Related papers: Improving sequence-based genotype calls with linka…
Family history is a major risk factor for many types of cancer. Mendelian risk prediction models translate family histories into cancer risk predictions based on knowledge of cancer susceptibility genes. These models are widely used in…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
Mendelian randomization uses genetic variants to make causal inferences about the effect of a risk factor on an outcome. With fine-mapped genetic data, there may be hundreds of genetic variants in a single gene region any of which could be…
This paper presents an efficient program for checking Mendelian consistency in a pedigree. Since pedigrees may contain incomplete and/or erroneous information, geneticists need to pre-process them before performing linkage analysis.…
In genetic studies, haplotype data provide more refined information than data about separate genetic markers. However, large-scale studies that genotype hundreds to thousands of individuals may only provide results of pooled data, where…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
Genotype imputation enhances genetic data by predicting missing SNPs using reference haplotype information. Traditional methods leverage linkage disequilibrium (LD) to infer untyped SNP genotypes, relying on the similarity of LD structures…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…
Many DNA profiles recovered from crime scene samples are of a quality that does not allow them to be searched against, nor entered into, databases. We propose a method for the comparison of profiles arising from two DNA samples, one or both…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Background: The learning of genotype-phenotype associations and history of human disease by doing detailed and precise analysis of phenotypic abnormalities can be defined as deep phenotyping. To understand and detect this interaction…
The standard paradigm for the analysis of genome-wide association studies involves carrying out association tests at both typed and imputed SNPs. These methods will not be optimal for detecting the signal of association at SNPs that are not…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
Substantial progress has been made in identifying single genetic variants predisposing to common complex diseases. Nonetheless, the genetic etiology of human diseases remains largely unknown. Human complex diseases are likely influenced by…
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…
The ability to quickly and accurately identify microbial species in a sample, known as metagenomic profiling, is critical across various fields, from healthcare to environmental science. This paper introduces a novel method to profile…