple validation framework of shared DNA controls. The sequence coverage obtained was extensive for the bulk of SNPs targeted by the HID-Ion AmpliSeq™ Identity Panel. Sensitivity studies showed 90–95% of SNP genotypes could be obtained from 25 to 100 pg of input DNA. Genotyping concordance tests included Coriell cell-line control DNA analyses checked against whole-genome sequencing data from 1000 Genomes and Complete Genomics, indicating a very high concordance rate of 99.8%. Discordant genotypes detected in rs1979255, rs1004357, rs938283, rs2032597 and rs2399332 indicate these loci should be excluded from the panel. Therefore, the HID-Ion AmpliSeq™ Identity Panel and Ion PGM™ system provide a sensitive and accurate forensic SNP genotyping assay. However, low-level DNA produced much more varied sequence coverage and in forensic use the Ion PGM™ system will require careful calibration of the total samples loaded per chip to preserve the genotyping reliability seen in routine forensic DNA. Furthermore, assessments of mixed DNA indicate the user’s control of sequence analysis parameter settings is necessary to ensure mixtures are detected robustly. Given the sensitivity of Ion PGM™, this aspect of forensic genotyping requires further optimisation before massively parallel sequencing is applied to routine casework.
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Genetic structure and forensic parameters of 38 Indels for human identification purposes in eight Mexican populations  Available online 2 May 2015
Insertion-deletions for human identification purposes (HID-Indels) offer advantages to solve particular forensic situations and complex paternity cases. In Mexico, admixed population known as Mestizos is the largest (∼90 %), plus a number of Amerindian groups (∼ 10%), which have not been studied with HID-Indels. For this reason, allele frequencies and forensic parameters for 38HID-Indels were estimated in 531 unrelated individuals from one Amerindian (Purépecha) and seven Mestizo populations from different regions of the country. Genotype distribution was in agreement with Hardy-Weinberg expectations in almost all loci/populations. The linkage disequilibrium (LD) test did not reveal possible associations between loci pairs in all eight Mexican populations. The combined power of discrimination was high in all populations (PD > 99.99999999998%). However, the power of exclusion of the 38HID-Indel system (PE > 99.6863%) was reduced regarding most of autosomal STR kits. The assessment of genetic structure (AMOVA) and relationships between populations (FST) demonstrated significant differences among Mexican populations, mainly of the Purépecha Amerindian group. Among Mexican-Mestizos, three population clusters consistent with geography were defined: i) North-West region: Chihuahua, Sinaloa, and Jalisco; ii) Central-Southern region: Mexico City, Veracruz and Yucatan; iii) South region: Chiapas. In brief, this report validates the inclusion of the 38HID-Indel system in forensic casework and paternity cases in seven Mexican-Mestizo populations from different regions, and in one Mexican Amerindian group.
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Assessing the impact of common forensic presumptive tests on the ability to obtain results using a novel rapid DNA platform  Volume 17, July 2015, Pages 87–90
The rise of DNA evidence to the forefront of forensic science has led to high sample numbers being submitted for profiling by investigators to casework laboratories: bottleneck effects are often seen resulting in slow turnaround times and sample backlog. The ParaDNA® Screening and Intelligence Tests have been designed to guide investigators on the viability of potential sources of DNA allowing them to determine which samples should be sent for full DNA analysis. Both tests are designed to augment the arsenal of available forensic tests for end users and be used concurrently to those commonly available. Therefore, assessing the impact that common forensic tests have on such novel technology is important to measure. The systems were tested against various potential inhibitors to which samples may be exposed as part of the investigative process. Presumptive test agents for biological materials (blood, semen and saliva) and those used as fingerprint enhancement agents were both used. The Screening Test showed a drop in performance following application of aluminium powder and cyanoacrylate (CNA) on fingerprints samples; however this drop in performance was not replicated with high template DNA. No significant effect was observed for any agent using the Intelligence Test. Therefore, both tests stand up well to the chemical agents applied and can be used by investigators with confidence that system performance will be maintained.
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Rapid Processing of Casework and Reference DNA Samples Using Standard Protocols

Kutranov, S. et al. Rapid Processing of Casework and Reference DNA Samples Using Standard Protocols. Promega Corporation Web site. http://au.promega.com/resources/profiles-in-dna/2015/rapid-processing-of-casework-and-reference-dna-samples-using-standardprotocols/
Updated 2015.

In this article, we demonstrate the use of the PowerPlex® ESX 17 Fast System to rapidly process casework and reference DNA samples in an operational forensic DNA laboratory using the manufacturer’s recommended protocols.   Reference samples included buccal cells on FTA® cards, OmniSwab™ buccal scrapes and cotton swab buccal scrapes. FTA® samples were amplified directly in half-volume (12.5µl) and full-volume (25µl) reactions. Swabs were pretreated with SwabSolution™ Reagent prior to amplification. The total time from sample to analysis for 21 FTA® card punches, in duplicate, or 21 buccal swabs (including time to process swabs with SwabSolution™ Reagent) and PCR controls was 2 hours and 30 minutes. Casework samples were chosen from a batch processed the previous day using the laboratory’s standard procedures. Amplification required approximately 55 minutes.

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Reference Manual on Scientific Evidence: Third Edition (2011)

National Academies Press  ISBN: 978-0-309-21421-6

The Reference Manual on Scientific Evidence, Third Edition, assists judges in managing cases involving complex scientific and technical evidence by describing the basic tenets of key scientific fields from which legal evidence is typically derived and by providing examples of cases in which that evidence has been used.

First published in 1994 by the Federal Judicial Center, the Reference Manual on Scientific Evidence has been relied upon in the legal and academic communities and is often cited by various courts and others. Judges faced with disputes over the admissibility of scientific and technical evidence refer to the manual to help them better understand and evaluate the relevance, reliability and usefulness of the evidence being proffered. The manual is not intended to tell judges what is good science and what is not. Instead, it serves to help judges identify issues on which experts are likely to differ and to guide the inquiry of the court in seeking an informed resolution of the conflict.

The core of the manual consists of a series of chapters (reference guides) on various scientific topics, each authored by an expert in that field. The topics have been chosen by an oversight committee because of their complexity and frequency in litigation. Each chapter is intended to provide a general overview of the topic in lay terms, identifying issues that will be useful to judges and others in the legal profession. They are written for a non-technical audience and are not intended as exhaustive presentations of the topic. Rather, the chapters seek to provide judges with the basic information in an area of science, to allow them to have an informed conversation with the experts and attorneys.

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Differentiating between monozygotic twins through DNA methylation-specific high-resolution melt curve analysis

Analytical Biochemistry Available online 10 February 2015;  doi:10.1016/j.ab.2015.02.001

Although short tandem repeat profiling is extremely powerful in identifying individuals from crime scene stains, it is unable to differentiate between monozygotic (MZ) twins. Efforts to address this include mutation analysis through whole genome sequencing and through DNA methylation studies. Methylation of DNA is affected by environmental factors; thus, as MZ twins age, their DNA methylation patterns change. This can be characterized by bisulfite treatment followed by pyrosequencing. However, this can be time-consuming and expensive; thus, it is unlikely to be widely used by investigators. If the sequences are different, then in theory the melting temperature should be different. Thus, the aim of this study was to assess whether high-resolution melt curve analysis can be used to differentiate between MZ twins. Five sets of MZ twins provided buccal swabs that underwent extraction, quantification, bisulfite treatment, polymerase chain reaction amplification and high-resolution melting curve analysis targeting two markers, Alu-E2F3 and Alu-SP. Significant differences were observed between all MZ twins targeting Alu-E2F3 and in four of five MZ twins targeting Alu-SP (P < 0.05). Thus, it has been demonstrated that bisulfite treatment followed by high-resolution melting curve analysis could be used to differentiate between MZ twins.

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Case of the month – Academic Forensic Pathology

*Please click on the title link to request a copy of the article* (QH staff only)

Volume 5, number 1. March 2015

Acute coronary artery thrombosis associated with synthetic cannabinoid intoxication / Stephanie A. Dean [et al…]

Postmortem diagnosis of primary small bowel volvulus in an adult / F. Garavan & H. Hameed

 Beyond the boundaries of forensic toxicology – the use of an atypical consultant in a rare case of cerberin poisoning / E. R. Severson [et al…]

Homicide versus hypothermia? An unusual case of hypothermia related to colloid cyst of the third ventricle / E. J. Schafer & J. A. Prahlow

The importance of genetic testing in a case of sudden death in hypertrophic cardiomyopathy due to troponin I mutation / Vivian Snyder [et al…]

 

Forensic intelligence: articles from Australian Journal of Forensic Sciences Volume 47, Issue 1, 2015

Forensic intelligence: commentary

The term ‘forensic intelligence’ and the benefits it brings do seem somewhat axiomatic; however, my perspective on this has evolved from my time as a police director of intelligence and a scientific support manager, followed by six years as the UK Forensic Science Regulator (for details of the role see http://www.gov.uk/government/organisations/forensic-science-regulator). Having lived through the introduction of the UK national intelligence model I have seen at first hand the benefits of well modelled intelligence strategies and systems. I have long believed that forensic practitioners and methods, both within the police and their supporting forensic science laboratories, have endless potential to feed timely and accurate information into the investigation and detection of crime at all stages of the process. The police objective of community safety is achieved through a range of actions that, in modern policing, involves much more than crime investigation and detection. We have learnt the benefits of proactive approaches that feed into and from intelligence that is focused and timely. Sadly, though, forensic science has remained largely a reactive tool that is deployed after the event and in support of a particular investigation. This series of papers seeks to change this paradigm and is to be applauded for the visionary use of forensic science as an intelligence tool that breaks free from the traditional reactive model.
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Introduction

Intelligence began as a military tool and has been in practice for centuries. David Kuhn1 refers to Sun Tzu who is credited with writing ‘The Art of War’ in the sixth century AD and quotes Tzu as saying:
Now the reason the enlightened prince and the wise general conquer the enemy wherever they move and their achievements surpass those of ordinary men is foreknowledge.
Intelligence has also been a law enforcement tool over many years. References date back to policing practices in the time of Louis XIV of France (1667) and Thames policing in the UK in the eighteenth century. David L. Carter2 refers to law enforcement intelligence units in US police forces in the 1920s producing dossiers on known criminals as early forms of the tool and there are many other examples through history.
The production and use of intelligence from a forensic science perspective is more recent again. It was brought into focus through a study ‘Using Forensic Science Effectively’ by the Association of Chief Police Officers (ACPO) and the Forensic Science Service (FSS)3 in 1996. This was at a time when the DNA database was being established in the UK.
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Elements of a forensic intelligence model

Intelligence began as a military tool and has been in practice for centuries. Relatively speaking, forensic intelligence is in its infancy as the focus of forensic science has traditionally been the courts and the resolution of crime. The focus for forensic intelligence is crime prevention, crime disruption and a reduced fear of crime and there is an emphasis on quick results. The usual chronic backlogs that haunt forensic science prevent quick results and so the default position is courts and crime resolution. However, in a number of jurisdictions in Australia, the introduction of at-scene or on-submission triaging and the digital capture, transmission and comparison of fingerprints is leading to a marked reduction in turnaround times for forensic science results; particularly those that are effective sources of intelligence. Aspects of forensic science service delivery such as organisational structure and culture, IT capability, the relationship between police and scientists and interim reporting need to be re-considered as key elements in a forensic intelligence model. However, forensic intelligence should not stand on its own. It should become an integral part of the overall investigative tool and intelligence-led strategies.
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The landscape of forensic intelligence research

Criminology, forensic science and policing scholars have a significant role to play in exploring new developments and directions in modern policing. Yet while the concept of forensic intelligence has caught the attention of a number of policing agencies around the world, it has yet to become a mainstream undertaking. In part this is an artefact of a pragmatic policing culture that only institutes new practices based on demonstrable, research and practice-based effectiveness. Here, we seek to draw attention to efforts in the scholarly community to accumulate a body of evidence on the efficacy of forensic intelligence. The article describes the international landscape of research pertaining to the development of forensic intelligence. We outline the key use of digitised, triangulated data on biometrics, scene of crime and illicit substances. In doing so, we draw attention to the challenges remaining for scholars and professionals to further understand and advance the use of forensic intelligence in mainstream policing.
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Forensic informatics enabling forensic intelligence

The utility of forensic informatics gained momentum in Queensland over a decade ago and was instrumental in identifying leakage points in forensic performance, the removal of backlogs and the provision of real-time feedback to forensic practitioners and investigating police. This paper provides insight into the evolution of forensic practice in Queensland, highlighting both the organisational challenges and the information system architecture, which established workflows tailored to the timely production of forensic intelligence to reduce, disrupt and prevent crime.
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Forensic data exchange: ensuring integrity

A growing chorus of forensic professionals believe that forensic science has undersold its potential contribution to crime reduction and has a more significant role to play in policing, with collation and analysis of forensic information used to inform policing tactics, operations or strategy. Domestic law enforcement agencies, as producers, consumers and purveyors of forensic information and intelligence, are also responding to political pressures to expand and accelerate their technological abilities to gather and disseminate forensic information and intelligence within expanding operational boundaries.
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Education and training in forensic intelligence: a new challenge

From recent calls for positioning forensic scientists within the criminal justice system, but also policing and intelligence missions, this paper emphasises the need for the development of educational and training programmes in the area of forensic intelligence. It is argued that an imbalance exists between perceived and actual understanding of forensic intelligence by police and forensic science managers, and that this imbalance can only be overcome through education. The challenge for forensic intelligence education and training is therefore to devise programmes that increase forensic intelligence awareness, firstly for managers to help prevent poor decisions on how to develop information processing. Two recent European courses are presented as examples of education offerings, along with lessons learned and suggested paths forward. It is concluded that the new focus on forensic intelligence could restore a pro-active approach to forensic science, better quantify its efficiency and let it get more involved in investigative and managerial decisions. A new educational challenge is opened to forensic science university programmes around the world: to refocus criminal trace analysis on a more holistic security problem solving approach.
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Forensic intelligence: deregulation or return to the roots of forensic science?

This paper presents an overview of forensic intelligence through historical, operational and academic considerations. While forensic intelligence is thriving through new traceability of human activities, theoretical developments in policing and innovative technologies, it should mainly be seen as an opportunity for forensic science to contribute to making policing more ‘scientific’ in the broad sense. This paper supports the development of a modern framework to holistically use the information conveyed by forensic case data to inform policing processes, support decision-making and ensure transparency. It is argued that the scientific information, the trace, has to be privileged, rather than rejected from current debates, despite the potential fears prompted by the misinterpretation of the term ‘intelligence’. Ultimately, forensic intelligence enables the emergence of a modern conception of forensic science.
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The applied use of forensic intelligence for community and organised crime

This paper describes the implementation of Forensic Intelligence (FORINT) practices over a two-year period within the Australian Federal Police. As an example of this, it looks at FORINT as applied to community crime within the capital city of Canberra and an innovative FORINT approach to combatting the use of the parcel post system by organised crime to import illicit goods into Australia. The paper explores the optimal environment required to enable FORINT to survive and thrive within a policing and forensic laboratory context.
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