ArticleGenetics2016
Incorporating Functional Annotations for Fine-Mapping Causal Variants in a Bayesian Framework Using Summary Statistics.
Article in Genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 4 of them syntheses that pooled it.
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Who cites it
40 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Genome-wide meta-analyses of restless legs syndrome yield insights into genetic architecture, disease biology and risk prediction.Nature genetics · 2024Pooled it
- Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals.Nature genetics · 2018Pooled it
- Proper conditional analysis in the presence of missing data: Application to large scale meta-analysis of tobacco use phenotypes.PLoS genetics · 2018Pooled it
- Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants.Nature communications · 2018Pooled it
- Correlations between causal effect sizes of proximal SNPs vary with functional annotations and implicate stabilizing selection.Nature genetics · 2026Article
- Early and late RNA eQTL are driven by different genetic mechanisms.Nature communications · 2026Article
- A machine-learning framework to characterize functional disease architectures and prioritize disease variants.medRxiv : the preprint server for health sciences · 2025Article
- BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across >1000s of omics datasets.Bioinformatics (Oxford, England) · 2025Article
- reg-eQTL: Integrating transcription factor effects to unveil regulatory variants.American journal of human genetics · 2025Article
- Refining fine-mapping: Effect sizes and regional heritability.PLoS genetics · 2025Article
- Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles.Nature genetics · 2024Article
- Pervasive correlations between causal disease effects of proximal SNPs vary with functional annotations and implicate stabilizing selection.Research square · 2023Article
- Pervasive correlations between causal disease effects of proximal SNPs vary with functional annotations and implicate stabilizing selection.medRxiv : the preprint server for health sciences · 2023Article
- Interpreting non-coding disease-associated human variants using single-cell epigenomics.Nature reviews. Genetics · 2023Review
- A unifying statistical framework to discover disease genes from GWASs.Cell genomics · 2023Article
- Advances and Applications of Polygenic Scores for Coronary Artery Disease.Annual review of medicine · 2023Review
- Article
- SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease.Cell genomics · 2022Article
- Article
- Methods for statistical fine-mapping and their applications to auto-immune diseases.Seminars in immunopathology · 2022Review
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5 authors.
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Abstract
Functional annotations have been shown to improve both the discovery power and fine-mapping accuracy in genome-wide association studies. However, the optimal strategy to incorporate the large number of existing annotations is still not clear. In this study, we propose a Bayesian framework to incorporate functional annotations in a systematic manner. We compute the maximum a posteriori solution and use cross validation to find the optimal penalty parameters. By extending our previous fine-mapping method CAVIARBF into this framework, we require only summary statistics as input. We also derived an exact calculation of Bayes factors using summary statistics for quantitative traits, which is necessary when a large proportion of trait variance is explained by the variants of interest, such as in fine mapping expression quantitative trait loci (eQTL). We compared the proposed method with PAINTOR using different strategies to combine annotations. Simulation results show that the proposed method achieves the best accuracy in identifying causal variants among the different strategies and methods compared. We also find that for annotations with moderate effects from a large annotation pool, screening annotations individually and then combining the top annotations can produce overly optimistic results. We applied these methods on two real data sets: a meta-analysis result of lipid traits and a cis-eQTL study of normal prostate tissues. For the eQTL data, incorporating annotations significantly increased the number of potential causal variants with high probabilities.
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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.