Methods for fine-mapping with chromatin and expression data

Recent studies have identified thousands of regions in the genome associated with chromatin modifications, which may in turn be affecting gene expression. Existing works have used heuristic methods to investigate the relationships between genome, epigenome, and gene expression, but, to our knowledge, none have explicitly modeled the chain of causality whereby genetic variants impact chromatin, which impacts gene expression. In this work we introduce a new hierarchical fine-mapping framework that integrates information across all three levels of data to better identify the causal variant and chromatin mark that are concordantly influencing gene expression. In simulations we show that our method is more accurate than existing approaches at identifying the causal mark influencing expression. We analyze empirical genetic, chromatin, and gene expression data from 65 African-ancestry and 47 European-ancestry individuals and show that many of the paths prioritized by our method are consistent with the proposed causal model and often lie in likely functional regions.Author summary: Genome-wide association studies (GWAS) have revealed that the majority of variants associated with complex disease lie in noncoding regulatory sequences. More recent studies have identified thousands of quantitative trait loci (QTLs) associated with chromatin modifications, which in turn are associated with changes in gene regulation. Thus, one proposed mechanism by which genetic variants act on trait is through chromatin, which may in turn have downstream effects on transcription. In this work, we propose a method that assumes a causal path from genetic variation to chromatin to expression and integrates information across all three levels of data in order to identify the causal variant and chromatin mark that are likely influencing gene expression. We demonstrate in simulations that our probabilistic approach produces well-calibrated posterior probabilities and outperforms existing methods with respect to SNP-, mark-, and overall path-mapping.