Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation.
Eric R GamazonAyellet V SegrèMartijn van de BuntXiaoquan WenHualin S XiFarhad HormozdiariHalit OngenAnuar KonkashbaevEske M DerksFrançois AguetJie Quannull nullDan L NicolaeEleazar EskinManolis KellisGad A GetzMark I McCarthyEmmanouil T DermitzakisNancy J CoxKristin G ArdliePublished in: Nature genetics (2018)
We apply integrative approaches to expression quantitative loci (eQTLs) from 44 tissues from the Genotype-Tissue Expression project and genome-wide association study data. About 60% of known trait-associated loci are in linkage disequilibrium with a cis-eQTL, over half of which were not found in previous large-scale whole blood studies. Applying polygenic analyses to metabolic, cardiovascular, anthropometric, autoimmune, and neurodegenerative traits, we find that eQTLs are significantly enriched for trait associations in relevant pathogenic tissues and explain a substantial proportion of the heritability (40-80%). For most traits, tissue-shared eQTLs underlie a greater proportion of trait associations, although tissue-specific eQTLs have a greater contribution to some traits, such as blood pressure. By integrating information from biological pathways with eQTL target genes and applying a gene-based approach, we validate previously implicated causal genes and pathways, and propose new variant and gene associations for several complex traits, which we replicate in the UK BioBank and BioVU.
Keyphrases
- genome wide
- dna methylation
- genome wide association study
- copy number
- gene expression
- poor prognosis
- blood pressure
- endothelial cells
- healthcare
- multiple sclerosis
- electronic health record
- quality improvement
- machine learning
- cross sectional
- high resolution
- long non coding rna
- type diabetes
- metabolic syndrome
- social media
- heart rate
- single cell
- genome wide identification
- blood glucose
- hiv infected
- adipose tissue
- mass spectrometry
- pluripotent stem cells
- induced pluripotent stem cells