ArticlePloS one2014
A Bayesian method to incorporate hundreds of functional characteristics with association evidence to improve variant prioritization.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation.PloS one · 2015Pooled it
- iFunMed: Integrative functional mediation analysis of GWAS and eQTL studies.Genetic epidemiology · 2019Article
- A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types.Genome biology · 2019Article
- Fitness Landscape of the Fission Yeast Genome.Molecular biology and evolution · 2019Article
- Exploring the underlying biology of intrinsic cardiorespiratory fitness through integrative analysis of genomic variants and muscle gene expression profiling.Journal of applied physiology (Bethesda, Md. : 1985) · 2019Article
- Colocalization analyses of genomic elements: approaches, recommendations and challenges.Bioinformatics (Oxford, England) · 2019Article
- Leveraging genome characteristics to improve gene discovery for putamen subcortical brain structure.Scientific reports · 2017Article
- Annotation Regression for Genome-Wide Association Studies with an Application to Psychiatric Genomic Consortium Data.Statistics in biosciences · 2017Article
- Genomics implicates adaptive and innate immunity in Alzheimer's and Parkinson's diseases.Annals of clinical and translational neurology · 2016Article
- Genetics and Genomics of Coronary Artery Disease.Current cardiology reports · 2016Review
- The genetics of drug efficacy: opportunities and challenges.Nature reviews. Genetics · 2016Review
- Autoimmune diseases - connecting risk alleles with molecular traits of the immune system.Nature reviews. Genetics · 2016Review
- Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus.Nature genetics · 2015Article
- Strategies for fine-mapping complex traits.Human molecular genetics · 2015Review
- Smoking Gun or Circumstantial Evidence? Comparison of Statistical Learning Methods using Functional Annotations for Prioritizing Risk Variants.Scientific reports · 2015Article
- Assessing models for genetic prediction of complex traits: a comparison of visualization and quantitative methods.BMC genomics · 2015Article
- The role of regulatory variation in complex traits and disease.Nature reviews. Genetics · 2015Review
- Genetics and brain morphology.Neuropsychology review · 2015Article
- FRAS1-related extracellular matrix 3 (FREM3) single-nucleotide polymorphism effects on gene expression, amygdala reactivity and perceptual processing speed: An accelerated aging pathway of depression risk.Frontiers in psychology · 2015Article
- Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases.American journal of human genetics · 2014Article
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4 authors.
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Abstract
The increasing quantity and quality of functional genomic information motivate the assessment and integration of these data with association data, including data originating from genome-wide association studies (GWAS). We used previously described GWAS signals ("hits") to train a regularized logistic model in order to predict SNP causality on the basis of a large multivariate functional dataset. We show how this model can be used to derive Bayes factors for integrating functional and association data into a combined Bayesian analysis. Functional characteristics were obtained from the Encyclopedia of DNA Elements (ENCODE), from published expression quantitative trait loci (eQTL), and from other sources of genome-wide characteristics. We trained the model using all GWAS signals combined, and also using phenotype specific signals for autoimmune, brain-related, cancer, and cardiovascular disorders. The non-phenotype specific and the autoimmune GWAS signals gave the most reliable results. We found SNPs with higher probabilities of causality from functional characteristics showed an enrichment of more significant p-values compared to all GWAS SNPs in three large GWAS studies of complex traits. We investigated the ability of our Bayesian method to improve the identification of true causal signals in a psoriasis GWAS dataset and found that combining functional data with association data improves the ability to prioritise novel hits. We used the predictions from the penalized logistic regression model to calculate Bayes factors relating to functional characteristics and supply these online alongside resources to integrate these data with association data.
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