Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
Cell 2017;
167:1398-1414.e24. [PMID:
27863251 PMCID:
PMC5119954 DOI:
10.1016/j.cell.2016.10.026]
[Citation(s) in RCA: 389] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 08/19/2016] [Accepted: 10/14/2016] [Indexed: 12/20/2022]
Abstract
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14+ monocytes, CD16+ neutrophils, and naive CD4+ T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk.
Genome, transcriptome, and epigenome reference panel in three human immune cell types
Identified 4,418 genes associated with epigenetic changes independent of genetics
Described genome-epigenome coordination defining cell-type-specific regulatory events
Functionally mapped disease mechanisms at 345 unique autoimmune disease loci
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