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- Title
Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype.
- Authors
Tragante, Vinicius; Gho, Johannes M. I. H.; Felix, Janine F.; Vasan, Ramachandran S.; Smith, Nicholas L.; Voight, Benjamin F.; Palmer, Colin; van der Harst, Pim; Moore, Jason H.; Asselbergs, Folkert W.
- Abstract
Background: Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Analysis (GSEA) aims to address this by identifying sets of genes or biological pathways contributing to a phenotype, through gene-gene interactions or other mechanisms, which are not the focus of conventional association methods. Results: Approaches that utilize GSEA can now take input from array chips, either gene-centric or genome-wide, but are highly sensitive to study design, SNP selection and pruning strategies, SNP-to-gene mapping, and pathway definitions. Here, we present lessons learned from our experience with GSEA of heart failure, a particularly challenging phenotype due to its underlying heterogeneous etiology. Conclusions: This case study shows that proper data handling is essential to avoid false-positive results. Well-defined pipelines for quality control are needed to avoid reporting spurious results using GSEA.
- Subjects
HEART failure; HEART failure risk factors; SINGLE nucleotide polymorphisms; GENE mapping; DISEASE susceptibility; DISEASE incidence; GENETICS
- Publication
BioData Mining, 2017, Vol 10, p1
- ISSN
1756-0381
- Publication type
Article
- DOI
10.1186/s13040-017-0137-5