ORCID Profile
0000-0003-0633-7424
Current Organisations
Forensic Science SA
,
Flinders University
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Publisher: Elsevier BV
Date: 09-2023
Publisher: Elsevier BV
Date: 09-2023
Publisher: Wiley
Date: 14-07-2015
Abstract: We report on successful lification of canine STR DNA profiles from single dog hairs. Dog hairs are commonly found on clothing or items of interest in forensic casework and may be crucial associative evidence if linked to an in idual dog. We used direct lification from these hairs to increase the DNA yield of the s le, as well as greatly reducing analysis time. Hairs from different somatic regions were used from several different dog breeds to lify a selection of eight loci from the validated DogFiler multiplex. Naturally shed canine hairs were processed, with a mix of coarse topcoat (guard) hairs and thinner soft undercoat hairs. Multiple sections of single hairs were lified in 5 mm segments to determine the viability of DNA recovery from the shaft of the hair. Single guard hairs were cut into 5 mm sections and added directly into a PCR tube. Undercoat hairs, which are very fine, were lified together in a single tube (approximately ten small hairs). Coarse hairs were found to be the most successful in producing full DNA profiles at all eight loci, matching the corresponding reference profile for that dog.
Publisher: Elsevier BV
Date: 11-2017
DOI: 10.1016/J.FSIGEN.2017.09.002
Abstract: The introduction of probabilistic DNA interpretation systems has made it possible to evaluate many profiles that previously (under a manual interpretation system) were not. These probabilistic systems have been around for a number of years and it is becoming more common that their use within a laboratory has spanned at least one technology change. This may be a change in laboratory hardware, the DNA profiling kit used, or the manner in which the profile is generated. Up until this point, when replicates DNA profiles are generated, that span a technological change, the ability to utilise all the information in all replicates has been limited or non-existent. In this work we explain and derive the models required to evaluate (what we term) multi-kit analysis problems. We demonstrate the use of the multi-kit feature on a number of scenarios where such an analysis would be desired within a laboratory. Allowing the combination of profiling data that spans a technological change will further increase the amount of DNA profile information produced in a laboratory that can be evaluated.
Publisher: Elsevier BV
Date: 11-2020
Publisher: Wiley
Date: 02-10-2014
Abstract: Forward stutter, or over stutter, one repeat unit length larger than the parent allele (N + 1 stutter), is a relatively rare product of the PCR lification of STRs used in forensic DNA analysis. We have investigated possible explanatory variables for the occurrence and size of forward stutter for four different autosomal multiplexes. In addition, we have investigated models used to predict the expected heights of forward stutter. For all tetra and penta-nucleotide repeats we can find no correlation between allelic peak height, marker, or longest uninterrupted sequence in the allele. The data fit a gamma distribution with no explanatory variables. For the single trinucleotide repeat present in two of the four multiplexes (D22S1045) forward stutter is much more common and the best explanatory variable appears to be back stutter height. This suggests some fundamental cocausation of high backward and forward stutter for this locus.
Publisher: Elsevier BV
Date: 09-2020
Publisher: Elsevier BV
Date: 05-2020
Publisher: Elsevier BV
Date: 07-2016
DOI: 10.1016/J.FSIGEN.2016.02.011
Abstract: Advances in technology to both generate and interpret DNA profiles has seen the expansion of the ability to provide opinions about results obtained from very low levels of starting biological material. The response in court has been to question the mode by which the DNA came to be on an item, rather than questioning its presence. This brings into play a number of real-world aspects such as transfer of biological material, persistence of biological material on items, shedding ability of in iduals, just to name a few. There have been a number of studies that investigate different aspects relating the mode of DNA deposition and transfer, mostly under tightly controlled conditions. We add to this knowledge pool by investigating the extent to which in iduals at Forensic Science SA (FSSA) deposit their DNA on objects throughout the floor of the building where DNA examinations take place. We find that the results obtained in our minimally controlled study allow us to comment on a number of published concepts.
Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.FSIGEN.2018.10.019
Abstract: Previous work has shown that artificial neural networks can be used to classify signal in an electropherogram into categories that have interpretational meaning (such as allele, baseline, pull-up or stutter). The previous work trained the neural networks on a single data type, produced under a single laboratory condition and applied it to data that was matched in these factors. In this work we investigate the ability of neural networks to be trained on data of different types (i.e. single sourced profiles or mixed DNA profiles) and from different laboratory conditions (specifically the model of electrophoresis instrument) to determine whether a set of neural networks is required for each different type of data produced or whether a single neural network can be used for a broad range of data and still achieve the same level of performance. The results of our study have implications as to how a laboratory would choose to train and apply neural networks to classify data in electropherograms produced in their laboratory.
Publisher: Frontiers Media SA
Date: 12-12-2016
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.FSIGEN.2013.12.001
Abstract: 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 s le could only be searched for in a database of in iduals 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 s les 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 s les that were previously unsuitable for database comparison. We show that effective management of the selection of s les for searching and the interpretation of the output can be highly informative.
Publisher: Elsevier BV
Date: 03-2016
DOI: 10.1016/J.FSIGEN.2015.12.009
Abstract: In forensic DNA analysis a DNA extract is lified using polymerase chain reaction (PCR), separated using capillary electrophoresis and the resulting DNA products are detected using fluorescence. S ling variation occurs when the DNA molecules are aliquotted during the PCR setup stage and this translates to variability in peak heights in the resultant electropherogram or between electropherograms generated from a DNA extract. Beyond the variability caused by s ling variation it has been observed that there are factors in generating the DNA profile that can contribute to the magnitude of variability observed, most notably the number of PCR cycles. In this study we investigate a number of factors in the generation of a DNA profile to determine which contribute to levels of peak height variability.
Publisher: Elsevier BV
Date: 2013
Publisher: Wiley
Date: 06-08-2015
Abstract: The interpretation of complex DNA profiles is facilitated by a Bayesian approach. This approach requires the development of a pair of propositions: one aligned to the prosecution case and one to the defense case. This note explores the issue of proposition setting in an adversarial environment by a series of ex les. A set of guidelines generalize how to formulate propositions when there is a single person of interest and when there are multiple in iduals of interest. Additional explanations cover how to handle multiple defense propositions, relatives, and the transition from subsource level to activity level propositions. The propositions depend on case information and the allegations of each of the parties. The prosecution proposition is usually known. The authors suggest that a sensible proposition is selected for the defense that is consistent with their stance, if available, and consistent with a realistic defense if their position is not known.
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.FSIGEN.2017.12.006
Abstract: The hierarchy of propositions has been accepted amongst the forensic science community for some time. It is also accepted that the higher up the hierarchy the propositions are, against which the scientist are competent to evaluate their results, the more directly useful the testimony will be to the court. Because each case represents a unique set of circumstances and findings, it is difficult to come up with a standard structure for evaluation. One common tool that assists in this task is Bayesian networks (BNs). There is much ersity in the way that BN can be constructed. In this work, we develop a template for BN construction that allows sufficient flexibility to address most cases, but enough commonality and structure that the flow of information in the BN is readily recognised at a glance. We provide seven steps that can be used to construct BNs within this structure and demonstrate how they can be applied, using a case ex le.
Publisher: Informa UK Limited
Date: 18-11-2019
Publisher: Wiley
Date: 22-09-2021
Abstract: Likelihood ratios ( LR ) differences between the probabilistic genotyping software EuroForMix and STRmix™ are examined. After considering differences in the allele probabilities, the LRs from both software for an unambiguous single‐source profile were identical (four significant figures). LRs from both software for an unambiguous single‐source profile with alleles previously unseen in the allele frequency database (rare alleles) were the same (three significant figures) for θ = 0.01. Due to differences in the minimum allele frequencies, the LR s differed by three orders of magnitude when θ = 0. For both software, the LR s for a single‐source dilution series decreased as the input amount decreased. The LR s from both software were within an order of magnitude for known contributors. The largest difference was where the target input amount was 0.0156 ng: The LR EuroForMix was 2.1 × 10 25 and the LR STRmix was 8.0 × 10 24 . Both software show similar LR behavior with respect to mixture ratio. For two person mixtures the LR increases for both the major and the minor as the ratio moves away from 1:1. The LR for the major stabilizes at about 3:1 whereas the LR for the minor reaches its maximum at about 3:1 and then declines. Greater differences in LR were observed between EuroForMix and STRmix™ for mixtures. One‐hundred and twenty‐nine mixtures from the PROVEDIt dataset were compared. LR s for 84% of the comparisons for known contributors without rare alleles were within two orders of magnitude. Five ergent results were investigated, and a manual intervention approach was applied where appropriate.
Publisher: Elsevier BV
Date: 09-2017
DOI: 10.1016/J.FSIGEN.2017.07.002
Abstract: Electropherograms are produced in great numbers in forensic DNA laboratories as part of everyday criminal casework. Before the results of these electropherograms can be used they must be scrutinised by analysts to determine what the identified data tells them about the underlying DNA sequences and what is purely an artefact of the DNA profiling process. This process of interpreting the electropherograms can be time consuming and is prone to subjective differences between analysts. Recently it was demonstrated that artificial neural networks could be used to classify information within an electropherogram as allelic (i.e. representative of a DNA fragment present in the DNA extract) or as one of several different categories of artefactual fluorescence that arise as a result of generating an electropherogram. We extend that work here to demonstrate a series of algorithms and artificial neural networks that can be used to identify peaks on an electropherogram and classify them. We demonstrate the functioning of the system on several profiles and compare the results to a leading commercial DNA profile reading system.
Publisher: No publisher found
Date: 2019
DOI: 10.1016/J.FSIGEN.2019.102166
Abstract: Peaks in an electropherogram could represent alleles, stutter product, or a combination of allele and stutter. Continuous probabilistic genotyping (PG) systems model the heights of peaks in an additive manner: for a shared or composite peak, PG models assume that the peak height is the sum of the allelic component and the stutter component. In this work we examine the assumption that the heights of overlapping alleles from a minor contributor and stutter peaks from a major contributor are additive. Any peak below the analytical threshold is considered unobserved hence, in any dataset and particularly in low-template DNA profiles, some or many peaks may be unobserved or missing. Using simulation and empirical data, we show that an additive model can explain the heights of overlapping alleles from a minor contributor and stutter peaks from a major contributor as long as missing data are carefully considered. We use a naive method of imputation for the missing data which appears to perform adequately in this case. If missing data are ignored then the sum of stutter and allelic peaks is expected to be an overestimate of the average height of the composite peaks, as was observed in this study.
Publisher: Elsevier BV
Date: 09-2020
Publisher: Cold Spring Harbor Laboratory
Date: 25-06-2021
DOI: 10.1101/2021.06.25.449960
Abstract: In previously reported work a method for applying a lower bound to the variation induced by the Monte Carlo effect was trialled. This is implemented in the widely used probabilistic genotyping system, STRmix ™ . The approach did not give the desired 99% coverage. However, the method for assigning the lower bound to the MCMC variability is only one of a number of layers of conservativism applied in a typical application. We tested all but one of these sources of variability collectively and term the result the near global coverage. The near global coverage for all tested s les was greater than 99.5% for inclusionary average LR s of known donors. This suggests that when included in the probability interval method the other layers of conservativism are more than adequate to compensate for the intermittent underperformance of the MCMC variability component. Running for extended MCMC accepts was also shown to result in improved precision.
Publisher: Elsevier BV
Date: 03-2014
DOI: 10.1016/J.FSIGEN.2013.07.001
Abstract: Some advanced methods for DNA profile interpretation require a probability for the event of dropout. Methods have been suggested based on logistic regression. Two of these respectively use a proxy for template that is constant across loci and one that is modelled using an exponential curve. Both of these methods allow different modelling constants from each locus. A variant of the model using an exponential curve is discussed. This variant constrains the constants to be the same for every locus. We test these two methods and the variant by developing the constants (training) on one set of data and testing them on another. This mimics the likely use in casework. We find that the new variant appears to be the most useful in that it performs better than the other two options when trained on one data set and used on another. The hypothesised reason for this is that locus to locus variation in lification efficiency varies with time, multimix batch, or from s le to s le.
Publisher: Elsevier BV
Date: 05-2021
Publisher: Elsevier BV
Date: 07-2014
DOI: 10.1016/J.SCIJUS.2014.02.007
Abstract: The Bayesian paradigm is the preferred approach to evidence interpretation. It requires the evaluation of the probability of the evidence under at least two propositions. The value of the findings (i.e., our LR) will depend on these propositions and the case information, so it is crucial to identify which propositions are useful for the case at hand. Previously, a number of principles have been advanced and largely accepted for the evaluation of evidence. In the evaluation of traces involving DNA mixtures there may be more than two propositions possible. We apply these principles to some exemplar situations. We also show that in some cases, when there are no clear propositions or no defendant, a forensic scientist may be able to generate explanations to account for observations. In that case, the scientist plays a role of investigator, rather than evaluator. We believe that it is helpful for the scientist to distinguish those two roles.
Publisher: Elsevier BV
Date: 11-2014
DOI: 10.1016/J.FSIGEN.2014.08.015
Abstract: Sophisticated methods of DNA profile interpretation have enabled scientists to calculate weights for genotype sets proposed to explain some observed data. Using standard formulae these weights can be incorporated into an LR calculation that considers two competing propositions. We demonstrate here how consideration of relatedness to the person of interest can be incorporated into a LR calculation and how the same calculation can be used for familial searches of complex mixtures. We provide a general formula that can be used in semi or fully automated methods of calculation and demonstrate their use by working through an ex le.
Publisher: Elsevier BV
Date: 11-2014
DOI: 10.1016/J.FSIGEN.2014.08.014
Abstract: DNA profile interpretation has benefitted from recent improvements that use semi-continuous or fully continuous methods to interpret information within an electropherogram. These methods are likelihood ratio based and currently require that a number of contributors be assigned prior to analysis. Often there is ambiguity in the choice of number of contributors, and an analyst is left with the task of determining what they believe to be the most probable number. The choice can be particularly important when the difference between two possible contributor numbers means the difference between excluding a person of interest as being a possible contributor, and producing a statistic that favours their inclusion. Presenting both options in a court of law places the decision with the court. We demonstrate here an MCMC method of correctly weighting analyses of DNA profile data spanning a range of contributors. We explore the theoretical behaviour of such a weight and demonstrate these theories using practical ex les. We also highlight the issues with omitting this weight term from the LR calculation when considering different numbers of contributors in the one calculation.
Publisher: Springer Science and Business Media LLC
Date: 23-03-2017
DOI: 10.1007/S00414-017-1573-Y
Abstract: We present here the derivation of paternity index formulae that covers situations of a disputed paternity trio with a trisomic product of conception. We consider six possible mechanisms for trisomy to occur: dispermy, dieggy, paternal meiosis I or II, and maternal meiosis I or II in the calculation. We also provide a biological explanation for how each of the mechanisms could give rise to a trisomy. The paper is set out in a general manner so that the tables presented can be used on any instance of trisomic offspring. This work is motivated by a case of disputed paternity where the product of conception was trisomic, i.e. the electropherogram of the product of conception possessed three alleles at each locus. The outcome was extremely strong support for the alleged father's paternity of the product of conception.
Publisher: Elsevier BV
Date: 07-2019
DOI: 10.1016/J.FSIGEN.2019.02.020
Abstract: Standard practice in forensic science is to compare a person of interest's (POI) reference DNA profile with an evidence DNA profile and calculate a likelihood ratio that considers propositions including and excluding the POI as a DNA donor. A method has recently been published that provides the ability to compare two evidence profiles (of any number of contributors and of any level of resolution) comparing propositions that consider the profiles either have a common contributor, or do not have any common contributors. Using this method, forensic analysts can provide intelligence to law enforcement by linking crime scenes when no suspects may be available. The method could also be used as a quality assurance measure to identify potential s le to s le contamination. In this work we analyse a number of constructed mixtures, ranging from two to five contributors, and with known numbers of common contributors, in order to investigate the performance of using likelihood ratios for mixture to mixture comparisons. Our findings demonstrate the ability to identify common donors in DNA mixtures with the power of discrimination depending largely on the least informative mixture of the pair being considered. The ability to match mixtures to mixtures may provide intelligence information to investigators by identifying possible links between cases which otherwise may not have been considered connected.
Publisher: Elsevier BV
Date: 07-2014
DOI: 10.1016/J.FSIGEN.2014.02.003
Abstract: A typical assessment of the strength of forensic DNA evidence is based on a population genetic model and estimated allele frequencies determined from a population database. Some experts provide a confidence or credible interval which takes into account the s ling variation inherent in deriving these estimates from only a s le of a total population. This interval is given in conjunction with the statistic of interest, be it a likelihood ratio (LR), match probability, or cumulative probability of inclusion. Bayesian methods of addressing database s ling variation produce a distribution for the statistic from which the bound(s) of the desired interval can be determined. Population database s ling uncertainty represents only one of the sources of uncertainty that affects estimation of the strength of DNA evidence. There are other uncertainties which can potentially have a much larger effect on the statistic such as, those inherent in the value of Fst, the weights given to genotype combinations in a continuous interpretation model, and the composition of the relevant population. In this paper we model the effect of each of these sources of uncertainty on a likelihood ratio (LR) calculation and demonstrate how changes in the distribution of these parameters affect the reported value. In addition, we illustrate the impact the different approaches of accounting for s ling uncertainties has on the LR for a four person mixture.
Publisher: Elsevier BV
Date: 05-2019
DOI: 10.1016/J.FSIGEN.2019.02.021
Abstract: A recent publication has provided the ability to compare two mixed DNA profiles and consider their probability of occurrence if they do, compared to if they do not, have a common contributor. This ability has applications to both quality assurance (to test for s le to s le contamination) and for intelligence gathering purposes (did the same unknown offender donate DNA to multiple s les). We use a mixture to mixture comparison tool to investigate the prevalence of s le to s le contamination that could occur from two laboratory mechanisms, one during DNA extraction and one during electrophoresis. By carrying out pairwise comparisons of all s les (deconvoluted using probabilistic genotyping software STRmix™) within extraction or run batches we identify any potential common DNA donors and investigate these with respect to their risk of contamination from the two proposed mechanisms. While not identifying any contamination, we inadvertently find a potential intelligence link between s les, showing the use of a mixture to mixture comparison tool for investigative purposes.
Publisher: Elsevier BV
Date: 12-2009
Publisher: Elsevier BV
Date: 05-2019
Publisher: Elsevier BV
Date: 2021
Publisher: Elsevier BV
Date: 2013
Publisher: Informa UK Limited
Date: 21-12-2015
Publisher: Elsevier BV
Date: 07-2017
DOI: 10.1016/J.FSIGEN.2017.05.006
Abstract: Fingermarks are a source of human identification both through the ridge patterns and DNA profiling. Typing nuclear STR DNA markers from previously enhanced fingermarks provides an alternative method of utilising the limited fingermark deposit that can be left behind during a criminal act. Dusting with fingerprint powders is a standard method used in classical fingermark enhancement and can affect DNA data. The ability to generate informative DNA profiles from powdered fingerprints using direct PCR swabs was investigated. Direct PCR was used as the opportunity to generate usable DNA profiles after performing any of the standard DNA extraction processes is minimal. Omitting the extraction step will, for many s les, be the key to success if there is limited s le DNA. DNA profiles were generated by direct PCR from 160 fingermarks after treatment with one of the following dactyloscopic fingerprint powders: white hadonite silver aluminium HiFi Volcano silk black or black magnetic fingerprint powder. This was achieved by a combination of an optimised double-swabbing technique and swab media, omission of the extraction step to minimise loss of critical low-template DNA, and additional AmpliTaq Gold
Publisher: Elsevier BV
Date: 11-2018
DOI: 10.1016/J.FSIGEN.2018.07.014
Abstract: Many methods have been suggested for evaluating the evidential value of a matching Y-chromosomal DNA profile obtained from a biological stain associated with a crime scene and the Y-chromosomal DNA profile of a suspect. Most of these methods are based on estimating the population frequency of the Y-profile. The common independence assumption between loci for autosomal DNA profiles cannot be used for Y-chromosomal DNA profiles. In this paper we reconsider the problem of population frequency estimation by application of Bayesian networks and the Chow-Liu algorithm to model dependencies between loci. We found that the method based on the Chow-Liu algorithm performs almost as well as the discrete Laplace method. We have also made comparisons to the independence model and we have demonstrated once again that the independence method for Y-profiles cannot be supported.
Publisher: Elsevier BV
Date: 03-2021
Publisher: Oxford University Press (OUP)
Date: 11-07-2016
DOI: 10.1093/LPR/MGW004
Publisher: Springer Science and Business Media LLC
Date: 13-11-2014
DOI: 10.1007/S12024-014-9626-8
Abstract: We report on the successful routine lification of DNA profiles from small sections of fingernails using direct PCR. The data are from 40 nail clippings from eight donors where approximately 4 mm(2) of nail is added directly to the PCR. The NGM™ kit was used that lifies 15 STR loci plus amelogenin. No increase in cycle number was used and no enrichment of the PCR products was performed. Full DNA profiles were observed in 17 of the 40 profiles with 21 generating partial DNA profiles. The process omits the DNA extraction process, and hence there is no opportunity to quantify the DNA prior to lifying the STRs, but by not performing a DNA extraction step, the amount of DNA available for PCR is maximized. Single source DNA profiles were observed in 29 of the 38 profiles obtained. The source of the DNA is assumed to be adhering to the underside of the nail. This simple method offers a significant reduction in time to generate DNA profiles from nail clippings, such as those taken from victims of mass disasters, and should be included into a forensic process relatively easily as it requires no change to manufacturer's instructions for lification.
Publisher: Elsevier BV
Date: 09-2020
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.FSIGEN.2016.06.012
Abstract: Sexual assault cases are the type of case that often produces questions about the cellular source of DNA. In these cases multiple findings of microscopy, DNA profiling and presumptive testing need to be considered when addressing source level propositions. In this work, I consider a line of questioning that has been raised a number of times in the recent past, where in court it was disputed that low levels of sperm seen on a microscope slide were the cellular source of the male DNA profile component generated from the sperm fraction of a differential DNA extraction. I demonstrate how the cell scoring results and DNA profiling results can be considered together, in helping address this source level question through the use of Bayesian Networks.
Publisher: Elsevier BV
Date: 03-2017
DOI: 10.1016/J.FSIGEN.2016.12.004
Abstract: H
Publisher: Elsevier BV
Date: 09-2018
DOI: 10.1016/J.FSIGEN.2018.07.003
Abstract: The interpretation of evidence continues to be one of the biggest challenges facing the forensic community. This is the first of two papers intended to provide advice on difficult aspects of evaluation and in particular on the formulation of propositions. The scientist has a dual role: investigator (crime-focused), where often there is no suspect available and a database search may be required evaluator (suspect-focused), where the strength of evidence is assessed in the context of the case. In investigative mode, generally the aim is to produce leads regarding the source of the DNA. Sub-source level propositions will be adequate to help identify potential suspects who can be further investigated by the authorities. Once in evaluative mode, given the defence version of events of the person of interest, it may become necessary to consider alternatives that go beyond the source of the DNA (i.e., to consider activity level propositions). In the evaluation phase, it is crucial that formulation of propositions allows the assessment of all the results that will help with the issue at hand. Propositions should therefore be precise (indication of the number of contributors, information on the relevant population etc.), be about causes, not effects (e.g. a 'matching' DNA profile) and to avoid bias, must not be findings-led. This means that ideally, propositions should be decided based on the case information and before the results of the comparisons are known. This paper primarily reflects upon what has been coined as "sub-source level propositions". These are restricted to the evaluation of the DNA profiles themselves, and help answer the issue regarding the source of the DNA. It is to be emphasised that likelihood ratios given sub-source level propositions cannot be carried over to a different level - for ex le, activity level propositions, where the DNA evidence is put into the context of the alleged activities. This would be highly misleading and could give rise to miscarriages of justice this will be discussed in a second paper. The value of forensic results depends not only on propositions, but also on the type of results (e.g. allelic designations, peak heights, replicates) and upon the model used: it is therefore important to discuss these aspects. Finally, since communication is key to help understanding by courts, we will explore how to convey the value of the results and explain the importance of avoiding the practice of transposing the conditional.
Publisher: Wiley
Date: 12-08-2015
Abstract: This study reports on the comparison of a standard extraction process with the direct PCR approach of processing low-level DNA swabs typical in forensic investigations. Varying concentrations of control DNA were deposited onto three commonly encountered substrates, brass, plastic, and glass, left to dry, and swabbed using premoistened DNA-free nylon FLOQswabs(™) . Swabs (n = 90) were either processed using the DNA IQ(™) kit or, for direct PCR, swab fibers (~2 mm(2) ) were added directly to the PCR with no prior extraction. A significant increase in the height of the alleles (p < 0.005) was observed when using the direct PCR approach over the extraction methodology when controlling for surface type and mass of DNA deposited. The findings indicate the potential use of direct PCR for increasing the PCR product obtained from low-template DNA s les in addition to minimizing contamination and saving resources.
Publisher: Frontiers Media SA
Date: 15-03-2017
Publisher: Informa UK Limited
Date: 24-05-2018
Publisher: Elsevier BV
Date: 2023
DOI: 10.1016/J.FSIGEN.2022.102787
Abstract: Standard processing of electrophoretic data within a forensic DNA laboratory is for one (or two) analysts to designate peaks as either artefactual or non-artefactual in a process commonly referred to as profile 'reading'. Recently, FaSTR™ DNA has been developed to use artificial neural networks to automatically classify fluorescence within an electropherogram as baseline, allele, stutter or pull-up. These classifications are based on probabilities assigned to each timepoint (scan) within the electropherogram. Instead of using the probabilities to assign fluorescence into a category they can be used directly in the profile analysis. This has a number of advantages increased objectivity in DNA profile processing, the removal for the need for analysts to read profiles, the removal for the need of an analytical threshold. Models within STRmix™ were extended to incorporate the peak label probabilities assigned by FaSTR™ DNA. The performance of the model extensions was tested on a DNA mixture dataset, comprising 2-4 person s les. This dataset was processed in a 'standard' manner using an analytical threshold of 50rfu, analyst peak designations and STRmix™ V2.9 models. The same dataset was then processed in an automated manner using no analytical threshold, no analysts reading the profile and using the STRmix™ models extended to incorporate peak label probabilities. Both datasets were compared to the known DNA donors and a set of non-donors. The result between the two processes was a very close performance, but with a large efficiency gain in the 0rfu process. Utilising peak label probabilities opens up the possibility for a range of workflow process efficiency gains, but beyond this allows full use of all data within an electropherogram.
Publisher: Elsevier BV
Date: 03-2008
DOI: 10.1016/J.FSIGEN.2007.11.006
Abstract: The weighting of DNA evidence can be estimated using various models. Each model relies on allele frequencies, which are obtained from data accumulated in a population database. This report analyses sub-population data for 325 Aboriginal Australian residents of South Australia at nine autosomal Profiler Plus short tandem repeat (STR) loci.
Publisher: Elsevier BV
Date: 05-2015
DOI: 10.1016/J.FSIGEN.2014.11.001
Abstract: A set of low template mixed DNA profiles with known ground truths was examined using software that utilised peak heights (STRmix™ V2.3) and an adapted version that did not use peak heights and mimicked models based on a drop-out probability [1,2] (known as semi-continuous or 'drop' models) (STRmix™ lite). The use of peak heights increased the LR when Hp was true in the vast majority of cases. The effect was most notable at moderate template levels but was also present at quite low template levels. There is no level at which we can say that height information is totally uninformative. Even at the lowest levels the bulk of the data show some improvement from the inclusion of peak height information.
Publisher: Springer Science and Business Media LLC
Date: 25-03-2019
Publisher: Elsevier BV
Date: 09-2016
Publisher: Elsevier BV
Date: 07-2018
DOI: 10.1016/J.FSIGEN.2018.03.016
Abstract: Modern probabilistic genotyping (PG) software is capable of modeling stutter as part of the profile weighting statistic. This allows for peaks in stutter positions to be considered as allelic or stutter or both. However, prior to running any s le through a PG calculator, the examiner must first interpret the s le, considering such things as artifacts and number of contributors (NOC or N). Stutter can play a major role both during the assignment of the number of contributors, and the assessment of inclusion and exclusion. If stutter peaks are not filtered when they should be, it can lead to the assignment of an additional contributor, causing N contributors to be assigned as N + 1. If peaks in the stutter position of a major contributor are filtered using a threshold that is too high, true alleles of minor contributors can be lost. Until now, the software used to view the electropherogram stutter filters are based on a locus specific model. Combined stutter peaks occur when a peak could be the result of both back stutter (stutter one repeat shorter than the allele) and forward stutter (stutter one repeat unit larger than the allele). This can challenge existing filters. We present here a novel stutter filter model in the ArmedXpert™ software package that uses a linear model based on allele for back stutter and applies an additive filter for combined stutter. We term this the allele specific stutter model (AM). We compared AM with a traditional model based on locus specific stutter filters (termed LM). This improved stutter model has the benefit of: Instances of over filtering were reduced 78% from 101 for a traditional model (LM) to 22 for the allele specific model (AM) when scored against each other. Instances of under filtering were reduced 80% from 85 (LM) to 17 (AM) when scored against ground truth mixtures.
Publisher: Elsevier BV
Date: 09-2020
Publisher: Elsevier BV
Date: 2019
DOI: 10.1016/J.FSIGEN.2018.11.011
Abstract: Using a simplified model, we examine the effect of varying the number of contributors in the prosecution and alternate propositions for a number of simulated ex les. We compare the Slooten and Caliebe [1] solution, with several existing practices. Our own experience is that most laboratories, and ourselves, assign the number of contributors, N = n, by allele count and a manual examination of peak heights. The LR
Publisher: Elsevier BV
Date: 05-2015
DOI: 10.1016/J.FSIGEN.2015.01.008
Abstract: The performance of any model used to analyse DNA profile evidence should be tested using simulation, large scale validation studies based on ground-truth cases, or alignment with trends predicted by theory. We investigate a number of diagnostics to assess the performance of the model using Hd true tests. Of particular focus in this work is the proportion of comparisons to non-contributors that yield a likelihood ratio (LR) higher than or equal to the likelihood ratio of a known contributor (LRPOI), designated as p, and the average LR for Hd true tests. Theory predicts that p should always be less than or equal to 1/LRPOI and hence the observation of this in any particular case is of limited use. A better diagnostic is the average LR for Hd true which should be near to 1. We test the performance of a continuous interpretation model on nine DNA profiles of varying quality and complexity and verify the theoretical expectations.
Publisher: Elsevier BV
Date: 07-2019
Publisher: Elsevier BV
Date: 05-2019
DOI: 10.1016/J.FSIGEN.2019.01.006
Abstract: An intra and inter-laboratory study using the probabilistic genotyping (PG) software STRmix™ is reported. Two complex mixtures from the PROVEDIt set, analysed on an Applied Biosystems™ 3500 Series Genetic Analyzer, were selected. 174 participants responded. For S le 1 (low template, in the order of 200 rfu for major contributors) five participants described the comparison as inconclusive with respect to the POI or excluded him. Where LRs were assigned, the point estimates ranging from 2 × 10
Publisher: Elsevier BV
Date: 09-2012
DOI: 10.1016/J.FSIGEN.2012.01.001
Abstract: Y-chromosome specific STR profiling is increasingly used in forensic casework. However, the strong geographic clustering of Y haplogroups can lead to large differences in Y-STR haplotype frequencies between different ethnicities, which may have an impact on database composition in admixed populations. Aboriginal people have inhabited Australia for over 40,000 years and until ∼300 years ago they lived in almost complete isolation. Since the late 18th century Australia has experienced massive immigration, mainly from Europe, although in recent times from more widespread origins. This colonisation resulted in highly asymmetrical admixture between the immigrants and the indigenes. A State jurisdiction within Australia has created an Aboriginal Y-STR database in which assignment of ethnicity was by self-declaration. This criterion means that some males who identify culturally as members of a particular ethnic group may have a Y haplogroup characteristic of another ethnic group, as a result of admixture in their paternal line. As this may be frequent in Australia, an examination of the extent of genetic admixture within the database was performed. A Y haplogroup predictor program was first used to identify Y haplotypes that could be assigned to a European haplogroup. Of the 757 males (589 unique haplotypes), 445 (58.8%) were identified as European (354 haplotypes). The 312 non-assigned males (235 haplotypes) were then typed, in a hierarchical fashion, with a Y-SNP panel that detected the major Y haplogroups, C-S, as well as the Aboriginal subgroup of C, C4. Among these 96 males were found to have non-Aboriginal haplogroups. In total, ∼70% of Y chromosomes in the Aboriginal database could be classed as non-indigenous, with only 169 (129 unique haplotypes) or 22% of the total being associated with haplogroups denoting Aboriginal ancestry, C4 and K* or more correctly K(xL,M,N,O,P,Q,R,S). The relative frequencies of these indigenous haplogroups in South Australia (S.A.) were significantly different to those seen in s les from the Northern Territory and Western Australia. In S.A., K* (∼60%) has a much higher frequency than C4 (∼40%), and the subgroup of C4, C4(DYS390.1del), comprised only 17%. Clearly admixture in the paternal line is at high levels among males who identify themselves as Australian Aboriginals and this knowledge may have implications for the compilation and use of Y-STR databases in frequency estimates.
Publisher: Informa UK Limited
Date: 11-02-2014
Publisher: Elsevier BV
Date: 02-2013
DOI: 10.1016/J.FSIGEN.2012.11.013
Abstract: Traditional forensic DNA interpretation methods are restricted as they are unable to deal completely with complex low level or mixed DNA profiles. This type of data has become more prevalent as DNA typing technologies become more sensitive. In addition they do not make full use of the information available in peak heights. Existing methods of interpretation are often described as binary which describes the fact that the probability of the evidence is assigned as 0 or 1 (hence binary) (see for ex le [1] at 7.3.3). These methods are being replaced by more advanced interpretation methods such as continuous models. In this paper we describe a series of models that can be used to calculate expected values for allele and stutter peak heights, and their ratio SR. This model could inform methods which implement a continuous method for the interpretation of DNA profiling data.
Publisher: Springer Science and Business Media LLC
Date: 16-07-2016
DOI: 10.1007/S12024-016-9784-Y
Abstract: We report on the successful use of direct PCR lification of single fibers from items of worn clothing. Items of clothing were worn throughout the course of a day, with the in idual commencing regular activities. Single fibers were taken from the cuff of the clothing at regular intervals and lified directly. The same areas were subjected to tape-lifting, and also lified directly for comparison. The NGM™ kit that lifies 15 STR loci plus amelogenin was used. A total of 35 single fiber s les were processed and analyzed from five items of clothing, with 81 % of s les returning a profile of 14 alleles or more. All tape-lift s les lified directly produced DNA profiles of 15 alleles or more. The aim was to develop a simple, operational method that could be used routinely in forensic science casework and that has the potential to generate more complete profiles, which would not be detected using standard extraction methods on this type of s le. For ease of implementation, the process also adheres to standard methods with no increase in the cycle number.
Publisher: CRC Press
Date: 11-04-2023
Publisher: Elsevier BV
Date: 07-2014
DOI: 10.1016/J.FSIGEN.2014.03.008
Abstract: Continuous DNA interpretation systems make use of more information from DNA profiles than analysts have previously been able to with binary, threshold based systems. With these new continuous DNA interpretation systems and a new, more powerful, DNA profiling kit (GlobalFiler) there is an opportunity to re-examine the behaviour of a commonly used statistic in forensic science, the likelihood ratio (LR). The theoretical behaviour of the LR has been known for some time, although in many instances the behaviour has not been able to be thoroughly demonstrated due to limitations of the biological and mathematical models being used. In this paper the effects of profile complexity, replicate lifications, assuming contributors, adding incorrect information, and adding irrelevant information to the calculation of the LR are explored. The empirical results are compared to theoretical expectations and explained. The work finishes with the results being used to dispel common misconceptions around reliability, accuracy, informativeness and reproducibility.
Publisher: CRC Press
Date: 11-04-2023
Publisher: Elsevier BV
Date: 07-2020
Publisher: CRC Press
Date: 03-09-2018
Publisher: Elsevier BV
Date: 03-2016
DOI: 10.1016/J.FSIGEN.2015.11.010
Abstract: Y-STR profiling makes up a small but important proportion of forensic DNA casework. Often Y-STR profiles are used when autosomal profiling has failed to yield an informative result. Consequently Y-STR profiles are often from the most challenging s les. In addition to these points, Y-STR loci are linked, meaning that evaluation of haplotype probabilities are either based on overly simplified counting methods or computationally costly genetic models, neither of which extend well to the evaluation of mixed Y-STR data. For all of these reasons Y-STR data analysis has not seen the same advances as autosomal STR data. We present here a probabilistic model for the interpretation of Y-STR data. Due to the fact that probabilistic systems for Y-STR data are still some way from reaching active casework, we also describe how data can be analysed in a continuous way to generate interpretational thresholds and guidelines.
Publisher: Elsevier BV
Date: 11-2017
Publisher: Elsevier BV
Date: 12-2014
DOI: 10.1016/J.JTBI.2014.08.021
Abstract: A commonly used idea in forensic fields is known as the 'hierarchy of propositions'. DNA analysts commonly report at the sub-source level in the hierarchy. This means that they simply comment on the probability of the evidence for the given propositions that consider contributors that lead to a DNA profile and not on the source of specific biological components, not the activity that led to the transfer or the offence that is reported to have occurred. However DNA analysts also commonly report at a level even lower than the sub-source level. In this 'sub-sub-source' level only reference comparisons to components of a mixture are reported. The difference between the sub-source level and sub-sub-source level is the difference between comparing an in idual to a mixture as a whole, or comparing them to only one component of a mixture. This idea has been expressed in the past as the 'two trace' problem or the 'factor of two' problem. With the advent of expert systems that can provide a measure of weight of evidence in the form of a likelihood ratio (LR) for any mixture, resolvable or not, the distinction between these two levels becomes more important. In this paper we explore how the LR can be constructed to report correctly at the sub-source level, by taking contributor orders and genotype set orders into account. We include worked ex les of the LR calculation to help explain this confusing issue.
Publisher: Elsevier BV
Date: 07-2018
DOI: 10.1016/J.FSIGEN.2018.03.006
Abstract: In this paper we introduce a new likelihood ratio method for evaluating mixed Y-STR profiles that is based on the premise that, given a haplotype has been seen in the person of interest, the most likely source of a second haplotype, matching at all or most loci, is in an in idual with a recent common ancestor. We have called the new method the "Haplotype centred" (HC) method for likelihood ratio derivation. For single source, unambiguous haplotypes the HC method performs identically with the Kappa method proposed by Brenner. When attention is turned to mixtures we are required to assign a probability to many haplotypes seen neither in the database nor any person typed in the case. We derive a likelihood ratio formula in a way that allows a locus by locus approach. We demonstrate the application of the HC method on a series of Y-STR mixtures, originating from two to four in iduals, in a manner that is still calculated locus-by-locus in nature.
Publisher: Elsevier BV
Date: 07-2019
Publisher: Elsevier BV
Date: 07-2019
DOI: 10.1016/J.FSIGEN.2019.03.020
Abstract: We investigate the ability of the 31 SNP loci in the Global AIMs Nano set to distinguish self-declared Australian Aboriginal in iduals from European, Oceanic, African, Native American and East Asian populations. Human evolution suggests that Australian Aboriginal in iduals came to Australia approximately 50 000 years ago, during the time it made up part of Sahul. Since then the colonisation of Australia by Europeans has meant significant admixture within the Australian Aboriginal population. These two events present themselves in our study with the Aboriginal population creating a continuous genetic cline between the Oceanic and European groups. We also assigned the Aboriginal in iduals into their traditional regional groups to determine whether there was any ability to distinguish these from each other. We found similar results to studies using other markers, namely that the more remote regions (that have been less affected by admixture) erged from the rest. Overall, we found the ability of the GNano system to differentiate self-declared Australian Aboriginal in iduals was reasonable but had limitations that need to be recognised if these assignments are applied to unknown in iduals.
Publisher: CRC Press
Date: 17-03-2016
DOI: 10.1201/B19680
Publisher: Elsevier BV
Date: 07-2016
Publisher: CRC Press
Date: 11-04-2023
Publisher: Elsevier BV
Date: 03-2016
DOI: 10.1016/J.FSIGEN.2015.11.009
Abstract: The evaluation of forensic evidence can occur at any level within the hierarchy of propositions depending on the question being asked and the amount and type of information that is taken into account within the evaluation. Commonly DNA evidence is reported given propositions that deal with the sub-source level in the hierarchy, which deals only with the possibility that a nominated in idual is a source of DNA in a trace (or contributor to the DNA in the case of a mixed DNA trace). We explore the use of information obtained from examinations, presumptive and discriminating tests for body fluids, DNA concentrations and some case circumstances within a Bayesian network in order to provide assistance to the Courts that have to consider propositions at source level. We use a scenario in which the presence of blood is of interest as an exemplar and consider how DNA profiling results and the potential for laboratory error can be taken into account. We finish with ex les of how the results of these reports could be presented in court using either numerical values or verbal descriptions of the results.
Publisher: CRC Press
Date: 11-04-2023
Publisher: Elsevier BV
Date: 09-2013
DOI: 10.1016/J.FSIGEN.2013.05.011
Abstract: A method for interpreting autosomal mixed DNA profiles based on continuous modelling of peak heights is described. MCMC is applied with a model for allelic and stutter heights to produce a probability for the data given a specified genotype combination. The theory extends to handle any number of contributors and replicates, although practical implementation limits analyses to four contributors. The probability of the peak data given a genotype combination has proven to be a highly intuitive probability that may be assessed subjectively by experienced caseworkers. Whilst caseworkers will not assess the probabilities per se, they can broadly judge genotypes that fit the observed data well, and those that fit relatively less well. These probabilities are used when calculating a subsequent likelihood ratio. The method has been trialled on a number of mixed DNA profiles constructed from known contributors. The results have been assessed against a binary approach and also compared with the subjective judgement of an analyst.
Publisher: CRC Press
Date: 11-04-2023
Publisher: CRC Press
Date: 11-04-2023
Publisher: CRC Press
Date: 11-04-2023
Publisher: Elsevier BV
Date: 09-2019
DOI: 10.1016/J.FSIGEN.2019.06.006
Abstract: Trace DNA and the manner in which it is transferred from item to item is a common topic arising in forensic science, both in case evaluations, and in Court testimony. In order to assign the probability of obtaining DNA findings, given competing propositions that specify transfer mechanisms, consideration must be given to a number of factors. Previous work by the authors developed a simple Object-Oriented Bayesian Network (OOBN) that pooled numerous published studies in order to attempt evaluation of trace DNA results given such propositions. In this work, we expand on the previously published OOBN and formalise a number of class networks that can be used together in a logical way to consider DNA movement through complex chains of transfer events. Specifically, we develop an OOBN that considers the two-way transfer of DNA that occurs when two items contact, and allows for the s ling of intermediary items involved in the chain of transfers. The aim is to show that adopting an approach involving basic building blocks, we offer the possibility to tackle complex and various cases for which the OOBN will be obtained by combining their elementary blocks. We conclude with a demonstration of applying the OOBN being applied to a chain of transfers in a case scenario.
Publisher: Springer Science and Business Media LLC
Date: 30-12-2012
DOI: 10.1007/S12024-012-9402-6
Abstract: We report on successful lification of DNA profiles from a single hair. Direct lification was used on the root tip of both anagen and telogen hairs using a kit to lify 15 STR loci. All 30 anagen hairs tested from five different people gave full DNA profiles after 29 cycles with no allelic drop-in or heterozygous imbalance. Six of the 30 telogen hairs tested resulted in a full DNA profile, and a further four telogen hair s les tested produced a DNA profile of five or more complete loci that could be up-loaded to the National DNA Database (Australia). A full DNA profile was also obtained from the shaft of an anagen hair. Current practice for many laboratories is that a single hair may not be subjected to DNA testing as there is little chance of success, hence this 100 % success rate from anagen hairs is a significant advancement. A full DNA profile was obtained from a 5 year-old single hair illustrating the success when using direct PCR rather than attempting an extraction prior to the lification step. The process described deliberately uses current DNA profiling methods with no increase in cycle number, such that the methodology can be incorporated readily into operational practice. For the first time in the field of human identification, single hairs can be analyzed with confidence that a meaningful DNA profile will be generated and the data accepted by the criminal justice system.
Publisher: CRC Press
Date: 11-04-2023
Publisher: CRC Press
Date: 11-04-2023
Publisher: Informa UK Limited
Date: 07-01-2020
Publisher: Elsevier BV
Date: 2020
DOI: 10.1016/J.FSIGEN.2019.102199
Abstract: In this short publication we address the topic of evaluation of biological results given activity level propositions, particularly when the source of the biological material is not in question. When the issue regards the mechanisms or actions that led to the deposition of the biological material concerned, there is a need for more case information than when the issue pertains to the source of the DNA. It is up to the scientist to structure the provided case information into propositions, assumptions and undisputed case information. In our statements, deciding what goes in the propositions and what will be part of the paragraph dedicated to case information is partly personal. It may however affect the way we think about a case and thereby have consequences for the evaluation of the results as well as for the communication of the information to the recipient. In particular we highlight the importance of considering and communicating all DNA transfer mechanisms that are relevant to the evaluation under each proposition, and how the way the propositions are thought about (and expressed) can assist in this endeavour.
Publisher: Elsevier BV
Date: 2019
Publisher: Informa UK Limited
Date: 29-01-2019
Publisher: Elsevier BV
Date: 2015
DOI: 10.1016/J.FSIGEN.2014.09.019
Abstract: There has been a recent push from many jurisdictions for the standardisation of forensic DNA interpretation methods. Current research is moving from threshold-based interpretation strategies towards continuous interpretation strategies. However laboratory uptake of software employing probabilistic models is slow. Some of this reluctance could be due to the perceived intimidating calculations to replicate the software answers and the lack of formal internal validation requirements for interpretation software. In this paper we describe a set of experiments which may be used to internally validate in part probabilistic interpretation software. These experiments included both single source and mixed profiles calculated with and without dropout and drop-in and studies to determine the reproducibility of the software with replicate analyses. We do this by way of ex le using three software packages: STRmix™, LRmix, and Lab Retriever. We outline and demonstrate the profile ex les where the expected answer may be calculated and provide all calculations.
Publisher: Elsevier BV
Date: 11-2016
DOI: 10.1016/J.FSIGEN.2016.07.013
Abstract: Electropherograms are produced in great numbers in forensic DNA laboratories as part of everyday criminal casework. Before the results of these electropherograms can be used they must be scrutinised by analysts to determine what the identified data tells us about the underlying DNA sequences and what is purely an artefact of the DNA profiling process. A technique that lends itself well to such a task of classification in the face of vast amounts of data is the use of artificial neural networks. These networks, inspired by the workings of the human brain, have been increasingly successful in analysing large datasets, performing medical diagnoses, identifying handwriting, playing games, or recognising images. In this work we demonstrate the use of an artificial neural network which we train to 'read' electropherograms and show that it can generalise to unseen profiles.
Publisher: Elsevier BV
Date: 11-2020
Publisher: Elsevier BV
Date: 05-2020
Publisher: Elsevier BV
Date: 09-2016
DOI: 10.1016/J.SCIJUS.2016.06.010
Abstract: Bayesian networks are being increasingly used to address complex questions of forensic interest. Like all probabilities, those that underlie the nodes within a network rely on structured data and knowledge. Obviously, the more structured data we have, the better. But, in real life, the numbers of experiments that can be carried out are limited. It is thus important to know if/when our knowledge is sufficient and when one needs to perform further experiments to be in a position to report the value of the observations made. To explore the impact of the amount of data that are available for assessing results, we have constructed Bayesian Networks and explored the sensitivity of the likelihood ratios to changes to the data that underlie each node. Bayesian networks are constructed and sensitivity analyses performed using freely available R libraries (gRain and BNlearn). We demonstrate how the analyses can be used to yield information about the robustness provided by the data used to inform the conditional probability table, and also how they can be used to direct further research for maximum effect. By maximum effect, we mean to contribute with the least investment to an increased robustness. In addition, the paper investigates the consequences of the sensitivity analysis to the discussion on how the evidence shall be reported for a given state of knowledge in terms of underpinning data.
Publisher: Elsevier BV
Date: 07-2018
DOI: 10.1016/J.FSIGEN.2018.04.009
Abstract: STRmix™ uses several laboratory specific parameters to calibrate the stochastic model for peak heights. These are modelled on empirical observations specific to the instruments and protocol used in the analysis. The extent to which these parameters can be borrowed from laboratories with similar technology and protocols without affecting the accuracy of the system is investigated using a sensitivity analysis. Parameters are first calibrated to a publicly available dataset, after which a large number of likelihood ratios are computed for true contributors and non-contributors using both the calibrated parameters and several borrowed parameters. Differences in the LR caused by using different sets of parameter values are found to be negligible.
Publisher: Springer Science and Business Media LLC
Date: 19-09-2013
DOI: 10.1007/S00414-013-0911-Y
Abstract: Y-chromosome short tandem repeats (Y-STRs) are used in forensic science laboratories all over the world, as their application is wide and often vital in solving casework. Analysis of an in-house database of South Australian self-declared Aboriginal males held by Forensic Science South Australia (FSSA) using the Applied Biosystem's AmpFℓSTR® Yfiler™ PCR Amplification Kit revealed 43 variant Y-STR alleles at 6 of the 17 loci. All variant alleles were sequenced to determine the exact repeat structure for each. As a high level of admixture has previously been found within the SA Aboriginal database, s les were haplogrouped using Y-SNPs to determine their likely geographical origin. Although a number of variant alleles were associated with non-Aboriginal Y-haplogroups, a high frequency was observed within the Australian K-M9 lineage. Detailed knowledge of these variant alleles may have further application in the development of new DNA markers for identification purposes, and in population and evolutionary studies of Australian Aborigines.
Publisher: Elsevier BV
Date: 07-2017
DOI: 10.1016/J.FSIGEN.2017.04.004
Abstract: The interpretation of DNA evidence can entail analysis of challenging STR typing results. Genotypes inferred from low quality or quantity specimens, or mixed DNA s les originating from multiple contributors, can result in weak or inconclusive match probabilities when a binary interpretation method and necessary thresholds (such as a stochastic threshold) are employed. Probabilistic genotyping approaches, such as fully continuous methods that incorporate empirically determined biological parameter models, enable usage of more of the profile information and reduce subjectivity in interpretation. As a result, software-based probabilistic analyses tend to produce more consistent and more informative results regarding potential contributors to DNA evidence. Studies to assess and internally validate the probabilistic genotyping software STRmix™ for casework usage at the Federal Bureau of Investigation Laboratory were conducted using lab-specific parameters and more than 300 single-source and mixed contributor profiles. Simulated forensic specimens, including constructed mixtures that included DNA from two to five donors across a broad range of template amounts and contributor proportions, were used to examine the sensitivity and specificity of the system via more than 60,000 tests comparing hundreds of known contributors and non-contributors to the specimens. Conditioned analyses, concurrent interpretation of lification replicates, and application of an incorrect contributor number were also performed to further investigate software performance and probe the limitations of the system. In addition, the results from manual and probabilistic interpretation of both prepared and evidentiary mixtures were compared. The findings support that STRmix™ is sufficiently robust for implementation in forensic laboratories, offering numerous advantages over historical methods of DNA profile analysis and greater statistical power for the estimation of evidentiary weight, and can be used reliably in human identification testing. With few exceptions, likelihood ratio results reflected intuitively correct estimates of the weight of the genotype possibilities and known contributor genotypes. This comprehensive evaluation provides a model in accordance with SWGDAM recommendations for internal validation of a probabilistic genotyping system for DNA evidence interpretation.
Publisher: Springer Science and Business Media LLC
Date: 07-03-2022
DOI: 10.1007/S12024-022-00465-6
Abstract: The sensitivity and discrimination power of modern DNA profiling systems means that very small amounts of DNA from an in idual can be detected on an item leading to large inclusionary statistics for that person. The sensitivity of these systems has significant benefits in the investigation of crime but also can be highly sensitive to contamination of exhibits or crime scenes. It becomes critical to distinguish between deposition during commission of a crime or deposition via some other method unrelated to the crime. This study investigates methodologies used in crime scene examination and the potential for them to cause non-crime-related transfer of DNA. Factors assessed include the source of DNA, the handling time, the amount of movement during contact, and the substrate type. The amount of movement and the number of transfer steps are the most critical in determining whether, and how much, DNA is transferred. This study provides information for crime scene examiners and also scientists assessing transfer scenarios.
Publisher: Elsevier BV
Date: 07-2018
Publisher: Wiley
Date: 30-10-2015
DOI: 10.1002/AJPA.22886
Abstract: Understanding the origins of Aboriginal Australians is crucial in reconstructing the evolution and spread of Homo sapiens as evidence suggests they represent the descendants of the earliest group to leave Africa. This study analyzed a large s le of Y-chromosomes to answer questions relating to the migration routes of their ancestors, the age of Y-haplogroups, date of colonization, as well as the extent of male-specific variation. Knowledge of Y-chromosome variation among Aboriginal Australians is extremely limited. This study examined Y-SNP and Y-STR variation among 657 self-declared Aboriginal males from locations across the continent. 17 Y-STR loci and 47 Y-SNPs spanning the Y-chromosome phylogeny were typed in total. The proportion of non-indigenous Y-chromosomes of assumed Eurasian origin was high, at 56%. Y lineages of indigenous Sahul origin belonged to haplogroups C-M130*(xM8,M38,M217,M347) (1%), C-M347 (19%), K-M526*(xM147,P308,P79,P261,P256,M231,M175,M45,P202) (12%), S-P308 (12%), and M-M186 (0.9%). Haplogroups C-M347, K-M526*, and S-P308 are Aboriginal Australian-specific. Dating of C-M347, K-M526*, and S-P308 indicates that all are at least 40,000 years old, confirming their long-term presence in Australia. Haplogroup C-M347 comprised at least three sub-haplogroups: C-DYS390.1del, C-M210, and the unresolved paragroup C-M347*(xDYS390.1del,M210). There was some geographic structure to the Y-haplogroup variation, but most haplogroups were present throughout Australia. The age of the Australian-specific Y-haplogroups suggests New Guineans and Aboriginal Australians have been isolated for over 30,000 years, supporting findings based on mitochondrial DNA data. Our data support the hypothesis of more than one route (via New Guinea) for males entering Sahul some 50,000 years ago and give no support for colonization events during the Holocene, from either India or elsewhere.
Publisher: Elsevier BV
Date: 12-2015
Publisher: Informa UK Limited
Date: 26-02-2019
Publisher: Elsevier BV
Date: 2020
DOI: 10.1016/J.FSIGEN.2019.102186
Abstract: The value of the evidence depends critically on propositions. In the second of two papers intended to provide advice to the community on difficult aspects of evaluation and the formulation of propositions, we focus primarily on activity level propositions. This helps the court address the question of "How did an in idual's cell material get there?". In order to do this, we expand the framework outlined in the first companion paper. First, it is important not to conflate results and propositions. Statements given activity level propositions aim to help address issues of indirect vs direct transfer, and the time of the activity, but it is important to avoid use of the word 'transfer' in propositions. This is because propositions are assessed by the Court, but DNA transfer is a factor that scientists need to take into account for the interpretation of their results. Suitable activity level propositions are ideally set before knowledge of the results and address issues like: X stabbed Y vs. an unknown person stabbed Y but X met Y the day before. The scientist assigns the probability of the evidence, if each of the alternate propositions is true, to derive a likelihood ratio. To do this, the scientist asks: a) "what are the expectations if each of the propositions is true?" b) "What data are available to assist in the evaluation of the results given the propositions?" When presenting evidence, scientists work within the hierarchy of propositions framework. The value of evidence calculated for a DNA profile cannot be carried over to higher levels in the hierarchy - the calculations given sub-source, source and activity level propositions are all separate. A number of ex les are provided to illustrate the principles espoused, and the criteria that such assessments should meet. Ideally in order to assign probabilities, the analyst should have/collect data that are relevant to the case in question. These data must be relevant to the case at hand and we encourage further research and collection of data to form knowledge bases. Bayesian Networks are extremely useful to help us think about a problem, because they force us to consider all relevant possibilities in a logical way. An ex le is provided.
Publisher: Elsevier BV
Date: 12-2012
DOI: 10.1016/J.FSIGEN.2012.05.005
Abstract: Y-STR haplotype data was obtained using the AmpFlSTR(®) YFiler™ PCR Amplification Kit (Applied Biosystems, Foster City, CA) for 1079 Caucasian and 766 Australian Aboriginal in iduals. Haplotype ersity was similar in both populations, however discrimination capacity was higher in Caucasians than Aborigines (0.946 compared to 0.692). Locus DYS385, which was considered as a single locus, was the most erse marker in both populations (0.836 in Caucasians and 0.905 in Aborigines). The South Australian Aboriginal and Caucasian databases were compiled from casework reference profile information held on the South Australian Criminal, Reference and Evidence DNA Database (SACREDD). Ethnicity was assigned based on self-declaration.
Publisher: Cold Spring Harbor Laboratory
Date: 26-06-2021
DOI: 10.1101/2021.06.25.450000
Abstract: Two methods for applying a lower bound to the variation induced by the Monte Carlo effect are trialled. One of these is implemented in the widely used probabilistic genotyping system, STRmix ™ . Neither approach is giving the desired 99% coverage. In some cases the coverage is much lower than the desired 99%. The discrepancy (i.e. the distance between the LR corresponding to the desired coverage and the LR observed coverage at 99%) is not large. For ex le, the discrepancy of 0.23 for approach 1 suggests the lower bounds should be moved downwards by a factor of 1.7 to achieve the desired 99% coverage. Although less effective than desired these methods provide a layer of conservatism that is additional to the other layers. These other layers are from factors such as the conservatism within the sub-population model, the choice of conservative measures of co-ancestry, the consideration of relatives within the population and the res ling method used for allele probabilities, all of which tend to understate the strength of the findings. Two methods for quantifying Monte Carlo variability are tested, Both give less than the desired 99% coverage, The magnitude of possible discrepancy is small, For ex le an LR of 4.3 × 10 11 could be reported as 1.8 × 10 12 An LR of 18 could be reported as 22.
Publisher: Informa UK Limited
Date: 12-2013
Publisher: Elsevier BV
Date: 05-2017
DOI: 10.1016/J.FSIGEN.2017.02.008
Abstract: DNA is routinely recovered in criminal investigations. The sensitivity of laboratory equipment and DNA profiling kits means that it is possible to generate DNA profiles from very small amounts of cellular material. As a consequence, it has been shown that DNA we detect may not have arisen from a direct contact with an item, but rather through one or more intermediaries. Naturally the questions arising in court, particularly when considering trace DNA, are of how DNA may have come to be on an item. While scientists cannot directly answer this question, forensic biological results can help in discriminating between alleged activities. Much experimental research has been published showing the transfer and persistence of DNA under varying conditions, but as of yet the results of these studies have not been combined to deal with broad questions about transfer mechanisms. In this work we use published data and Bayesian networks to develop a statistical logical framework by which questions of transfer mechanism can be approached probabilistically. We also identify a number of areas where further work could be carried out in order to improve our knowledge base when helping to address questions about transfer mechanisms. Finally, we apply the constructed Bayesian network to ground truth known data to determine if, with current knowledge, there is any power in DNA quantities to distinguish primary and secondary transfer events.
Publisher: Elsevier BV
Date: 09-2018
DOI: 10.1016/J.FSIGEN.2018.06.002
Abstract: Direct PCR from touch DNA has a range of potential applications in the field of forensic investigation for exhibit examination that, under standard extraction methods, rarely produce informative DNA profiles. Previous studies from 'touch DNA' have focussed on fingermarks created under laboratory conditions. Here we report on successful STR DNA profiling from a range of touched items. Direct PCR, with no increase in cycle number, was performed after eight different s le types, typical of those submitted for forensic investigation, were handled by volunteers for a maximum of 15 s to deposit trace amounts of their DNA. Amplifications were performed using either GlobalFiler
Publisher: MDPI AG
Date: 30-09-2021
Abstract: Probabilistic genotyping has become widespread. EuroForMix and DNAStatistX are both based upon maximum likelihood estimation using a γ model, whereas STRmix™ is a Bayesian approach that specifies prior distributions on the unknown model parameters. A general overview is provided of the historical development of probabilistic genotyping. Some general principles of interpretation are described, including: the application to investigative vs. evaluative reporting detection of contamination events inter and intra laboratory studies numbers of contributors proposition setting and validation of software and its performance. This is followed by details of the evolution, utility, practice and adoption of the software discussed.
Publisher: Elsevier BV
Date: 09-2018
DOI: 10.1016/J.FSIGEN.2018.06.001
Abstract: The evaluation of results of forensic genetic analyses given activity level propositions is an emerging discipline in forensic genetics. Although it is a topic with a long history, it has never been considered to be such a critically important topic for the field, as today. With the increasing sensitivity of analysis techniques, and advances in data interpretation using probabilistic models ('probabilistic genotyping'), there is an increasing demand on forensic biologists to share specialised knowledge to help recipients of expert information address mode and timing of transfer and persistence of traces in court. Scientists thereby have a critical role in the assessment of their findings in the context of the case. This helps the judiciary with activity level inferences in a balanced, robust and transparent way, when based on (1) proper case assessment and interpretation respecting the hierarchy of propositions (supported by, for ex le, the use of Bayesian networks as graphical models), (2) use of appropriate data to inform probabilities, and (3) reporting guidelines by international bodies. This critical review of current literature shows that with certain prerequisites for training and quality assurance, there is a solid foundation for evidence interpretation when propositions of interest are at the 'activity level'.
Publisher: Elsevier BV
Date: 2013
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