LDexpress: an online tool for integrating population-specific linkage disequilibrium patterns with tissue-specific expression data.
Shu-Hong LinRohit ThakurMitchell J MachielaPublished in: BMC bioinformatics (2021)
Genome-wide association studies have identified thousands of genetic susceptibility loci associated with cancer as well as other traits and diseases. Mapping germline variation in identified genetic susceptibility regions to alterations in nearby gene expression nominates candidate genes potentially related to disease risk for further functional investigation. We developed LDexpress as an online resource that integrates population-specific linkage disequilibrium data from the 1000 Genomes (1000G) project and tissue-specific expression data from the Genotype-Tissue Expression project to better study regional germline variation impacting gene expression. LDexpress is a publicly available web tool designed to be easy to use, flexible to conduct a wide range of variant queries, and quick to efficiently investigate dozens of query variants across multiple tissue types. We demonstrate the utility of LDexpress using example genomic queries and anticipate this tool will accelerate understanding of disease etiology by uncovering associations of regional germline variation to nearby gene expression.
Keyphrases
- gene expression
- genome wide
- dna methylation
- poor prognosis
- copy number
- genome wide association
- electronic health record
- dna repair
- big data
- quality improvement
- binding protein
- long non coding rna
- high resolution
- papillary thyroid
- data analysis
- squamous cell carcinoma
- oxidative stress
- machine learning
- squamous cell
- case control
- lymph node metastasis
- antiretroviral therapy
- childhood cancer