Impact of allelic dropout on evidential value of forensic DNA profiles using RMNE

Motivation: Two methods are commonly used to report on evidence carried by forensic DNA profiles: the ‘Random Man Not Excluded’ (RMNE) approach and the likelihood ratio (LR) approach. It is often claimed a major advantage of the LR method that dropout can be assessed probabilistically

Evaluation of forensic evidence in DNA mixture using RMNE

Invited Paper Sessions (IPS) 21: Statistical reasoning in lawTo establish the link between an arrested suspect and a crime case based on a DNA mixture, one of the two main statistical tools used by forensic scientists is the random man not excluded (RMNE) probability. The tradi- tional RMNE approach omits any knowledge on the number of contributors and is commonly regarded as being less powerful than the likelihood (LR) approach. In view of the simplicity of interpretation of RMNE, which is the major advantage of using it to present DNA evidences in court, we present a new concept for the interpretation and calculation of the RMNE proba- bility. A new approach for determining the non-exclusion of a random man is proposed, upon which a general formula for the calculation of RMNE probability is developed. By taking account of the number of contributors, the new RMNE probability can be much more powerful for evaluating the evidentiary value of non excluded suspects, compared to the traditional RMNE approach. As illustrated by an example based on a real rape case, our approach can be easily implemented and can shorten the gap between the two approaches by utilizing more information of the case.published_or_final_versio

Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles.

BackgroundTechnological advances have enabled the analysis of very small amounts of DNA in forensic cases. However, the DNA profiles from such evidence are frequently incomplete and can contain contributions from multiple individuals. The complexity of such samples confounds the assessment of the statistical weight of such evidence. One approach to account for this uncertainty is to use a likelihood ratio framework to compare the probability of the evidence profile under different scenarios. While researchers favor the likelihood ratio framework, few open-source software solutions with a graphical user interface implementing these calculations are available for practicing forensic scientists.ResultsTo address this need, we developed Lab Retriever, an open-source, freely available program that forensic scientists can use to calculate likelihood ratios for complex DNA profiles. Lab Retriever adds a graphical user interface, written primarily in JavaScript, on top of a C++ implementation of the previously published R code of Balding. We redesigned parts of the original Balding algorithm to improve computational speed. In addition to incorporating a probability of allelic drop-out and other critical parameters, Lab Retriever computes likelihood ratios for hypotheses that can include up to four unknown contributors to a mixed sample. These computations are completed nearly instantaneously on a modern PC or Mac computer.ConclusionsLab Retriever provides a practical software solution to forensic scientists who wish to assess the statistical weight of evidence for complex DNA profiles. Executable versions of the program are freely available for Mac OSX and Windows operating systems

Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles

BACKGROUND: Technological advances have enabled the analysis of very small amounts of DNA in forensic cases. However, the DNA profiles from such evidence are frequently incomplete and can contain contributions from multiple individuals. The complexity of such samples confounds the assessment of the statistical weight of such evidence. One approach to account for this uncertainty is to use a likelihood ratio framework to compare the probability of the evidence profile under different scenarios. While researchers favor the likelihood ratio framework, few open-source software solutions with a graphical user interface implementing these calculations are available for practicing forensic scientists. RESULTS: To address this need, we developed Lab Retriever, an open-source, freely available program that forensic scientists can use to calculate likelihood ratios for complex DNA profiles. Lab Retriever adds a graphical user interface, written primarily in JavaScript, on top of a C++ implementation of the previously published R code of Balding. We redesigned parts of the original Balding algorithm to improve computational speed. In addition to incorporating a probability of allelic drop-out and other critical parameters, Lab Retriever computes likelihood ratios for hypotheses that can include up to four unknown contributors to a mixed sample. These computations are completed nearly instantaneously on a modern PC or Mac computer. CONCLUSIONS: Lab Retriever provides a practical software solution to forensic scientists who wish to assess the statistical weight of evidence for complex DNA profiles. Executable versions of the program are freely available for Mac OSX and Windows operating systems. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0740-8) contains supplementary material, which is available to authorized users

Statistical aspects of forensic genetics:Models for qualitative and quantitative STR data

This PhD thesis deals with statistical models intended for forensic genetics, which is the part of forensic medicine concerned with analysis of DNA evidence from criminal cases together with calculation of alleged paternity and affinity in family reunification cases. The main focus of the thesis is on crime cases as these differ from the other types of cases since the biological material often is used for person identification contrary to affinity. Common to all cases, however, is that the DNA is used as evidence in order to assess the prob-ability of observing the biological material given different hypotheses. Most countries use com-mercially manufactured DNA kits for typing a person’s DNA profile. Using these kits the DNA profile is constituted by the state of 10-15 DNA loci which has a large variation from person to person in the population. Thus, only a small fraction of the genome is typed, but due to the large variability, it is possible to identify individuals with very high probability. These probabil-ities are used when calculating the weight of evidence, which in some cases corresponds to the likelihood of observing a given suspect’s DNA profile in the population. By assessing the probability of the DNA evidence under competing hypotheses the biologica

Progress in Forensic Genetics: New Markers Validation Studies and Population Data

Los objetivos de esta tesis son: - validar una pentaplex de nueva generación que incluya los cinco nuevos marcadores recomendados por el Consejo de la Unión Europea para la extensión del lo European Standard Set (ESS) mediante evaluación del nivel de información de los datos y del éxito del análisis sobre una amplia gama de muestras forenses y también comparar su funcionamiento con el que de otros equipos disponibles comercialmente. - crear una base de datos demográfica útil en forense que incluye una estimación de la frecuencia de cada allelo posible y genotipo (o haplotipo), estudiando la variabilidad en el Área mediterránea de 15 STRs autosómicosl bien establecidos juntos con los 5 nuevos marcadores EES, el sumamente discriminante SE33 y algún STRs de los chromosomes sexuales comúnemente usados en la investigación forense. Finalmente pretendemos evaluar la variabilidad de la 52 SNPplex recientemente introducida para usos forense

Porting forensic DNA analysis to deep sequencing

Forensic DNA profiles of short tandem repeat (STR) loci are currently obtained using PCR followed by capillary electrophoresis (CE). Massively parallel sequencing (MPS) technologies do not rely on size separation and thus relieve the limitations on locus multiplexy. Deep sequencing with MPS creates possibilities within forensics for analyzing degraded samples and mixed samples. Furthermore, in the same analysis single nucleotide polymorphism (SNP) markers can be included, which can generate phenotypic or ancestry leads for forensic investigators. Data analysis of raw sequencer reads, resulting in a reliable and usable forensic human identification report is still in early development. The aim of the doctoral research was to develop a program for forensic DNA data analysis. The main results are the data analysis framework MyFLq (My Forensic Loci queries) and nomenclature service FLAD (Forensic Loci Allele Database). MyFLq and FLAD can be used together in a forensic workflow that has backward compatibility with CE. To my knowledge, this is the first open-source and complete solution for forensic MPS raw data analysis

Helping with inquiries: theory and practice in forensic science

This thesis investigates the reasoning practices of forensic scientists, with specific focus on the application of the Bayesian form of probabilistic reasoning to forensic science matters. Facilitated in part by the insights of evidence scholarship, Bayes Theorem has been advocated as an essential resource for the interpretation and evaluation of forensic evidence, and has been used to support the production of specific technologies designed to aid forensic scientists in these processes. In the course of this research I have explored the ways in which Bayesian reasoning can be regarded as a socially constructed collection of practices, despite proposals that it is simply a logical way to reason about evidence. My data are drawn from two case studies. In the first, I demonstrate how the Bayesian algorithms used for the interpretation of complex DNA profiles are themselves elaborately constructed devices necessary for the anchoring of scientific practice to forensic contexts. In the second case study, an investigation of a more generalised framework of forensic investigation known as the Case Assessment and Interpretation (CAI) model, I show how the enactment of Bayesian reasoning is dependent on a series of embodied, experiential and intersubjective knowledge-forming activities. Whilst these practices may seem to be largely independent of theoretical representations of Bayesian reasoning, they are nonetheless necessary to bring the latter into being. This is at least partially due to the ambiguities and liminalities encountered in the process of applying Bayesianism to forensic investigation, and also may result from the heavy informational demands placed on the reasoner. I argue that these practices, or 'forms of Bayes', are necessary in order to negotiate areas of ontological uncertainty. The results of this thesis therefore challenge prevailing conceptions of Bayes Theorem as a universal, immutable signifier, able to be put to work unproblematically in any substantive domain, Instead, I have been able to highlight the diverse range of practices required for 'Bayesian' reasoners to negotiate the sociomaterial contingencies exposed in the process of its application

Evaluation of DNA Polymorphisms for Kinship Testing in the Population of Saudi Arabia

Short Tandem Repeats (STRs) have been the standard DNA marker employed in forensic laboratories for more than two decades. Due to the advances in the kit chemistries and separation technologies (capillary electrophoresis (CE) systems), the number of STRs that can be simultaneously typed has grown to 21-26; this provides sufficient confidence in the conclusions of most kinship cases. However, more complex cases (e.g. testing distant relatives, potential mutations, deficient cases or incest cases) or when the target population shows an increased level of consanguinity, the genetic evidence may prove inconclusive. This necessitates testing additional STRs included in supplementary STR kits. Another option is by using Massively Parallel Sequencing (MPS) systems that allow simultaneous sequencing of additional DNA markers. A total 500 samples from the population of Saudi Arabia were collected. Two CE-based STR kits were used: Globalfiler™ PCR amplification kit (AB, USA) and SureID® 23 comp Human Identification kit (Health Gene Technologies, China) that together allowed 38 aSTRs to be analysed. In addition, as the SureID® 23 comp kit has not been validated either by an independent laboratory or by the manufacturer, the kit was validated following the minimum criteria of the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM). Moreover, the ForenSeq™ DNA Signature Prep Kit (Verogen) was used to sequence 87 samples and to generate sequence-based data for 122 autosomal markers included in the kit. The project allowed, in total, obtaining size-based data for 136 autosomal markers (42 aSTRs and 94 iiSNPs) and sequence-based data for 122 autosomal markers (28 aSTRs including SE33 and 94 iiSNPs). The data were evaluated for human identification and kinship testing in Saudi Arabia Although Globalfiler™ kit provided combined match probability (CMP) of 1.42E-26 that is much higher than the kit currently used in Saudi Arabia that has a CMP of 2.23E-18 (Identifiler plus kit), the availability of data for 42 aSTRs allowed other commercially available kits to be evaluated (based on the loci they contain). The study suggests adopting VeriFilerTM Plus (AB) or PowerPlex Fusion 6C system (Promega Corporation, USA) as a standard STR kit that would provide the lowest CMPs (9.26E-29 and 1.03E-29, respectively). Adopting any of the three kits would provide sufficient confidence in most parent-child cases (trio or duo). The validation of the SureID® 23 comp has shown that the kit met the criteria commonly used in forensic genetics laboratories. In addition, the kit can benefit from some developments that were identified by the validation, in particular the addition of extra alleles in the allelic ladder and also to increase the amount of input DNA that can be added to an amplification. The kit can be used if any kinship cases showed inconclusive results with GlobalFilerTM, VeriFilerTM Plus or PowerPlex Fusion 6C allowing 38-40 aSTRs to be analysed. The ForenSeq™ DNA Signature Prep Kit provided CMP of 1.97E-68 and 3.65E-77 for the size and sequencebased data respectively, where 1.24E-37 (size-based data) and 5.6E-41 (sequence-based data) were provided from the iiSNPs alone. The kit can be used when two or three mismatches were suspected to be mutations or when testing distant relationships. The study highlighted 220 syntenic pairs, 46 of which would have significant impact on LR estimation due to lower RFs (< 0.12). The case-specific impact of linkage should be included in the estimation of LRs by using the RFs values estimated in this project