Related papers: A simple genome-wide association study algorithm
In genetic association studies, detecting phenotype-genotype association is a primary goal. We assume that the relationship between the data -phenotype, genetic markers and environmental covariates - can be modelled by a generalized linear…
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…
The objective of a genome-wide association study (GWAS) is to associate subsequences of individuals' genomes to the observable characteristics called phenotypes (e.g., high blood pressure). Motivated by the GWAS problem, in this paper we…
Although genome-wide association studies (GWAS) on complex traits have achieved great successes, the current leading GWAS approaches simply perform to test each genotype-phenotype association separately for each genetic variant. Curiously,…
Ancestry-specific proteome-wide association studies (PWAS) based on genetically predicted protein expression can reveal complex disease etiology specific to certain ancestral groups. These studies require ancestry-specific models for…
Adaptation in response to selection on polygenic phenotypes may occur via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional…
Drug development is a very costly and lengthy process, while repositioned or repurposed drugs could be brought into clinical practice within a shorter time-frame and at a much reduced cost. The past decade has observed a massive growth in…
The SNPs (Single Nucleotide Polymorphisms) genotyping platforms are of great value for gene mapping of complex diseases. Nowadays, the high-density of these molecular markers enables studies of dependence patterns between loci over the…
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…
Investigating the genetic architecture of complex diseases is challenging due to the multifactorial and interactive landscape of genomic and environmental influences. Although genome-wide association studies (GWAS) have identified thousands…
Motivated by empirical arguments that are well-known from the genome-wide association studies (GWAS) literature, we study the statistical properties of linear mixed models (LMMs) applied to GWAS. First, we study the sensitivity of LMMs to…
Genetic Gaussian network of multiple phenotypes constructed through the genetic correlation matrix is informative for understanding their biological dependencies. However, its interpretation may be challenging because the estimated genetic…
This R package evaluates main and pair-wise interaction effect of single nucleotide polymorphisms (SNPs) via the W-test, scalable to whole genome-wide data sets. The package provides fast and accurate p-value estimation of genetic markers,…
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…
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…
To uncover the genetic basis of complex disease, individuals are often measured at a large number of genetic variants (usually SNPs) across the genome. GemTools provides computationally efficient tools for modeling genetic ancestry based on…
Many complex disease syndromes such as asthma consist of a large number of highly related, rather than independent, clinical phenotypes, raising a new technical challenge in identifying genetic variations associated simultaneously with…
The paramount importance of replicating associations is well recognized in the genome-wide associaton (GWA) research community, yet methods for assessing replicability of associations are scarce. Published GWA studies often combine…