ArticleNucleic acids research2016
Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 6 of them syntheses that pooled it.
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Who cites it
44 citing papers in PubMed, 6 syntheses or guidelines pooled it, 82 citations in OpenAlex.
- Leveraging pleiotropic association using sparse group variable selection in genomics data.BMC medical research methodology · 2022Pooled it
- Genome-wide association study of cognitive function in diverse Hispanics/Latinos: results from the Hispanic Community Health Study/Study of Latinos.Translational psychiatry · 2020Pooled it
- A Review of Statistical Methods for Identifying Trait-Relevant Tissues and Cell Types.Frontiers in genetics · 2020Pooled it
- Methods for the Analysis and Interpretation for Rare Variants Associated with Complex Traits.Current protocols in human genetics · 2019Pooled it
- Proper conditional analysis in the presence of missing data: Application to large scale meta-analysis of tobacco use phenotypes.PLoS genetics · 2018Pooled it
- Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.Nature genetics · 2018Pooled it
- BAYESIAN VARIABLE SELECTION IN A COX PROPORTIONAL HAZARDS MODEL WITH THE "SUM OF SINGLE EFFECTS" PRIOR.ArXiv · 2025Article
- The goldmine of GWAS summary statistics: a systematic review of methods and tools.BioData mining · 2024Article
- Novel insight into the etiology of ischemic stroke gained by integrative multiome-wide association study.Human molecular genetics · 2024Article
- Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease.Nature genetics · 2023Article
- Interpreting non-coding disease-associated human variants using single-cell epigenomics.Nature reviews. Genetics · 2023Review
- Novel insight into the etiology of ischemic stroke gained by integrative transcriptome-wide association study.medRxiv : the preprint server for health sciences · 2023Article
- Identifying enhancer properties associated with genetic risk for complex traits using regulome-wide association studies.PLoS computational biology · 2022Article
- Leveraging the local genetic structure for trans-ancestry association mapping.American journal of human genetics · 2022Article
- Fine-mapping from summary data with the "Sum of Single Effects" model.PLoS genetics · 2022Article
- Methods for statistical fine-mapping and their applications to auto-immune diseases.Seminars in immunopathology · 2022Review
- EPISPOT: An epigenome-driven approach for detecting and interpreting hotspots in molecular QTL studies.American journal of human genetics · 2021Article
- Article
- B1a and B2 cells are characterized by distinct CpG modification states at DNMT3A-maintained enhancers.Nature communications · 2021Article
- Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human.BMC biology · 2020Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Genome wide association studies (GWAS) provide a powerful approach for uncovering disease-associated variants in human, but fine-mapping the causal variants remains a challenge. This is partly remedied by prioritization of disease-associated variants that overlap GWAS-enriched epigenomic annotations. Here, we introduce a new Bayesian model RiVIERA (Risk Variant Inference using Epigenomic Reference Annotations) for inference of driver variants from summary statistics across multiple traits using hundreds of epigenomic annotations. In simulation, RiVIERA promising power in detecting causal variants and causal annotations, the multi-trait joint inference further improved the detection power. We applied RiVIERA to model the existing GWAS summary statistics of 9 autoimmune diseases and Schizophrenia by jointly harnessing the potential causal enrichments among 848 tissue-specific epigenomics annotations from ENCODE/Roadmap consortium covering 127 cell/tissue types and 8 major epigenomic marks. RiVIERA identified meaningful tissue-specific enrichments for enhancer regions defined by H3K4me1 and H3K27ac for Blood T-Cell specifically in the nine autoimmune diseases and Brain-specific enhancer activities exclusively in Schizophrenia. Moreover, the variants from the 95% credible sets exhibited high conservation and enrichments for GTEx whole-blood eQTLs located within transcription-factor-binding-sites and DNA-hypersensitive-sites. Furthermore, joint modeling the nine immune traits by simultaneously inferring and exploiting the underlying epigenomic correlation between traits further improved the functional enrichments compared to single-trait models.
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