ArticleNucleic acids research2018
Power, false discovery rate and Winner's Curse in eQTL studies.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers, 2 of them syntheses that pooled it.
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Who cites it
88 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- An atlas of genome-wide gene expression and metabolite associations and possible mediation effects towards body mass index.Journal of molecular medicine (Berlin, Germany) · 2023Pooled it
- The incubation period of COVID-19: a global meta-analysis of 53 studies and a Chinese observation study of 11 545 patients.Infectious diseases of poverty · 2021Pooled it
- Machine learning and statistical methods for molecular quantitative trait loci.Nature reviews. Genetics · 2026Review
- Accelerated Evolution of Context-Dependent Gene Expression in Primate Immune Cells.bioRxiv : the preprint server for biology · 2026Article
- FHL3 Regulates Vascular Smooth Muscle Cell Phenotypic Switching Through the MRTFB-SRF Signaling Axis.Cells · 2026Article
- BMI-genome interactions regulate global gene expression with emphasis in brain and gut.Cell genomics · 2026Article
- A TAD-informed aging-brain xQTL atlas of multi-modal and cell-type-resolved regulatory variation.medRxiv : the preprint server for health sciences · 2026Article
- Higher eQTL power reveals signals that boost GWAS colocalization.American journal of human genetics · 2026Article
- Mapping epigenetic gene variant dynamics: comparative analysis of frequency, functional impact and trait associations in African and European populations.Scientific reports · 2026Article
- Multi-tissue transcriptome-wide association study identifies 29 risk genes associated with attention-deficit/hyperactivity disorder.medRxiv : the preprint server for health sciences · 2026Article
- Integrative functional genomics analysis identifies pleiotropic genes for vascular diseases.Nature communications · 2026Article
- Expanded chromatin accessibility mapping explains genetic variation associated with complex traits in liver.American journal of human genetics · 2026Article
- Article
- A deep dive into statistical modeling of RNA splicing QTLs reveals variants that explain neurodegenerative disease.American journal of human genetics · 2025Article
- Distributional genetic effects reveal context-dependent molecular regulation in human brain aging and Alzheimer's disease.Research square · 2025Article
- Genetic determinants of monocyte splicing are enriched for disease susceptibility loci.Nature communications · 2025Article
- Expanded Chromatin Accessibility Mapping Explains Genetic Variation Associated with Complex Traits in Liver.medRxiv : the preprint server for health sciences · 2025Article
- Beware of counter-intuitive levels of false discoveries in datasets with strong intra-correlations.Genome biology · 2025Article
- ClipperQTL: ultrafast and powerful eGene identification method.Genome biology · 2025Article
- Protein quantitative trait locus analysis in African American and non-Hispanic White individuals.Genome biology · 2025Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Investigation of the genetic architecture of gene expression traits has aided interpretation of disease and trait-associated genetic variants; however, key aspects of expression quantitative trait loci (eQTL) study design and analysis remain understudied. We used extensive, empirically driven simulations to explore eQTL study design and the performance of various analysis strategies. Across multiple testing correction methods, false discoveries of genes with eQTLs (eGenes) were substantially inflated when false discovery rate (FDR) control was applied to all tests and only appropriately controlled using hierarchical procedures. All multiple testing correction procedures had low power and inflated FDR for eGenes whose causal SNPs had small allele frequencies using small sample sizes (e.g. frequency <10% in 100 samples), indicating that even moderately low frequency eQTL SNPs (eSNPs) in these studies are enriched for false discoveries. In scenarios with ≥80% power, the top eSNP was the true simulated eSNP 90% of the time, but substantially less frequently for very common eSNPs (minor allele frequencies >25%). Overestimation of eQTL effect sizes, so-called 'Winner's Curse', was common in low and moderate power settings. To address this, we developed a bootstrap method (BootstrapQTL) that led to more accurate effect size estimation. These insights provide a foundation for future eQTL studies, especially those with sampling constraints and subtly different conditions.
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