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- Title
Integration of methylation QTL and enhancer–target gene maps with schizophrenia GWAS summary results identifies novel genes.
- Authors
Wu, Chong; Pan, Wei
- Abstract
Motivation Most trait-associated genetic variants identified in genome-wide association studies (GWASs) are located in non-coding regions of the genome and thought to act through their regulatory roles. Results To account for enriched association signals in DNA regulatory elements, we propose a novel and general gene-based association testing strategy that integrates enhancer-target gene pairs and methylation quantitative trait locus data with GWAS summary results; it aims to both boost statistical power for new discoveries and enhance mechanistic interpretability of any new discovery. By reanalyzing two large-scale schizophrenia GWAS summary datasets, we demonstrate that the proposed method could identify some significant and novel genes (containing no genome-wide significant SNPs nearby) that would have been missed by other competing approaches, including the standard and some integrative gene-based association methods, such as one incorporating enhancer-target gene pairs and one integrating expression quantitative trait loci. Availability and implementation Software: wuchong.org/egmethyl.html Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
GENE mapping; CIS-regulatory elements (Genetics); METHYLATION; GENES; SCHIZOPHRENIA; STATISTICAL power analysis
- Publication
Bioinformatics, 2019, Vol 35, Issue 19, p3576
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btz161