PedExpert: a computer program for the application of Bayesian networks to human paternity testing

Gomes, Raquel Regina de Freitas Magalhães; Campos, S.V.A.; Pena, Sérgio D. J.

doi:10.4238/vol8-1gmr555

Cited by 3 publications

(3 citation statements)

References 9 publications

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“…Computer programs designed for the analysis of pedigrees can be classified into two categories. The programs in the first category employ the distinctive pull-down menus [10,12,13,18,19]. Those in the second category use common software applications, such as Microsoft Excel [11], and the end users must perform manual operations, such as general computer manipulations and spreadsheet selections, to calculate the probability of paternity with these programs Figure 5: Script used for analysis of the standard trio case, which is the scenario described in Paternity Test Case 1.…”

Section: Resultsmentioning

confidence: 99%

“…However, a case is more complicated when the genotype of the alleged father is not available, but the genotype of one or more of the following individuals is available: his mother, his father, one or more of his siblings, his wife, or one or more of his biological children. Computer programs have been written for the purpose of determining paternity given genetic data from a complicated or incomplete pedigree [10][11][12][13][14][15][16][17][18][19][20][21][22]. However, most papers describing such programs provide only minimal and generalized calculations and are, therefore, accessible only to mathematicians and researchers with an excellent mathematical background.…”

Section: Programming Scripts For Simple and Complex Paternity Testingmentioning

confidence: 99%

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Programming Scripts for Simple and Complex Paternity Testing based on Open-Source Programming Language from the R Project

Takamiya¹,

Aoki²,

Dewa³

2014

JOURNAL OF FORENSIC SCIENCE & CRIMINOLOGY

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Programming scripts were written for the statistical analysis of genetic data from simple cases and complex cases of undetermined paternity. The methods presented here involve algorithms constructed with R, an open-source and increasingly popular programming language used for calculations and statistics; these methods also involve conditional probability analysis, Bayes' Theorem, and pedigree analysis. Previous computer programs for assessing probable paternity in complex cases of undetermined paternity have been written; however, only minimal or generalized formulas are described in the papers presenting these programs. Therefore, these previously published programs are difficult to understand for most forensic researchers. Here, we present the details of the calculations used to evaluate probabilities of paternity and the details of the R scripts used execute these calculations. These scripts were constructed not only for standard trio case where DNA typing of the mother, child, and the alleged father are available, but also for more complex cases where DNA typing of the alleged father is absent. In these more complex cases, the putative genotype of the alleged father is determined from the genotypes of his parents, his siblings, his wife, children known to be his biological children, or some combination of these people. This report provides concrete and orderly descriptions of the calculations and the R scripts so that each facet of this method is easily understood. Furthermore, access to these scripts will enable individual researchers to develop calculation systems of their own.

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Section: Resultsmentioning

confidence: 99%

Section: Programming Scripts For Simple and Complex Paternity Testingmentioning

confidence: 99%

Programming Scripts for Simple and Complex Paternity Testing based on Open-Source Programming Language from the R Project

Takamiya¹,

Aoki²,

Dewa³

2014

JOURNAL OF FORENSIC SCIENCE & CRIMINOLOGY

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show abstract

“…The nodes are connected to other nodes and the interplay is governed by probabilities within each node. Several studies have already shown the advantages of using OOBN in forensic contexts [15], [16], [17], [18], [19], [20]. Taroni et al [15] offers a thorough introduction to the basic methodology.…”

Section: Introductionmentioning

confidence: 99%

Using Object Oriented Bayesian Networks to Model Linkage, Linkage Disequilibrium and Mutations between STR Markers

2012

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In a number of applications there is a need to determine the most likely pedigree for a group of persons based on genetic markers. Adequate models are needed to reach this goal. The markers used to perform the statistical calculations can be linked and there may also be linkage disequilibrium (LD) in the population. The purpose of this paper is to present a graphical Bayesian Network framework to deal with such data. Potential LD is normally ignored and it is important to verify that the resulting calculations are not biased. Even if linkage does not influence results for regular paternity cases, it may have substantial impact on likelihood ratios involving other, more extended pedigrees. Models for LD influence likelihoods for all pedigrees to some degree and an initial estimate of the impact of ignoring LD and/or linkage is desirable, going beyond mere rules of thumb based on marker distance. Furthermore, we show how one can readily include a mutation model in the Bayesian Network; extending other programs or formulas to include such models may require considerable amounts of work and will in many case not be practical. As an example, we consider the two STR markers vWa and D12S391. We estimate probabilities for population haplotypes to account for LD using a method based on data from trios, while an estimate for the degree of linkage is taken from the literature. The results show that accounting for haplotype frequencies is unnecessary in most cases for this specific pair of markers. When doing calculations on regular paternity cases, the markers can be considered statistically independent. In more complex cases of disputed relatedness, for instance cases involving siblings or so-called deficient cases, or when small differences in the LR matter, independence should not be assumed. (The networks are freely available at http://arken.umb.no/~dakl/BayesianNetworks.)

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An optimized approach for Paternity Testing using rs numbers and whole genome

Mondy

Mohamed

Ehab

et al. 2022

2022 2nd International Mobile, Intelligent, and Ubiquitous Computing Conference (MIUCC)

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PedExpert: a computer program for the application of Bayesian networks to human paternity testing

Cited by 3 publications

References 9 publications

Programming Scripts for Simple and Complex Paternity Testing based on Open-Source Programming Language from the R Project

Programming Scripts for Simple and Complex Paternity Testing based on Open-Source Programming Language from the R Project

Using Object Oriented Bayesian Networks to Model Linkage, Linkage Disequilibrium and Mutations between STR Markers

An optimized approach for Paternity Testing using rs numbers and whole genome

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