Related papers: Combining allele frequency uncertainty and populat…
In this paper, we discuss the construction of a multivariate generalisation of the Dirichlet-multinomial distribution. An example from forensic genetics in the statistical analysis of DNA mixtures motivates the study of this multivariate…
DNA databases are widely used in forensic science to identify unknown offenders. When no exact match is found, familial DNA searches can help by identifying first-degree relatives using likelihood ratios. If multiple subpopulations are…
Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…
Estimation of the allele frequency at genetic markers is a key ingredient in biological and biomedical research, such as studies of human genetic variation or of the genetic etiology of heritable traits. As genetic data becomes increasingly…
Here we present an Italian criminal case that shows how statistical methods can be used to extract information from a series of mixed DNA profiles. The case involves several different individuals and a set of different DNA traces. The case…
Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele…
We present methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a basic example would be testing whether a contributor to a mixture is the father of a child of known…
When a defendant's DNA matches a sample found at a crime scene, how compelling is the match? To answer this question, DNA analysts typically use relative frequencies, random-match probabilities or likelihood ratios. They compute these…
Familial Searching is the process of searching in a DNA database for relatives of a certain individual. It is well known that in order to evaluate the genetic evidence in favour of a certain given form of relatedness between two…
It is becoming routine to obtain datasets on DNA sequence variation across several thousands of chromosomes, providing unprecedented opportunity to infer the underlying biological and demographic forces. Such data make it vital to study…
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic…
Many forensic genetics problems can be handled using structured systems of discrete variables, for which Bayesian networks offer an appealing practical modeling framework, and allow inferences to be computed by probability propagation…
Many applications in genetic analyses utilize sampling distributions, which describe the probability of observing a sample of DNA sequences randomly drawn from a population. In the one-locus case with special models of mutation such as the…
Approximate Bayesian computation (ABC) is a likelihood-free approach for Bayesian inferences based on a rejection algorithm method that applies a tolerance of dissimilarity between summary statistics from observed and simulated data.…
Sex difference in allele frequency is an emerging topic that is critical to our understanding of ascertainment bias, as well as data quality particularly of the largely overlooked X chromosome. To detect sex difference in allele frequency…
The likelihood ratio (LR) measures the relative weight of forensic data regarding two hypotheses. Several levels of uncertainty arise if frequentist methods are chosen for its assessment: the assumed population model only approximates the…
Recently-developed genotype imputation methods are a powerful tool for detecting untyped genetic variants that affect disease susceptibility in genetic association studies. However, existing imputation methods require individual-level…
Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…
In the Admixture Model, the probability of an individual having a certain number of alleles at a specific marker depends on the allele frequencies in $K$ ancestral populations and the fraction of the individual's genome originating from…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…