ArticleAmerican journal of human genetics2016
An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants.
Article in American journal of human genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers, 3 of them syntheses that pooled it.
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Who cites it
88 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Skeletal muscle eQTL meta-analysis implicates genes in the genetic architecture of muscular and cardiometabolic traits.American journal of human genetics · 2025Pooled it
- Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits.American journal of human genetics · 2024Pooled it
- Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology.Nature genetics · 2017Pooled it
- Machine learning and statistical methods for molecular quantitative trait loci.Nature reviews. Genetics · 2026Review
- Tissue-resident immune cells drive genetic risk in autoimmune and lung diseases.Nature immunology · 2026Article
- Mapping genetic regulation of gene expression to cellular contexts identifies long non-coding RNAs associated with brain disorders.Nature communications · 2026Article
- Article
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- BMI-genome interactions regulate global gene expression with emphasis in brain and gut.Cell genomics · 2026Article
- Cis-regulation of gene expression between sexes and life stages in Rumex hastatulus.Molecular biology and evolution · 2026Article
- Decoding common and rare noncoding variant effects across cellular and developmental contexts.Nature genetics · 2026Article
- OmiGA for ultra-efficient molecular quantitative trait loci mapping.Nature communications · 2026Article
- Construction of a Multitissue Cell Atlas Reveals Cell-Type-Specific Regulation of Molecular and Complex Phenotypes in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Linking the plasma proteome to genetics in individuals from continental Africa provides insights into type 2 diabetes pathogenesis.Nature genetics · 2026Article
- Relationships Between Circulating Lipids, Lipoproteins, and Lymphocyte Subsets in the Multi-Ethnic Study of Atherosclerosis.Global heart · 2026Article
- A nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon.BMC genomics · 2025Article
- Fast Probabilistic Whitening Transformation for Ultra-High Dimensional Genetic Data.bioRxiv : the preprint server for biology · 2025Article
- Mapping the landscape of cell type-dependent genetic regulation of DNA methylation across human tissues.Research square · 2025Article
- Integrative multi-omics uncovers skeletal muscle enhancer programming of cardiorespiratory fitness.bioRxiv : the preprint server for biology · 2025Article
- Genetic determinants of monocyte splicing are enriched for disease susceptibility loci.Nature communications · 2025Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Methods for multiple-testing correction in local expression quantitative trait locus (cis-eQTL) studies are a trade-off between statistical power and computational efficiency. Bonferroni correction, though computationally trivial, is overly conservative and fails to account for linkage disequilibrium between variants. Permutation-based methods are more powerful, though computationally far more intensive. We present an alternative correction method called eigenMT, which runs over 500 times faster than permutations and has adjusted p values that closely approximate empirical ones. To achieve this speed while also maintaining the accuracy of permutation-based methods, we estimate the effective number of independent variants tested for association with a particular gene, termed Meff, by using the eigenvalue decomposition of the genotype correlation matrix. We employ a regularized estimator of the correlation matrix to ensure Meff is robust and yields adjusted p values that closely approximate p values from permutations. Finally, using a common genotype matrix, we show that eigenMT can be applied with even greater efficiency to studies across tissues or conditions. Our method provides a simpler, more efficient approach to multiple-testing correction than existing methods and fits within existing pipelines for eQTL discovery.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.