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Goulart LF, Bettella F, Sønderby IE, Schork AJ, Thompson WK, Mattingsdal M, Steen VM, Zuber V, Wang Y, Dale AM, Andreassen OA, Djurovic S. MicroRNAs enrichment in GWAS of complex human phenotypes. BMC Genomics 2015; 16:304. [PMID: 25884492 PMCID: PMC4437677 DOI: 10.1186/s12864-015-1513-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/08/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The genotype information carried by Genome-wide association studies (GWAS) seems to have the potential to explain more of the 'missing heritability' of complex human phenotypes, given improved statistical approaches. Several lines of evidence support the involvement of microRNA (miRNA) and other non-coding RNA in complex human traits and diseases. We employed a novel, genetic annotation-informed enrichment method for GWAS that captures more polygenic effects than standard GWAS analysis, to investigate if miRNA-tagging Single Nucleotide Polymorphisms (SNPs) are enriched of associations with 15 complex human phenotypes. We then leveraged the enrichment using a conditional False Discovery Rate (condFDR) approach to assess any improvement in the detection of individual miRNA SNPs associated with the disorders. RESULTS We found SNPs tagging miRNA transcription regions to be significantly enriched of associations with 10 of 15 phenotypes. The enrichment remained significant after controlling for affiliation to other genomic categories, and was confirmed by replication. Albeit only nominally significant, enrichment was found also in miRNA binding sites for 10 phenotypes out of 15. Leveraging the enrichment in the condFDR framework, we observed a 2-4-fold increase in discovery of SNPs tagging miRNA regions. CONCLUSIONS Our results suggest that miRNAs play an important role in the polygenic architecture of complex human disorders and traits, and therefore that miRNAs are a genomic category that can and should be used to improve gene discovery.
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Affiliation(s)
- Luiz F Goulart
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
| | - Francesco Bettella
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
| | - Ida E Sønderby
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
| | - Andrew J Schork
- Multimodal Imaging Laboratory, University of California at San Diego, La Jolla, CA, 92037, USA.
- Cognitive Sciences Graduate Program, University of California at San Diego, La Jolla, CA, 92037, USA.
- Center for Human Development, University of California at San Diego, La Jolla, CA, 92037, USA.
| | - Wesley K Thompson
- Department of Psychiatry, University of California at San Diego, La Jolla, CA, 92037, USA.
| | - Morten Mattingsdal
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
| | - Vidar M Steen
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Dr. Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.
| | - Verena Zuber
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Yunpeng Wang
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
| | - Anders M Dale
- Multimodal Imaging Laboratory, University of California at San Diego, La Jolla, CA, 92037, USA.
- Department of Psychiatry, University of California at San Diego, La Jolla, CA, 92037, USA.
- Department of Neuroscience, University of California at San Diego, La Jolla, CA, 92037, USA.
- Department of Radiology, University of California at San Diego, La Jolla, CA, 92037, USA.
| | - Ole A Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
- Department of Psychiatry, University of California at San Diego, La Jolla, CA, 92037, USA.
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
- Division of Mental Health and Addiction, Oslo University Hospital, 0407, Oslo, Norway.
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