Related papers: Replicability analysis for genome-wide association…
Genetic variants identified to date by genome-wide association studies only explain a small fraction of total heritability. Gene-by-gene interaction is one important potential source of unexplained heritability. In the first part of this…
Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a…
Genome-wide Association Studies (GWASes) identify genomic variations that are statistically associated with a trait, such as a disease, in a group of individuals. Unfortunately, careless sharing of GWAS statistics might give rise to privacy…
Assessment of replicability is critical to ensure the quality and rigor of scientific research. In this paper, we discuss inference and modeling principles for replicability assessment. Targeting distinct application scenarios, we propose…
We consider the problems of hypothesis testing and model comparison under a flexible Bayesian linear regression model whose formulation is closely connected with the linear mixed effect model and the parametric models for SNP set analysis…
Replicability issues -- referring to the difficulty or failure of independent researchers to corroborate the results of published studies -- have hindered the meaningful progression of science and eroded public trust in scientific findings.…
Genome-wide association studies (GWAS) have been widely used to examine the association between single nucleotide polymorphisms (SNPs) and complex traits, where both the sample size n and the number of SNPs p can be very large. Recently,…
Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many…
Traditional GWAS has advanced our understanding of complex diseases but often misses nonlinear genetic interactions. Deep learning offers new opportunities to capture complex genomic patterns, yet existing methods mostly depend on feature…
Bacteria pose unique challenges for genome-wide association studies (GWAS) because of strong structuring into distinct strains and substantial linkage disequilibrium across the genome. While methods developed for human studies can correct…
Genome-wide association studies (GWAS) have led to the discovery of numerous single nucleotide polymorphisms (SNPs) associated with various phenotypes and complex diseases. However, the identified genetic variants do not fully explain the…
Genome-wide association studies (GWAS) have successfully identified over two hundred thousand genotype-trait associations. Yet some challenges remain. First, complex traits are often associated with many single nucleotide polymorphisms…
Generalized linear mixed-effects models in the context of genome-wide association studies (GWAS) represent a formidable computational challenge: the solution of millions of correlated generalized least-squares problems, and the processing…
Network meta-analysis (NMA) is a useful tool to compare multiple interventions simultaneously in a single meta-analysis, it can be very helpful for medical decision making when the study aims to find the best therapy among several active…
We present an alternative method for genome-wide association studies (GWAS) that is more powerful than the regular GWAS method for locus detection. The regular GWAS method suffers from a substantial multiple-testing burden because of the…
Genome Wide Association Studies (GWAS) are used to identify statistically significant genetic variants in case-control studies. GWAS typically use a p-value threshold of 5 x 10-8 to identify highly ranked single nucleotide polymorphisms…
Association testing aims to discover the underlying relationship between genotypes (usually Single Nucleotide Polymorphisms, or SNPs) and phenotypes (attributes, or traits). The typically large data sets used in association testing often…
Genetic association analyses often involve data from multiple potentially-heterogeneous subgroups. The expected amount of heterogeneity can vary from modest (e.g., a typical meta-analysis) to large (e.g., a strong gene--environment…
Subgroup-specific meta-analysis synthesizes treatment effects for patient subgroups across randomized trials. Methods include joint or separate modeling of subgroup effects and treatment-by-subgroup interactions, but inconsistencies arise…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…