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Agnostic pathway/gene set analysis of genome-wide association data identifies associations for pancreatic cancer

Journal of the National Cancer Institute Dec 18, 2018

Walsh N, et al. - Researchers performed a large agnostic pathway and gene set analysis of genome-wide association studies (GWAS) data integrated with functional annotation and expression quantitative trait loci (eQTL) analysis, to identify gene sets and pathways related to pancreatic ductal adenocarcinoma (PDAC) in 9,040 cases and 12,496 controls. At a false discovery rate of less than 0.05, 14 pathways and gene sets related to PDAC were discovered. Five pathways and gene sets showed the strongest associations after Bonferroni correction, including maturity-onset diabetes of the young, regulation of beta-cell development, role of epidermal growth factor (EGF) receptor transactivation by G protein–coupled receptors in cardiac hypertrophy pathways, and the Nikolsky breast cancer chr17q11-q21 amplicon and Pujana ATM Pearson correlation coefficient (PCC) network gene sets. As eQTLs in two normal derived pancreas tissue datasets, rs876493 and three correlating SNPs (PGAP3) and rs3124737 (CASP7) from the Pujana ATM PCC gene set were identified and validated.
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