Related papers: Multiple-trait Adaptive Fisher's Method for Genome…
Where causal SNPs (single nucleotide polymorphisms) tend to accumulate within biological pathways, the incorporation of prior pathways information into a statistical model is expected to increase the power to detect true associations in a…
Estimating the sharing of genetic effects across different conditions is important to many statistical analyses of genomic data. The patterns of sharing arising from these data are often highly heterogeneous. To flexibly model these…
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…
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…
In the past decade, Genome-Wide Association Studies (GWAS) have delivered an increasingly broad view of the genetic basis of human phenotypic variation. One of the major developments from GWAS is polygenic scores, a genetic predictor of an…
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) have proven powerful for comprehending the genetic architecture of complex traits, they are challenged by a high dimension of single-nucleotide polymorphisms (SNPs) as predictors, the presence…
Identifying shared genetic risk factors for multiple measured traits has been of great interest in studying complex disorders. Marlow's (2003) method for detecting shared gene effects on complex traits has been highly influential in the…
Heritability is a central parameter in quantitative genetics, both from an evolutionary and a breeding perspective. For plant traits heritability is traditionally estimated by comparing within and between genotype variability. This approach…
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…
Transcriptome-wide association studies (TWAS) link genetic variation to complex traits by leveraging expression quantitative trait loci (eQTL) data. However, most implementations are typically limited to local (cis-acting) effects and fail…
In genome wide association studies (GWAS), researchers are often dealing with non-normally distributed traits or a mixture of discrete-continuous traits. However, most of the current region-based methods rely on multivariate linear mixed…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
After the completion of human genome sequence was anounced, it is evident that interpretation of DNA sequences is an immediate task to work on. For understanding their signals, improvement of present sequence analysis tools and developing…
Gene/pathway-based methods are drawing significant attention due to their usefulness in detecting rare and common variants that affect disease susceptibility. The biological mechanism of drug responses indicates that a gene-based analysis…
Gene-based testing is a commonly employed strategy in many genetic association studies. Gene-trait associations can be complex due to underlying population heterogeneity, gene-environment interactions, and various other reasons. Existing…
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…
Replication helps ensure that a genotype-phenotype association observed in a genome-wide association (GWA) study represents a credible association and is not a chance finding or an artifact due to uncontrolled biases. We discuss…
Gene expression prediction plays a vital role in transcriptome-wide association studies (TWAS), which seek to establish associations between tissue gene expression and complex traits. Traditional models rely on genetic variants in close…
Transcriptome-wide association studies based on genetically predicted gene expression have the potential to identify novel regions associated with various complex traits. It has been shown that incorporating expression quantitative trait…