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

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http://hdl.handle.net/10138/323913

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PanScan PanC4 consortia , Walsh , N , Zhang , H , Männistö , S & Weiderpass , E 2019 , ' Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer ' , Journal of the National Cancer Institute , vol. 111 , no. 6 , 155 , pp. 557-567 . https://doi.org/10.1093/jnci/djy155

Title: Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer
Author: PanScan PanC4 consortia; Walsh, Naomi; Zhang, Han; Männistö, Satu; Weiderpass, Elisabete
Contributor: University of Helsinki, Department of Medical and Clinical Genetics
Date: 2019-06
Language: eng
Number of pages: 11
Belongs to series: Journal of the National Cancer Institute
ISSN: 0027-8874
URI: http://hdl.handle.net/10138/323913
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 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.
Subject: BREAST-CANCER
SUSCEPTIBILITY LOCI
GENES
ENDOTHELIN
RECEPTOR
MUTATIONS
VARIANTS
TRANSCRIPTOME
METASTASIS
EXPRESSION
3122 Cancers
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