ArticlePLoS genetics2020
Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses.
Article in PLoS genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 259 papers, 17 of them syntheses that pooled it.
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Who cites it
259 citing papers in PubMed, 17 syntheses or guidelines pooled it.
- Multi-ancestry genetic architecture of heart failure subtypes.Nature communications · 2026Pooled it
- The genetic architecture of brainstem structures.Nature communications · 2025Pooled it
- Pooled it
- Genome-wide association meta-analysis of age at onset of walking in over 70,000 infants of European ancestry.Nature human behaviour · 2025Pooled it
- Genome-wide analyses identify 30 loci associated with obsessive-compulsive disorder.Nature genetics · 2025Pooled it
- Genome-wide analyses identify 25 infertility loci and relationships with reproductive traits across the allele frequency spectrum.Nature genetics · 2025Pooled it
- Cross-ancestry analyses of Chinese and European populations reveal insights into the genetic architecture and disease implication of metabolites.Cell genomics · 2025Pooled it
- Genome-wide association and multi-omics analyses provide insights into the disease mechanisms of central serous chorioretinopathy.Scientific reports · 2025Pooled it
- Adipose tissue eQTL meta-analysis highlights the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits.Nature genetics · 2025Pooled it
- Novel Insights Into the Causal Effects and Shared Genetics Between Body Fat and Parkinson Disease.CNS neuroscience & therapeutics · 2024Pooled it
- Large-scale cross-ancestry genome-wide meta-analysis of serum urate.Nature communications · 2024Pooled it
- Genetic overlap and causality between COVID-19 and multi-site chronic pain: the importance of immunity.Frontiers in immunology · 2024Pooled it
- Investigating the shared genetic architecture between COVID-19 and obesity: a large-scale genome wide cross-trait analysis.Frontiers in endocrinology · 2024Pooled it
- Association between the LRP1B and APOE loci and the development of Parkinson's disease dementia.Brain : a journal of neurology · 2023Pooled it
- FHL5 Controls Vascular Disease-Associated Gene Programs in Smooth Muscle Cells.Circulation research · 2023Pooled it
- Genetic effects on the timing of parturition and links to fetal birth weight.Nature genetics · 2023Pooled it
- Genome-wide meta-analysis identifies 93 risk loci and enables risk prediction equivalent to monogenic forms of venous thromboembolism.Nature genetics · 2023Pooled it
- Cross-phenotype and cross-species integrative genomic prioritization of FOXF2 and FOXC1 at a cerebral small vessel disease locus.Functional & integrative genomics · 2026Article
- Article
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199 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
1 author.
Funding
Abstract
Horizontal integration of summary statistics from different GWAS traits can be used to evaluate evidence for their shared genetic causality. One popular method to do this is a Bayesian method, coloc, which is attractive in requiring only GWAS summary statistics and no linkage disequilibrium estimates and is now being used routinely to perform thousands of comparisons between traits. Here we show that while most users do not adjust default software values, misspecification of prior parameters can substantially alter posterior inference. We suggest data driven methods to derive sensible prior values, and demonstrate how sensitivity analysis can be used to assess robustness of posterior inference. The flexibility of coloc comes at the expense of an unrealistic assumption of a single causal variant per trait. This assumption can be relaxed by stepwise conditioning, but this requires external software and an LD matrix aligned to study alleles. We have now implemented conditioning within coloc, and propose a new alternative method, masking, that does not require LD and approximates conditioning when causal variants are independent. Importantly, masking can be used in combination with conditioning where allelically aligned LD estimates are available for only a single trait. We have implemented these developments in a new version of coloc which we hope will enable more informed choice of priors and overcome the restriction of the single causal variant assumptions in coloc analysis.
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Registered trials
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.