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An expression quantitative trait locus (eQTL) is a chromosomal region where genetic variants are associated with the expression levels of certain genes that can be both nearby or distant. The identifications of eQTLs for different tissues,…
Matched case-control studies are commonly employed in epidemiological research for their convenience and efficiency. Analysis of secondary outcomes can yield valuable insights into biological pathways and help identify genetic variants of…
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…
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…
Multiple types or views of data (e.g. genetics, proteomics) measured on the same set of individuals are now popularly generated in many biomedical studies. A particular interest might be the detection of sample subgroups (e.g. subtypes of…
In a mouse intercross with more than 500 animals and genome-wide gene expression data on six tissues, we identified a high proportion (18%) of sample mix-ups in the genotype data. Local expression quantitative trait loci (eQTL; genetic loci…
Reconstructing gene regulatory networks from large-scale heterogeneous data is a key challenge in biology. In multi-omics data analysis, networks based on pairwise statistical association measures remain popular, as they are easy to build…
Motivation: In spite of great success of genome-wide association studies (GWAS), multiple challenges still remain. First, complex traits are often associated with many single nucleotide polymorphisms (SNPs), each with small or moderate…
With the recent advent of high-throughput genotyping techniques, genetic data for genome-wide association studies (GWAS) have become increasingly available, which entails the development of efficient and effective statistical approaches.…
While progress has been made in identifying common genetic variants associated with human diseases, for most of common complex diseases, the identified genetic variants only account for a small proportion of heritability. Challenges remain…
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…
Integrating the summary statistics from genome-wide association study (\textsc{gwas}) and expression quantitative trait loci (e\textsc{qtl}) data provides a powerful way of identifying the genes whose expression levels are potentially…
Genome-wide eQTL mapping explores the relationship between gene expression values and DNA variants to understand genetic causes of human disease. Due to the large number of genes and DNA variants that need to be assessed simultaneously,…
Genetic differences between individuals associated to quantitative phenotypic traits, including disease states, are usually found in non-coding genomic regions. These genetic variants are often also associated to differences in expression…
In many transcriptomic studies, the correlation of genes might fluctuate with quantitative factors such as genetic ancestry. We propose a method that models the covariance between two variables to vary against a continuous covariate. For…
Genome-wide association studies (GWASs) have been extensively adopted to depict the underlying genetic architecture of complex diseases. Motivated by GWASs' limitations in identifying small effect loci to understand complex traits'…
Pooled analyses that aggregate data from multiple studies are becoming increasingly common in collaborative epidemiologic research in order to increase the size and diversity of the study population. However, biomarker measurements from…
Imputation using external reference panels is a widely used approach for increasing power in GWAS and meta-analysis. Existing HMM-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian…
With advancement of medicine, alternative exposures or interventions are emerging with respect to a common outcome, and there are needs to formally test the difference in the associations of multiple exposures. We propose a duplication…
Genetic association studies have been a popular approach for assessing the association between common Single Nucleotide Polymorphisms (SNPs) and complex diseases. However, other genomic data involved in the mechanism from SNPs to disease,…