ArticleNucleic acids research2018
INFERNO: inferring the molecular mechanisms of noncoding genetic variants.
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 43 papers, 1 of them a synthesis that pooled it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 63 citations in OpenAlex.
- Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing.Nature genetics · 2019Pooled it
- From correlation to causation: cell-type-specific gene regulatory networks in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Blood-based Transcriptomics Reveal Sex- and Amyloid-Modulated Biology of Plasma pTau217 in Preclinical Alzheimer's Disease.bioRxiv : the preprint server for biology · 2025Article
- A Modification to Two-Stage Least Squares With Genetic Applications.Statistics in medicine · 2025Article
- BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across >1000s of omics datasets.Bioinformatics (Oxford, England) · 2025Article
- From Correlation to Causation: Cell-Type-Specific Gene Regulatory Networks in Alzheimer's Disease.bioRxiv : the preprint server for biology · 2025Article
- Clinical and data-driven optimization of Genomiser for rare disease patients: experience from the Hong Kong Genome Project.Briefings in bioinformatics · 2025Article
- Integrated genomic analysis and CRISPRi implicatesNPJ dementia · 2025Article
- Genetic, transcriptomic, histological, and biochemical analysis of progressive supranuclear palsy implicates glial activation and novel risk genes.Nature communications · 2024Article
- The goldmine of GWAS summary statistics: a systematic review of methods and tools.BioData mining · 2024Article
- CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes.Human genomics · 2023Article
- Genome-wide association study in Alzheimer's disease: a bibliometric and visualization analysis.Frontiers in aging neuroscience · 2023Article
- Exploration of Tools for the Interpretation of Human Non-Coding Variants.International journal of molecular sciences · 2022Review
- Scalable approaches for functional analyses of whole-genome sequencing non-coding variants.Human molecular genetics · 2022Review
- Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling.iScience · 2022Article
- Large-Scale Multi-Omics Studies Provide New Insights into Blood Pressure Regulation.International journal of molecular sciences · 2022Article
- Article
- Association between WWOX/MAF variants and dementia-related neuropathologic endophenotypes.Neurobiology of aging · 2022Article
- FILER: a framework for harmonizing and querying large-scale functional genomics knowledge.NAR genomics and bioinformatics · 2022Article
- Comparative Investigation of Gene Regulatory Processes Underlying Avian Influenza Viruses in Chicken and Duck.Biology · 2022Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
The majority of variants identified by genome-wide association studies (GWAS) reside in the noncoding genome, affecting regulatory elements including transcriptional enhancers. However, characterizing their effects requires the integration of GWAS results with context-specific regulatory activity and linkage disequilibrium annotations to identify causal variants underlying noncoding association signals and the regulatory elements, tissue contexts, and target genes they affect. We propose INFERNO, a novel method which integrates hundreds of functional genomics datasets spanning enhancer activity, transcription factor binding sites, and expression quantitative trait loci with GWAS summary statistics. INFERNO includes novel statistical methods to quantify empirical enrichments of tissue-specific enhancer overlap and to identify co-regulatory networks of dysregulated long noncoding RNAs (lncRNAs). We applied INFERNO to two large GWAS studies. For schizophrenia (36,989 cases, 113,075 controls), INFERNO identified putatively causal variants affecting brain enhancers for known schizophrenia-related genes. For inflammatory bowel disease (IBD) (12,882 cases, 21,770 controls), INFERNO found enrichments of immune and digestive enhancers and lncRNAs involved in regulation of the adaptive immune response. In summary, INFERNO comprehensively infers the molecular mechanisms of causal noncoding variants, providing a sensitive hypothesis generation method for post-GWAS analysis. The software is available as an open source pipeline and a web server.
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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.