DNAxs/DNAStatistX: Development and validation of a software suite for the data management and probabilistic interpretation of DNA profiles

Benschop, Corina C.G.; Hoogenboom, Jerry; Hovers, Pauline; Slagter, Martin; Kruise, Dennis; Parag, Raymond; Steensma, Kristy; Slooten, Klaas; Nagel, Jord H.A.; Dieltjes, Patrick; Marion, Vincent; Paassen, Heidi Van; Jong, Jeroen de; Creeten, Christophe; Sijen, Titia; Kneppers, A. L. J.

doi:10.1016/j.fsigen.2019.06.015

Cited by 38 publications

(23 citation statements)

References 20 publications

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“…Increased complexity of DNA profile comparisons and interpretation demands fast and automated software tools to assist DNA experts in routine casework. eDNA is one such application [127], whose functionalities were an inspiration for the development of CaseSolver [21] and the DNA eXpert System DNAxs [128].…”

Section: Dnaxs and Related Modulesmentioning

confidence: 99%

“…By aggregating replicate profiles into one composite view (bar graphs) 2. By viewing the trace profile as bar graphs underneath which alleles of reference profiles are comparedThrough the match matrix option 3 By sending a DNA profile for a SmartRank search against the DNA database 4 By calculating LRs using DNAStatistX for a comparison of a person of interest to a trace DNA profile [128] DNAxs imports (pre-analyzed) DNA profiling data which is shown as the original electropherogram and is graphically represented as bar graphs with a color coding for reproduced and non-reproduced alleles in case of PCR replicates, and a color coding for alleles of the major component of a mixture through the LoCIM method (Locus Classification and Inference of the Major) [29]. This LoCIM method can be applied to one amplification of a DNA extract or to replicate DNA profiles.…”

Section: Dnaxs and Related Modulesmentioning

confidence: 99%

“…Lastly, through web APIs (Application Programming Interfaces) DNAxs can communicate with, for instance, CODIS, LIMS systems, SmartRank, and Bonaparte [128]. Additionally, as previously mentioned, for weight of evidence calculations, DNAxs implements DNAStatistX, which, alike EuroForMix, uses the γ distribution to model peak heights.…”

Section: Dnaxs and Related Modulesmentioning

confidence: 99%

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A Review of Probabilistic Genotyping Systems: EuroForMix, DNAStatistX and STRmix™

Gill

Benschop

Buckleton

et al. 2021

Genes

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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 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.

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Section: Dnaxs and Related Modulesmentioning

confidence: 99%

Section: Dnaxs and Related Modulesmentioning

confidence: 99%

Section: Dnaxs and Related Modulesmentioning

confidence: 99%

See 1 more Smart Citation

A Review of Probabilistic Genotyping Systems: EuroForMix, DNAStatistX and STRmix™

Gill

Benschop

Buckleton

et al. 2021

Genes

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“…Mixture deconvolution is one of the most engaging topics in forensics. Over previous years different methods have been developed to assist the process, both prior to [ 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 ] and after, DNA typing of a mixed trace [ 36 , 37 , 38 ]. The DEPArray System, which uses a dielectrophoresis grid to isolate single cells, is a promising cell separation technology for forensic analysis.…”

Section: Discussionmentioning

confidence: 99%

Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing

Diepenbroek

Bayer

Anslinger

2021

Genes

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Single-cell sequencing is a fast developing and very promising field; however, it is not commonly used in forensics. The main motivation behind introducing this technology into forensics is to improve mixture deconvolution, especially when a trace consists of the same cell type. Successful studies demonstrate the ability to analyze a mixture by separating single cells and obtaining CE-based STR profiles. This indicates a potential use of the method in other forensic investigations, like forensic DNA phenotyping, in which using mixed traces is not fully recommended. For this study, we collected single-source autopsy blood from which the white cells were first stained and later separated with the DEPArray™ N×T System. Groups of 20, 10, and 5 cells, as well as 20 single cells, were collected and submitted for DNA extraction. Libraries were prepared using the Ion AmpliSeq™ PhenoTrivium Panel, which includes both phenotype (HIrisPlex-S: eye, hair, and skin color) and ancestry-associated SNP-markers. Prior to sequencing, half of the single-cell-based libraries were additionally amplified and purified in order to improve the library concentrations. Ancestry and phenotype analysis resulted in nearly full consensus profiles resulting in correct predictions not only for the cells groups but also for the ten re-amplified single-cell libraries. Our results suggest that sequencing of single cells can be a promising tool used to deconvolute mixed traces submitted for forensic DNA phenotyping.

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“…These can then be used to generate likelihoods for propositions which can in turn be combined into LRs. There are a number of continuous PG algorithms available including DNA•VIEW ® [6], TrueAllele ® Casework [7,8] (Cybergenetics, Pittsburgh, PA, USA), STRmix™ [9] (Institute of Environmental Science and Research, Forensic Science South Australia, Adelaide, SA, Australia), EuroForMix [10] and DNAxs [11]. The latter two PG systems are an extended version of the model proposed by Cowell et al [12] which is open source while the other three require commercial licences [13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Proposed Framework for Comparison of Continuous Probabilistic Genotyping Systems amongst Different Laboratories

et al. 2021

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Continuous probabilistic genotyping (PG) systems are becoming the default method for calculating likelihood ratios (LRs) for competing propositions about DNA mixtures. Calculation of the LR relies on numerical methods and simultaneous probabilistic simulations of multiple variables rather than on analytical solutions alone. Some also require modelling of individual laboratory processes that give rise to electropherogram artefacts and peak height variance. For these reasons, it has been argued that any LR produced by continuous PG is unique and cannot be compared with another. We challenge this assumption and demonstrate that there are a set of conditions defining specific DNA mixtures which can produce an aspirational LR and thereby provide a measure of reproducibility for DNA profiling systems incorporating PG. Such DNA mixtures could serve as the basis for inter-laboratory comparisons, even when different STR amplification kits are employed. We propose a procedure for an inter-laboratory comparison consistent with these conditions.

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DNAxs/DNAStatistX: Development and validation of a software suite for the data management and probabilistic interpretation of DNA profiles

Cited by 38 publications

References 20 publications

A Review of Probabilistic Genotyping Systems: EuroForMix, DNAStatistX and STRmix™

A Review of Probabilistic Genotyping Systems: EuroForMix, DNAStatistX and STRmix™

Pushing the Boundaries: Forensic DNA Phenotyping Challenged by Single-Cell Sequencing

Proposed Framework for Comparison of Continuous Probabilistic Genotyping Systems amongst Different Laboratories

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