Classification of firing pin impressions using HOG-SVM.

Crimes, such as robbery and murder, often involve firearms. In order to assist with the investigation into the crime, firearm examiners are asked to determine whether cartridge cases found at a crime scene had been fired from a suspect's firearm. This examination is based on a comparison of the marks left on the surfaces of cartridge cases.

A comprehensive study into false positive rates for 'other' biological samples using common presumptive testing methods.

The identification of biological fluids or materials in forensic samples is a key requirement in forensic science that relies on chemical and biological based tests, most of which exhibit false positivity. When reporting results from such tests, Forensic Scientists use words such as probable, possible, and likely, without always being able to provide robust support for these conclusions. In collating information about false positive rates for a number of these tests, we found limited research into the cross reactions observed from 'other' biological samples in commonly encountered case sample stains.

On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime.

Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time.

Compatibility of the ForenSeq™ DNA Signature Prep Kit with laser microdissected cells: An exploration of issues that arise with samples containing low cell numbers.

Massively parallel sequencing is rapidly emerging as a valuable tool in forensic DNA analyses. As part of our validation of this technology, we established its compatibility with a laser microdissection cell collection method including a one-tube DNA extraction process. We also used the laser microdissector to explore the number of cells required to generate informative DNA sequence profiles and establish the limitations of the technology.

Forensic STR allele extraction using a machine learning paradigm.

We present a machine learning approach to short tandem repeat (STR) sequence detection and extraction from massively parallel sequencing data called Fragsifier. Using this approach, STRs are detected on each read by first locating the longest repeat stretches followed by locus prediction using k-mers in a machine learning sequence model. This is followed by reference flanking sequence alignment to determine precise STR boundaries.

Evaluation of massively parallel sequencing for forensic DNA methylation profiling.

Epigenetics is an emerging area of interest in forensic science. DNA methylation, a type of epigenetic modification, can be applied to chronological age estimation, identical twin differentiation and body fluid identification. However, there is not yet an agreed, established methodology for targeted detection and analysis of DNA methylation markers in forensic research.

A review of bioinformatic methods for forensic DNA analyses.

Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data.

The development of a method of suspension RNA-FISH for forensically relevant epithelial cells using LNA probes.

Messenger RNA profiling is becoming a common method for body fluid identification in forensic science but there are disadvantages when cell mixtures are present from more than one individual. A method that could identify and separate such cell mixtures would simplify downstream analysis. To do this, we have developed a novel method of RNA suspension-fluorescent in situ hybridization (RNA S-FISH) using a locked nucleic acid (LNA) probe for the keratin 10 (KRT10) mRNA that is suitable as a potential marker for epithelial cells.

A time-course analysis of mRNA expression during injury healing in human dermal injuries.

The determination of dermal injury age is important in forensic practice. It helps answer questions that are important to an investigation such as the timing of the injury and incident, the order of infliction (where there is more than one injury), the survival time after injury (post-infliction interval) and the relation of the injury to the incident. Despite the importance of injury age determination, there currently exists no reliable method to estimate dermal injury age.

SNP model development for the prediction of eye colour in New Zealand.

The ability to predict externally visible characteristics (EVCs) from DNA has appeal for use in forensic science, particularly where a forensic database match is not made and an eye witness account is unavailable. This technology has yet to be implemented in casework in New Zealand. The broad cultural diversity and likely population stratification within New Zealand dictates that any EVC predictions made using anonymous DNA must perform accurately in the absence of knowledge of the donor's ancestral background.

Detection of target-probe oligonucleotide hybridization using synthetic nanopore resistive pulse sensing.

Despite the plethora of DNA sensor platforms available, a portable, sensitive, selective and economic sensor able to rival current fluorescence-based techniques would find use in many applications. In this research, probe oligonucleotide-grafted particles are used to detect target DNA in solution through a resistive pulse nanopore detection technique. Using carbodiimide chemistry, functionalized probe DNA strands are attached to carboxylated dextran-based magnetic particles.

Development of an electrochemical polypyrrole-based DNA sensor and subsequent studies on the effects of probe and target length on performance.

DNA sensors have a wide scope of applications in the present and emerging medical and scientific fields, such as medical diagnostics and forensic investigations. However, much research-to-date on DNA sensor development has focused on short target DNA strands as model genes. In this communication we study the effect of the length of oligonucleotide probe and target strands as a significant step towards real world applications for DNA detection.

A comparison of stochastic variation in mixed and unmixed casework and synthetic samples.

Understanding the behaviour of mixed DNA profiles is of paramount importance in forensic DNA analysis. Key parameters are those of heterozygote balance and mixture proportion and its variability. These parameters have been previously explored as a function of the average peak height of the active alleles in single source and mixed samples derived from pristine DNA.

Characterising stutter in forensic STR multiplexes.

Stutter is an artefact seen when amplifying short tandem repeats and typically occurs at one repeat unit shorter in length than the parent allele. In forensic analysis, stutter complicates the analysis of DNA profiles from multiple contributors, known as mixed profiles, a common profile type. Consequently it is important to both understand and predict stutter behaviour in order to improve our understanding of the resolution and interpretation of these profiles.

The effect of cleaning agents on the ability to obtain DNA profiles using the Identifiler™ and PowerPlex® Y multiplex kits.

A year after the introduction of Identifiler™ into the forensic DNA laboratories of the Institute of Environmental Science and Research Limited (ESR), increasing occurrences of dropout of the three loci, D7S820, D18S51, and FGA, were observed in samples where the DNA was not degraded and sufficient DNA was present that full DNA profiles were to be expected. The dropout was either partial or complete at these loci. Full profiles could sometimes be obtained by reamplification of samples using the same input amount of DNA.

The use of bacteria for the identification of vaginal secretions.

We have used the 16S-23S rRNA intergenic spacer region for identifying vaginal specific bacteria. Lactobacillus crispatus and Lactobacillus gasseri were detected in vaginal secretions but not in semen, blood or saliva. Our data indicated that both L.

A method for DNA and RNA co-extraction for use on forensic samples using the Promega DNA IQ™ system.

The use of messenger RNA profiling to identify the origin of biological samples (e.g. blood, semen and saliva) from crime scenes is now at the stage of being implemented into routine forensic casework.

The development of a mRNA multiplex RT-PCR assay for the definitive identification of body fluids.

With current methodology, DNA profiling can identify an individual from a sample of biological material but it does not reveal what body fluid or tissue source the DNA profile originated from. We have developed a multiplex PCR system using messenger RNA (mRNA) that can identify blood, saliva, semen and menstrual blood in individual stains or in mixtures of body fluids. Messenger RNA transcripts specific to each type of body fluid have been identified and a multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) system developed to identify these body fluids along with three housekeeping genes.

Y STR haplotype data for New Zealand population groups using the Y-Plex 6 kit.

Allele and haplotype frequencies were obtained for the six Y STR loci DYS19, DYS389II, DYS390, DYS391, DYS393 and DYS385 in the New Zealand population. Ninety-two different haplotypes were found. The Maori population had a specific haplotype that occurred in over 30% of the population.

Rapid enumeration of Listeria monocytogenes in artificially contaminated cabbage using real-time polymerase chain reaction.

A quantitative real-time polymerase chain reaction (PCR) detection method specific for Listeria monocytogenes was developed, and studies involving pure culture showed that the response of the assay was linear over 7 log10 (log) cycles. The method was then applied to the detection of L. monocytogenes artificially inoculated onto cabbage, a vegetable chosen because it is a major component of coleslaw, which has been associated with an outbreak of listeriosis.