Literature DB >> 30541042

Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer.

Naomi Walsh1, Han Zhang2, Paula L Hyland2,3, Qi Yang2, Evelina Mocci4, Mingfeng Zhang5,6, Erica J Childs4, Irene Collins5, Zhaoming Wang5,7, Alan A Arslan8,9,10, Laura Beane-Freeman2, Paige M Bracci11, Paul Brennan12, Federico Canzian13, Eric J Duell14, Steven Gallinger15, Graham G Giles16,17,18, Michael Goggins19, Gary E Goodman20, Phyllis J Goodman21, Rayjean J Hung15, Charles Kooperberg20, Robert C Kurtz22, Núria Malats23,24, Loic LeMarchand25, Rachel E Neale26, Sara H Olson27, Ghislaine Scelo12, Xiao O Shu28, Stephen K Van Den Eeden29, Kala Visvanathan30, Emily White20,31, Wei Zheng28, Demetrius Albanes2, Gabriella Andreotti2, Ana Babic32, William R Bamlet33, Sonja I Berndt2, Ayelet Borgida15, Marie-Christine Boutron-Ruault34, Lauren Brais32, Paul Brennan12, Bas Bueno-de-Mesquita35,36,37, Julie Buring38,39, Kari G Chaffee33, Stephen Chanock2, Sean Cleary40, Michelle Cotterchio41,42, Lenka Foretova43, Charles Fuchs44, J Michael M Gaziano45,46, Edward Giovannucci32, Michael Goggins19, Thilo Hackert47, Christopher Haiman48, Patricia Hartge2, Manal Hasan49, Kathy J Helzlsouer50, Joseph Herman51, Ivana Holcatova52, Elizabeth A Holly11, Robert Hoover2, Rayjean J Hung15, Vladimir Janout53,54, Eric A Klein55, Robert C Kurtz22, Daniel Laheru4, I-Min Lee38,39, Lingeng Lu56, Núria Malats23,24, Satu Mannisto57, Roger L Milne16,17, Ann L Oberg33, Irene Orlow27, Alpa V Patel58, Ulrike Peters20, Miquel Porta59,60, Francisco X Real24,61,62, Nathaniel Rothman2, Howard D Sesso38,39, Gianluca Severi16,17,34, Debra Silverman2, Oliver Strobel47, Malin Sund63, Mark D Thornquist20, Geoffrey S Tobias2, Jean Wactawski-Wende64, Nick Wareham65, Elisabete Weiderpass66,67,68,69, Nicolas Wentzensen2, William Wheeler70, Herbert Yu71, Anne Zeleniuch-Jacquotte10,72, Peter Kraft39,73, Donghui Li73, Eric J Jacobs58, Gloria M Petersen33, Brian M Wolpin32, Harvey A Risch56, Laufey T Amundadottir5, Kai Yu2, Alison P Klein4,19, Rachael Z Stolzenberg-Solomon1.   

Abstract

BACKGROUND: Genome-wide association studies (GWAS) identify associations of individual single-nucleotide polymorphisms (SNPs) with cancer risk but usually only explain a fraction of the inherited variability. Pathway analysis of genetic variants is a powerful tool to identify networks of susceptibility genes.
METHODS: We conducted a large agnostic pathway-based meta-analysis of GWAS data using the summary-based adaptive rank truncated product method to identify gene sets and pathways associated with pancreatic ductal adenocarcinoma (PDAC) in 9040 cases and 12 496 controls. We performed expression quantitative trait loci (eQTL) analysis and functional annotation of the top SNPs in genes contributing to the top associated pathways and gene sets. All statistical tests were two-sided.
RESULTS: We identified 14 pathways and gene sets associated with PDAC at a false discovery rate of less than 0.05. After Bonferroni correction (P ≤ 1.3 × 10-5), the strongest associations were detected in five pathways and gene sets, 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. We identified and validated rs876493 and three correlating SNPs (PGAP3) and rs3124737 (CASP7) from the Pujana ATM PCC gene set as eQTLs in two normal derived pancreas tissue datasets.
CONCLUSION: Our agnostic pathway and gene set analysis integrated with functional annotation and eQTL analysis provides insight into genes and pathways that may be biologically relevant for risk of PDAC, including those not previously identified. Published by Oxford University Press 2018. This work is written by US Government employees and is in the public domain in the US.

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Year:  2019        PMID: 30541042      PMCID: PMC6579744          DOI: 10.1093/jnci/djy155

Source DB:  PubMed          Journal:  J Natl Cancer Inst        ISSN: 0027-8874            Impact factor:   13.506


  50 in total

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