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Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data

By Juan Fernéndez-Tajes, Kyle J Gaulton, Martijn van de Bunt, Jason Torres, Matthias Thurner, Anubha Mahajan, Anna L Gloyn, Kasper Lage, Mark I McCarthy

Posted 20 Jun 2018
bioRxiv DOI: 10.1101/350181 (published DOI: 10.1186/s13073-019-0628-8)

Genome wide association studies (GWAS) have identified several hundred susceptibility loci for Type 2 Diabetes (T2D). One critical, but unresolved, issue concerns the extent to which the mechanisms through which these diverse signals influencing T2D predisposition converge on a limited set of biological processes. However, the causal variants identified by GWAS mostly fall into non-coding sequence, complicating the task of defining the effector transcripts through which they operate. Here, we describe implementation of an analytical pipeline to address this question. First, we integrate multiple sources of genetic, genomic, and biological data to assign positional candidacy scores to the genes that map to T2D GWAS signals. Second, we introduce genes with high scores as seeds within a network optimization algorithm (the asymmetric prize-collecting Steiner Tree approach) which uses external, experimentally-confirmed protein-protein interaction (PPI) data to generate high confidence subnetworks. Third, we use GWAS data to test the T2D-association enrichment of the "non-seed" proteins introduced into the network, as a measure of the overall functional connectivity of the network. We find: (a) non-seed proteins in the T2D protein-interaction network generated (comprising 705 nodes) are enriched for association to T2D (p=0.0014) but not control traits; (b) stronger T2D-enrichment for islets than other tissues when we use RNA expression data to generate tissue-specific PPI networks ; and (c) enhanced enrichment (p=3.9x10-5) when we combine analysis of the islet-specific PPI network with a focus on the subset of T2D GWAS loci which act through defective insulin secretion. These analyses reveal a pattern of non-random functional connectivity between causal candidate genes at T2D GWAS loci, and highlight the products of genes including YWHAG, SMAD4 or CDK2 as contributors to T2D-relevant islet dysfunction. The approach we describe can be applied to other complex genetic and genomic data sets, facilitating integration of diverse data types into disease-associated networks

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