John Buckleton

John Buckleton
University of Auckland · Department of Mathematics

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317
Publications
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Introduction
Skills and Expertise

Publications

Publications (317)
Article
There is a general reluctance to use conditioning profiles when forming propositions for cases where the evidence is a DNA mixture. However, the use of conditioning profiles improves the ability to differentiate true from false donors. There are at least four situations where this decision making is at its most difficult. These are: •The unassociat...
Article
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The forensic community has devoted much effort over the last decades to the development of a logical framework for forensic interpretation, which is essential for the safe administration of justice. We review the research and guidelines that have been published and provide examples of how to implement them in casework. After a discussion on uncerta...
Preprint
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We discuss a range of miscodes found in probabilistic genotyping (PG) software and from other industries that have been reported in the literature and have been used to inform PG admissibility hearings. Every instance of the discovery of a miscode in PG software with which we have been associated has occurred either because of testing, use, or repe...
Article
The interpretation of mixtures containing related individuals can be difficult due to allele sharing between the contributors. Challenges include the assignment of the number of contributors (NoC) to the mixture with the under assignment of NoC resulting in false exclusions of true donors. Non-donating relatives of the true contributors to mixtures...
Article
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The identification of human remains belonging to missing persons is one of the main challenges for forensic genetics. Although other means of identification can be applied to missing person investigations, DNA is often extremely valuable to further support or refute potential associations. When reference DNA samples collected from personal items be...
Article
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Semaan et al. (J Forensic Res, 2020, 11, 453) discuss a mock case “where eight different individuals [P1 through P8] could not be excluded in a mixed DNA analysis. Even though … expert DNA mixture analysis software was used.” Two of these are the true donors. The LRs reported are incorrect due to the incorrect entry of propositions into LRmix Studi...
Article
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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 genera...
Article
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 profil...
Article
Cold case reinvestigations are a common occurrence. Occasionally some of the original work was conducted up to 30 years ago using profiling systems of the early 1990s, which targeted HLA-DQA1, ApoB, D1S80 and D17S5. When contemporary work is carried out, if a suspect is identified they will be profiled in contemporary profiling kits such as GlobalF...
Preprint
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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 betw...
Preprint
Full-text available
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...
Article
We describe an adaption of Bright et al.'s work modeling peak height variability in CE-DNA profiles to the modeling of allelic aSTR (autosomal short tandem repeats) read counts from NGS-DNA profiles, specifically for profiles generated from the ForenSeq™ DNA Signature Prep Kit, DNA Primer Mix B. Bright et al.'s model consists of three key component...
Article
Slooten described a method of targeting major contributors in mixed DNA profiles and comparing them to individuals on a DNA database. The method worked by taking incrementally more peak information from the profile (based on the peak contribution), and using a semi-continuous model, calculating likelihood ratios for the comparison to database indiv...
Article
Full-text available
In casework, laboratories may be asked to compare DNA mixtures to multiple persons of interest (POI). Guidelines on forensic DNA mixture interpretation recommend that analysts consider several pairs of propositions; however, it is unclear if several likelihood ratios (LRs) per person should be reported or not. The propositions communicated to the c...
Article
We describe a method to assign weights to genotype combinations at the Amelogenin locus. It is a typical practise in forensic laboratories that once the weight exceeds a threshold (such as 99%), then they can be considered to be resolve enough to interpret (for example to load onto a database). We found that unless an individual is a clear major (o...
Article
The assignment of the number of contributors (N) to a forensic DNA profile is undertaken as part of the interpretation process. There is no requirement for N to be the same for both propositions within the likelihood ratio framework. ISFG recommendations on mixture interpretation suggest that there may be times where prosecution and defence both sp...
Article
We seek to develop a rational approach to forming propositions when little information is available from the outset, as this often happens in casework. If propositions used when evaluating evidence are not exhaustive (in the context of the case), then there is a theoretical risk that an LR greater than one may be associated with a proposition in th...
Article
The interpretation of DNA profiles typically starts with an assessment of the number of contributors. In the last two decades, several methods have been proposed to assist with this assessment. We describe a relatively simple method using decision trees, that is fast to run and fully transparent to a forensic analyst. We use mixtures from the publi...
Article
DNA mixtures will have multiple donors under both the prosecution and alternate propositions when assigning a likelihood ratio for forensic DNA evidence. These donors are usually assumed to be unrelated to each other. In this paper, we make a small, preliminary examination of the potential effect of relaxing this assumption. We consider the simple...
Article
We reprise four significant software failures and examine these cases for lessons that can be transferred to the development of forensic software. All four case studies have been well examined and causes described. No one factor is common to all four case studies. The studies are the MIT Kerberos security software, the Mars Climate Orbiter (MCO), t...
Article
To answer the question “Are low likelihood ratios reliable?” requires both a definition of reliable and then a test of whether low likelihood ratios (LRs) meet that definition. We offer, from a purely statistical standpoint, that reliability can be determined by assessing whether the expected rate of inclusionary support for non-donors over many ca...
Article
Uncertainty in the assignment of the number of contributors (NoC) can be encountered, particularly in higher-order mixtures, where alleles may be shared between contributors, may have dropped out, or may be masked by the stutter artefacts or allelic peaks of a more dominant contributor. Most probabilistic genotyping software requires the assignment...
Article
There has been an increase in the number of laboratories and researchers adopting new sequencing technologies, known as next-generation sequencing (NGS). An understanding of the behaviour of NGS DNA profiles is needed to enable for the development of probabilistic genotyping methods for the interpretation of such profiles. In this work, we investig...
Article
Probabilistic methods of DNA profile interpretation are being adopted by forensic laboratories worldwide. One commonality to all probabilistic genotyping software is an assignment of the strength of evidence using the likelihood ratio (LR). The probabilistic genotyping software STRmix™ reports a number of LRs that differ based on the propositions c...
Article
Stiffelman [1] gives a broad critique of the application of likelihood ratios (LRs) in forensic science, in particular their use in probabilistic genotyping (PG) software. These are discussed in this review. LRs do not infringe on the ultimate issue. The Bayesian paradigm clearly separates the role of the scientist from that of the decision makers...
Article
It is routinely assumed when interpreting forensic DNA profiles that peaks of the same molecular size, whether allelic or stutter in origin, ‘stack’. That is, the height of a composite peak is approximately equal to the sum of its parts. There is strong theoretical reason to believe that this assumption should hold across the range of peak heights...
Article
The advent of DNA profiling in the 1980s has revolutionised forensic science. Forensic DNA profiling is a powerful tool that is used to both exonerate and implicate persons of interest in criminal cases. The technologies used to recover and detect DNA from crime scene stains have evolved over time. Whereas 30 years ago most forensic profiles were g...
Article
Ramos and Gonzalez-Rodriguez introduce the concept of calibration in order to determine whether a system of evidence presentation is a reliable assessor of evidential weight. In this paper, we apply this calibration method to a dataset of mixed forensic DNA profiles generated using the QIAGEN Investigator® 24plex QS Kit and interpreted using the pr...
Article
The probabilistic genotyping software Forensic Statistical Tool implements a semi‐continuous model for DNA interpretation. This software omits any locus where the sum of the allele probabilities equals or exceeds .97. There has been criticism that this function is neither signaled by the software nor disclosed in publications. We investigate the ef...
Article
We report the interpretation of three-person mixed DNA profiles constructed from DNA from one mother, father, and child trio using the probabilistic genotyping software STRmix™. A total of 40 mixtures were examined, with varying total template and mixture proportions of the three contributors. In addition, mixtures were artificially degraded at fou...
Article
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...
Article
Until recently, forensic DNA profile interpretation was predominantly a manual, time‐consuming process undertaken by analysts using heuristics to determine those genotype combinations that could reasonably explain a recovered profile. Probabilistic genotyping (PG) has now become commonplace in the interpretation of DNA profiling evidence. As the co...
Article
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 Sample 1 (low template, in the order of 200 rfu for major contributors) five participant...
Article
Probabilistic genotyping typically proceeds by first deconvoluting a mixture into separate components and then computing a likelihood ratio for a potential contributor. The typical range of likelihood ratios for contributors and unrelated profiles depends, to a large extent, on how well the mixture is resolved. This in turn depends on the quality a...
Article
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 numbe...
Article
Modern interpretation strategies typically require an assignment of the number of contributors (N) to a DNA profile. This can prove to be a difficult task, particularly when dealing with higher order mixtures or mixtures where one or more contributors have donated low amounts of DNA. Differences in the assigned N at interpretation can lead to diffe...
Article
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 sample to sample contamination) and for intelligence gathering purposes (did the same unk...
Article
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 examples. 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 =...
Book
Now in its second edition, Forensic DNA Evidence Interpretation is the most comprehensive resource for DNA casework available today. Written by leaders in the fields of biology and statistics, including a contribution from Peter Gill, the father of DNA analysis, the book emphasizes the interpretation of test results and provides the necessary formu...
Article
Full-text available
Rapid growth in world trade has enabled transnational criminal networks to conceal their contraband among the 1 billion containers shipped worldwide annually. Forensic methods are needed to identify the major cartels moving the contraband into transit. We combine DNA-based sample matching and geographic assignment of tusks to show that the two tusk...
Article
Forensic DNA interpretation is transitioning from manual interpretation based usually on binary decision‐making toward computer‐based systems that model the probability of the profile given different explanations for it, termed probabilistic genotyping (PG). Decision‐making by laboratories to implement probability‐based interpretation should be bas...
Article
MIX13 was an interlaboratory exercise directed by NIST in 2013. The goal of the exercise was to evaluate the general state of interpretation methods in use at the time across the forensic community within the US and Canada and to measure the consistency in mixture interpretation. The findings were that there was a large variation in analysts’ inter...
Article
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 betwee...
Article
Full-text available
Recently, Lund and Iyer (L&I) raised an argument regarding the use of likelihood ratios in court. In our view, their argument is based on a lack of understanding of the paradigm. L&I argue that the decision maker should not accept the expert's likelihood ratio without further consideration. This is agreed by all parties. In normal practice, there i...
Article
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 individual with a recent common ancestor. We have called the new method the “H...
Article
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 accurac...
Article
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 sample through a PG calculator, the examiner must first interpret the sample, considering such things as art...
Article
We report a large compilation of the internal validations of the probabilistic genotyping software STRmix™. Thirty one laboratories contributed data resulting in 2825 mixtures comprising three to six donors and a wide range of multiplex, equipment, mixture proportions and templates. Previously reported trends in the LR were confirmed including less...
Article
Full-text available
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...
Article
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....
Article
Full-text available
A recent report by the US President’s Council of Advisors on Science and Technology (PCAST) [1] has made a number of recommendations for the future development of forensic science. Whereas we all agree that there is much need for change, we find that the PCAST report recommendations are founded on serious misunderstandings. We explain the tradition...
Article
The interpretation of DNA evidence can entail analysis of challenging STR typing results. Genotypes inferred from low quality or quantity specimens, or mixed DNA samples originating from multiple contributors, can result in weak or inconclusive match probabilities when a binary interpretation method and necessary thresholds (such as a stochastic th...
Article
An update was performed of the classic experiments that led to the view that profile probability assignments are usually within a factor of 10 of each other. The data used in this study consist of 15 Identifiler loci collected from a wide range of forensic populations. Following Budowle et al. [1], the terms cognate and non-cognate are used. The co...
Article
Full-text available
Background The evaluation and interpretation of forensic DNA mixture evidence faces greater interpretational challenges due to increasingly complex mixture evidence. Such challenges include: casework involving low quantity or degraded evidence leading to allele and locus dropout; allele sharing of contributors leading to allele stacking; and differ...
Article
Hd true testing is a way of assessing the performance of a model, or DNA profile interpretation system. These tests involve simulating DNA profiles of non-donors to a DNA mixture and calculating a likelihood ratio (LR) with one proposition postulating their contribution and the alternative postulating their non-contribution. Following Turing it is...
Article
The use of biostatistical software programs to assist in data interpretation and calculate likelihood ratios is essential to forensic geneticists and part of the daily case work flow for both kinship and DNA identification laboratories. Previous recommendations issued by the DNA Commission of the International Society for Forensic Genetics (ISFG) c...
Article
Full-text available
Allele distributions for twenty-three autosomal short tandem repeat (STR) loci - D1S1656, D2S441, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D10S1248, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, D22S1045, CSF1PO, FGA, Penta D, Penta E, SE33, TH01, TPOX and vWA - were determined in Caucasians, Southwestern Hispanics, Southeastern Hispanics,...