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Comprehensive Multiple eQTL Detection and Its Application to GWAS Interpretation
- Source :
- Genetics, Genetics, 212(3), 905-918. GENETICS SOCIETY AMERICA
- Publication Year :
- 2019
- Publisher :
- Genetics Society of America, 2019.
-
Abstract
- Expression QTL (eQTL) detection has emerged as an important tool for unraveling the relationship between genetic risk factors and disease or clinical phenotypes. Most studies are predicated on the assumption that only a single causal variant explains the association signal in each interval. This greatly simplifies the statistical modeling, but is liable to biases in scenarios where multiple local causal-variants are responsible. Here, our primary goal was to address the prevalence of secondary cis-eQTL signals regulating peripheral blood gene expression locally, utilizing two large human cohort studies, each >2500 samples with accompanying whole genome genotypes. The CAGE (Consortium for the Architecture of Gene Expression) dataset is a compendium of Illumina microarray studies, and the Framingham Heart Study is a two-generation Affymetrix dataset. We also describe Bayesian colocalization analysis of the extent of sharing of cis-eQTL detected in both studies as well as with the BIOS RNAseq dataset. Stepwise conditional modeling demonstrates that multiple eQTL signals are present for ∼40% of over 3500 eGenes in both microarray datasets, and that the number of loci with additional signals reduces by approximately two-thirds with each conditioning step. Although
- Subjects :
- Multifactorial Inheritance
Microarray
conditional association
Quantitative Trait Loci
LOCI
Genome-wide association study
Single-nucleotide polymorphism
ANNOTATION DATA
Biology
Quantitative trait locus
Investigations
colocalization
Linkage Disequilibrium
03 medical and health sciences
0302 clinical medicine
Genetics
Humans
Genetic Predisposition to Disease
GENOME-WIDE ASSOCIATION
030304 developmental biology
GENE-EXPRESSION
SNPS
Regulation of gene expression
0303 health sciences
ARCHITECTURE
IDENTIFICATION
HERITABILITY
Gene Expression Profiling
Colocalization
PolyQTL
Phenotype
ALIGNMENT
Expression quantitative trait loci
fine mapping
gene regulation
030217 neurology & neurosurgery
Algorithms
INFLAMMATORY-BOWEL-DISEASE
Genome-Wide Association Study
Subjects
Details
- Language :
- English
- ISSN :
- 00166731
- Database :
- OpenAIRE
- Journal :
- Genetics, Genetics, 212(3), 905-918. GENETICS SOCIETY AMERICA
- Accession number :
- edsair.doi.dedup.....b3545281b46f7c04843c88dbb4acfabb