Thore Egeland

Thore Egeland
Norwegian University of Life Sciences (NMBU) · Research Group for Biostatistics

PhD

About

279
Publications
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Publications

Publications (279)
Article
Full-text available
We address computational and statistical aspects of DNA-based identification of victims in the aftermath of disasters. Current methods and software for such identification typically consider each victim individually, leading to suboptimal power of identification and potential inconsistencies in the statistical summary of the evidence. We resolve th...
Article
The present work proposes a general strategy for dealing with missing person identi- fication cases through DNA-database search. Our main example is the identification of abducted children in the last civic-dictatorship of Argentina, known as the “Miss- ing Grandchildren of Argentina”. Particularly we focus on those pedigrees where few, or only dis...
Article
Full-text available
Missing person identification typically involves genetic matching of a person of interest against relatives of the missing person. In cases with few available relatives, exhumations or other substantial efforts may be necessary in order to secure adequate statistical power. We propose a simulation approach for solving prioritisation problems arisin...
Article
Full-text available
In both criminal cases and relationship inference there is an increasing demand for analysis of DNA mixtures where relatives are involved. The goal might be to identify the contributors to a mixture where the donors may or may not be related, or to determine the relationship between individuals based on a mixture. relMix is an open source software...
Article
Full-text available
This paper describes a strategy for estimating chronological age of individuals based on age indicators of X-ray of the hand and the third molar tooth. The great majority of studies in the field provide group-wise data of different formats, which makes them difficult to compare and utilize in a model. In this paper, we have provided a framework to...
Article
Methods and implementations of DNA-based identification are well established in several forensic contexts. However, assessing the statistical power of these methods has been largely overlooked, except in the simplest cases. In this paper we outline general methods for such power evaluation, and apply them to a large set of family reunification case...
Article
Forensic genetic laboratories perform an increasing amount of genetic analyses of the X chromosome, in particular to solve complex cases of kinship analysis. For some biological relationships X-chromosomal markers can be more informative than autosomal markers, and there are a large number of markers, methods and databases that have been described...
Article
Some practical and theoretical aspects of evaluation of evidence based on the likelihood ratio (LR) in kinship cases are discussed. If relationships are complex or if complicating factors like mutation, correction for population structure or silent alleles need to be accounted for, available software may fail. We present an explicit general formula...
Article
Full-text available
Simulation experiments were used to show the impact of varying extraction efficiency, aliquot proportion, and PCR efficiency on the heterozygote balance of a range of diploid and haploid cells. Reducing either parameters introduces variance. It is well-known that the variance in heterozygote balance increases as the amount of DNA is reduced. Surpri...
Article
The existence of pedigrees belonging to the same kinship class (i.e. indistinguishable through independent markers) is well known in the forensic community, and theoretical frameworks for autosomal and X-chromosomal markers were already developed for a pair of individuals. Nevertheless, studies for the cases where a greater number of individuals is...
Article
In court questions are often raised related to how trace DNA was deposited, directly during the crime or innocently for instance by secondary transfer. It is therefore of interest to have knowledge of the probability of transfer or secondary transfer in different situations. Factors that could influence transfer probabilities are background DNA and...
Article
Routine forensic analysis using STRs will fail if the DNA is too degraded. The DNA degradation process in biological stain material is not well understood. In this study we sequenced old semen and blood stains by massively parallel sequencing. The sequence data coverage was used to measure degradation across the genome. The results supported the co...
Chapter
The chapter introduces the concept of dependency between markers and alleles. With the constant increase in the number of genetic markers analyzed, linkage is unavoidable. Efficient computational models to handle linked markers exist, and we explain the Lander–Green algorithm as well as present an extension to account for association between allele...
Chapter
The chapter provides a theoretical overview of the models most commonly used in the computation of the probability of DNA test data given a pedigree. We divide such models into three types: a population-level model, a pedigree-level model, and an observational-level model. Uncertainty of allele frequencies is modeled using Dirichlet distributions,...
Chapter
The chapter extends the ideas from the first chapters and puts the inference of relationships in a broader context. Searching for relatives in databases is introduced by means of familial searching and disaster victim identification. The same ideas may also be applied to missing person identifications.
Chapter
This final chapter applies decision theory to relationship inference problems. Specifically, it is shown how decision theory can help not only with the basic question of which pedigree should be chosen, but also in more complex questions such as which typing technology to use for relationship inference. In the question of whether one should acquire...
Chapter
The chapter contains examples of procedures for estimation of parameters in probability models for relationship inference. The main examples are the theta correction parameter, the lambda parameter for haplotype estimation, and the mutation rate parameter. The same general Bayesian framework is applied to all these, and can be extended to other par...
Chapter
The purpose of the chapter is to provide a first introduction to the basic methods for relationship inference. Following an introduction to forensic markers, the likelihood ratio (LR) is introduced and exemplified, first for a standard paternity case. The LR is widely used to summarize the statistical evidence in a wide range of forensic applicatio...
Chapter
The main part of the chapter is a sequence of introductory examples that use the Familias R package. The first example presents the most basic functions, such as building pedigrees, specifying marker information, specifying case data, and computing likelihoods and posterior probabilities. The following examples look more closely at things such as m...
Chapter
The chapter presents the aim of the book: to describe and discuss a statistical framework for relationship inference based on DNA data. The purpose is to convey a comprehensive theoretical understanding of some of the most commonly used models and to enable practitioners to perform statistical calculations on real-life case data. Some background in...
Article
Full-text available
The likelihood ratio is the fundamental quantity that summarizes the evidence in forensic cases. Therefore, it is important to understand the theoretical properties of this statistic. This paper is the last in a series of three, and the first to study linked markers. We show that for all non-inbred pairwise kinship comparisons, the expected likelih...
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
Mixture DNA profiles commonly appear in forensic genetics, and a large number of statistical methods and software are available for such cases. However, most of the literature concerns mixtures where the contributors are assumed unrelated and the genetic markers are unlinked. In this paper, we consider mixtures of linked markers and related contrib...
Article
As the profiling systems used in forensic analyses have become more sensitive in recent years, the risk of detecting a contamination in a DNA sample has increased proportionally. This requires more stringent work protocols and awareness to minimize the chance of contamination. Although there is high consciousness on contamination and best practice...
Article
Full-text available
Background: High-Density Lipoprotein (HDL)-cholesterol, has been associated with breast cancer development, but the association is under debate, and whether lipoprotein subfractions is associated with breast tumor characteristics remains unclear. Methods: Among 56 women with newly diagnosed invasive breast cancer stage I/II, aged 35-75 years, pr...
Article
Full-text available
Today, there exists a number of tools for solving kinship cases. But what happens when information comes from a mixture? DNA mixtures are in general rarely seen in kinship cases, but in a case presented to the Norwegian Institute of Public Health, sample DNA was obtained after a rape case that resulted in an unwanted pregnancy and abortion. The onl...
Article
The statistical evidence obtained from mixed DNA profiles can be summarised in several ways in forensic casework including the likelihood ratio (LR) and the Random Man Not Excluded (RMNE) probability. The literature has seen a discussion of the advantages and disadvantages of likelihood ratios and exclusion probabilities, and part of our aim is to...
Article
Full-text available
There is a large number of applications where family relationships need to be determined from DNA data. In forensic science, competing ideas are in general verbally formulated as the two hypotheses of a test. For the most common paternity case, the null hypothesis states that the alleged father is the true father against the alternative hypothesis...
Article
There has been recent interest in the exploitation of readily available dense genome scan marker data for the identification of relatives. However, there are conflicting findings on how informative these data are in practical situations and, in particular, sets of thinned markers are often used with no concrete justification for the chosen spacing....
Article
Caesarean section (CS) on maternal request is increasing. There is a need to understand why, and find measures to help women give birth vaginally. The purpose of this study was to compare the rate of complications in the first birth of 129 second time mothers wanting caesarean section with the rate of complications in the general population; to det...
Article
With the introduction of new multiplex PCR kits and instrumentation such as the Applied Biosystems 3500xl, there has recently been a rapid change in technology that has greatly increased sensitivity of detection so that a DNA profile can routinely be obtained from only a few cells. Research to evaluate the risks of passive transfer has not kept pac...
Article
The introduction of Short Tandem Repeat (STR) DNA was a revolution within a revolution that transformed forensic DNA profiling into a tool that could be used, for the first time, to create National DNA databases. This transformation would not have been possible without the concurrent development of fluorescent automated sequencers, combined with th...
Article
Full-text available
High-density lipoprotein-cholesterol (HDL-C) may influence the proliferation of breast tumor cells, but it is unclear whether low HDL-C levels, alone or in combination with cyclic estrogen and progesterone, is associated with mammographic density, a strong predictor of breast cancer development. Fasting morning serum concentrations of HDL-C were as...
Book
Relationship Inference in Familias and R discusses the use of Familias and R software to understand genetic kinship of two or more DNA samples. This software is commonly used for forensic cases to establish paternity, identify victims or analyze genetic evidence at crime scenes when kinship is involved. The book explores utilizing Familias software...
Article
Full-text available
IntroductionHigh mammographic density is an established breast cancer risk factor, and circulating oestrogen influence oestrogen-regulating gene expression in breast cancer development. However, less is known about the interrelationships of common variants in the CYP19A1 gene, daily levels of oestrogens, mammographic density phenotypes, and body ma...
Article
Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available t...
Article
In relationship testing the aim is to determine the most probable pedigree structure given genetic marker data for a set of persons. Disaster Victim Identification (DVI) based on DNA data from presumed relatives of the missing persons can be considered to be a collection of relationship problems. Forensic calculations in investigative mode address...
Article
Full-text available
Allelic dropout in relationship problems may commonly appear in areas such as disaster victim identification and the identification of missing persons. If dropout is not accounted for, the results may be incorrect interpretation of profiles, loss of valuable information and biased results. In this paper, we explore different models for dropout in k...
Article
Likelihood ratio (LR) methods to interpret multi-contributor, low template, complex DNA mixtures are becoming standard practice. The next major development will be to introduce search engines based on the new methods to interrogate very large national DNA databases, such as those held by China, the USA and the UK. Here we describe a rapid method th...
Conference Paper
Full-text available
The recent development of high-throughput systems for genotyping SNP in Eukaryote has led to an extraordinary amount of research activity, particularly in areas such as whole-genome selection of livestock and genome-wide association studies for detection of quantitative trait. Recent technological advances allow us to rapidly genotype more than 10...
Article
Background: High-Density Lipoprotein Cholesterol (HDL-C), and ovarian steroid hormones and mammographic density have independently been associated with breast cancer development. However, little is known regarding the association between HDL-C, ovarian hormones and mammographic density in premenopausal women. Material and Methods: We assessed fasti...
Article
This paper deals with the statistical interpretation of DNA mixture evidence. The conventional methods used in forensic casework today use something like 16 STR-markers. Power can be increased by rather using SNP-markers. New statistical methods are then needed, and we present a regression framework. The basic idea is that the traditional forensic...
Article
If complex DNA profiles, conditioned on multiple individuals are evaluated, it may be difficult to assess the strength of the evidence based on the likelihood ratio. A likelihood ratio does not give information about the relative weights that are provided by separate contributors. Alternatively, the observed likelihood ratio can be evaluated with r...
Article
DNA mixture evidence pertains to cases where several individuals may have contributed to a biological stain. Statistical methods and software for such problems are available and a large number of cases can be handled adequately. However, one class of mixture problems remains untreated in full generality in the literature, namely when the contributo...
Article
Full-text available
In forensic genetics, DNA profiles are compared in order to make inferences, paternity cases being a standard example. The statistical evidence can be summarised and reported in several ways. For example, in a paternity case, the likelihood ratio ($LR$) and the probability of not excluding a random man as father ($RMNE$) are two common summary stat...
Article
There is general lack of awareness that high LR based on complex propositions e.g. three contributors, does not necessarily translate into probative evidence against a suspect. In some cases there is an increased chance of false inclusion of a person of interest. This is an issue for all LR-based models. One way to address this issue is to further...
Article
Likelihood ratios used for the analysis of complex DNA mixtures depend on a number of modeling assumptions and parameter estimates. In particular, the LR does not give information about the relative weight of the separate contributors for hypotheses conditioned on several contributors. An alternative is to evaluate the observed LR with respect to l...
Conference Paper
Inferential studies on genetic relatedness fall into two broad approaches: (a) the genetic types of the individuals are used to compare the likelihood of their relatedness through specific genealogies; or (b) the genetic information is evaluated to infer the degree (or level) of relatedness between the individuals without specifying any pedigree. A...
Article
Full-text available
The statistical evidence obtained from mixed DNA profiles can be summarised in several ways in forensic casework including the likelihood ratio (LR) and the Random Man Not Excluded (RMNE) probability. The literature has seen a discussion of the advantages and disadvantages of likelihood ratios and exclusion probabilities, and part of our aim is to...
Article
Background: Dyslipidemia, excess weight, and high mammographic density have independently been associated with breast cancer development. However, little is known regarding the combined effect of dyslipidemia, excess weight and mammographic density on cyclic variation in estrogen and progesterone. Material and Methods: 202 premenopausal women (25-3...
Article
This paper is motivated by power considerations in connection with relationship testing. Given the true relationship between a set of individuals, a claimed relationship between the same individuals, and a set of genetic markers, we compute the power of exclusion, i.e., the probability that the genotypes will be incompatible with the claimed relati...
Article
Full-text available
The statistical interpretation of the forensic genetic evidence requires the use of allelic frequency estimates in the reference population for the studied markers. Differences in the genetic make up of the populations can be reflected in statistically different allelic frequency distributions. One can easily figure out that collecting such informa...
Article
Full-text available
Bifidobacteria are a major microbial component of infant gut microbiota, which is believed to promote health benefits for the host and stimulate maturation of the immune system. Despite their perceived importance, very little is known about the natural development of and possible correlations between bifidobacteria in human populations. To address...
Article
Full-text available
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...
Data
Observed haplotype frequencies. (DOC)
Data
Expected haplotype frequencies. (DOC)
Data
Bayesian network describing a sibling case, where the children are known to share the same mother. The nodes P/M tell whether the vWa paternal or maternal allele is inherited. The P/M node connected to the D12S391 allele also contains the recombination frequency. The LD node is connected to the paternal and maternal allele nodes and decides whether...
Article
The present number of STR loci adopted in relationship testing is chiefly limited to unlinked markers, in most cases residing on different chromosomes. In order to solve more complex cases of relatedness, e.g. deficient paternities and disputed sibships, the number of core loci can be extended. The inclusion of multiple loci on the same chromosome...