Related papers: Replicability analysis for genome-wide association…
In genome-wide association studies (GWASs) of common diseases/traits, we often analyze multiple GWASs with the same phenotype together to discover associated genetic variants with higher power. Since it is difficult to access data with…
A large number of recent genome-wide association studies (GWASs) for complex phenotypes confirm the early conjecture for polygenicity, suggesting the presence of large number of variants with only tiny or moderate effects. However, due to…
Large-scale genome-wide association studies (GWAS) have offered an exciting opportunity to discover putative causal genes or risk factors associated with diseases by using SNPs as instrumental variables (IVs). However, conventional…
Genome-wide association studies(GWAS) have proven to be highly useful in revealing the genetic basis of complex diseases. At present, most GWAS are studies of a particular single disease diagnosis against controls. However, in practice, an…
Experimental reproducibility and replicability are critical topics in machine learning. Authors have often raised concerns about their lack in scientific publications to improve the quality of the field. Recently, the graph representation…
Meta-analyses are commonly performed based on random-effects models, while in certain cases one might also argue in favour of a common-effect model. One such case may be given by the example of two "study twins" that are performed according…
The genetic basis of multiple phenotypes such as gene expression, metabolite levels, or imaging features is often investigated by testing a large collection of hypotheses, probing the existence of association between each of the traits and…
Gene set analysis methods rely on knowledge-based representations of genetic interactions in the form of both gene set collections and protein-protein interaction (PPI) networks. Explicit representations of genetic interactions often fail…
In genome-wide association studies (GWASs), there is an increasing need for detecting the associations between a genetic variant and multiple traits. In studies of complex diseases, it is common to measure several potentially correlated…
Background: Although Alzheimer's disease (AD) is a central nervous system disease and type 2 diabetes mellitus (T2DM) is a metabolic disorder, an increasing number of genetic epidemiological studies show clear link between AD and T2DM. The…
Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can…
Statistical significance of both the original and the replication study is a commonly used criterion to assess replication attempts, also known as the two-trials rule in drug development. However, replication studies are sometimes conducted…
As the meta-analysis of more than one diagnostic tests can impact clinical decision making and patient health, there is an increasing body of research in models and methods for meta-analysis of studies comparing multiple diagnostic tests.…
The aetiology of polygenic obesity is multifactorial, which indicates that life-style and environmental factors may influence multiples genes to aggravate this disorder. Several low-risk single nucleotide polymorphisms (SNPs) have been…
Taking advantages of high-throughput genotyping technology of single nucleotide polymorphism (SNP), large genome-wide association studies (GWASs) have been considered as the promise to unravel the complex relationships between genotypes and…
Sequencing-based studies are emerging as a major tool for genetic association studies of complex diseases. These studies pose great challenges to the traditional statistical methods (e.g., single-locus analyses based on regression methods)…
Context: Researchers from different groups and institutions are collaborating towards the construction of groups of interrelated replications. Applying unsuitable techniques to aggregate interrelated replications' results may impact the…
Given a large graph, how can we determine similarity between nodes in a fast and accurate way? Random walk with restart (RWR) is a popular measure for this purpose and has been exploited in numerous data mining applications including…
Network meta-analysis (NMA) is widely used to compare multiple interventions simultaneously by synthesizing direct and indirect evidence. The general fixed or random effects contrast-based NMA model can be applied to different outcomes and…
While the individuals chosen for a genome-wide association study (GWAS) may not be closely related to each other, there can be distant (cryptic) relationships that confound the evidence of disease association. These cryptic relationships…