Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background

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  • dc.contributor.author Menashe, Idanca
  • dc.contributor.author Real, Francisco X.ca
  • dc.contributor.author Kogevinas, Manolisca
  • dc.contributor.author Serra, Consolca
  • dc.contributor.author Lloreta, Josep, 1958-ca
  • dc.contributor.author Rothman, Nathanielca
  • dc.date.accessioned 2015-05-04T09:34:24Z
  • dc.date.available 2015-05-04T09:34:24Z
  • dc.date.issued 2012ca
  • dc.description.abstract Pathway analysis of genome-wide association studies (GWAS) offer a unique opportunity to collectively evaluate genetic variants with effects that are too small to be detected individually. We applied a pathway analysis to a bladder cancer GWAS containing data from 3,532 cases and 5,120 controls of European background (n = 5 studies). Thirteen hundred and ninety-nine pathways were drawn from five publicly available resources (Biocarta, Kegg, NCI-PID, HumanCyc, and Reactome), and we constructed 22 additional candidate pathways previously hypothesized to be related to bladder cancer. In total, 1421 pathways, 5647 genes and 90,000 SNPs were included in our study. Logistic regression model adjusting for age, sex, study, DNA source, and smoking status was used to assess the marginal trend effect of SNPs on bladder cancer risk. Two complementary pathway-based methods (gene-set enrichment analysis [GSEA], and adapted rank-truncated product [ARTP]) were used to assess the enrichment of association signals within each pathway. Eighteen pathways were detected by either GSEA or ARTP at P≤0.01. To minimize false positives, we used the I2 statistic to identify SNPs displaying heterogeneous effects across the five studies. After removing these SNPs, seven pathways (‘Aromatic amine metabolism’ [PGSEA = 0.0100, PARTP = 0.0020], ‘NAD biosynthesis’ [PGSEA = 0.0018, PARTP = 0.0086], ‘NAD salvage’ [PARTP = 0.0068], ‘Clathrin derived vesicle budding’ [PARTP = 0.0018], ‘Lysosome vesicle biogenesis’ [PGSEA = 0.0023, PARTP<0.00012], ’Retrograde neurotrophin signaling’ [PGSEA = 0.00840], and ‘Mitotic metaphase/anaphase transition’ [PGSEA = 0.0040]) remained. These pathways seem to belong to three fundamental cellular processes (metabolic detoxification, mitosis, and clathrin-mediated vesicles). Identification of the aromatic amine metabolism pathway provides support for the ability of this approach to identify pathways with established relevance to bladderen
  • dc.description.sponsorship This project has been funded in part with federal funds from the Natio nal Cancer Institute, National Institutes of Health, under Contract No. HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government. Support for individual studies that participated in the effort is as follows: SBCS (Dr. Silverman) - Intramural Research Program of the National Institutes of Health, National Cancer Institute, Division of Cancer Epidemiology and Genetics and intramural contract number NCI N02-CP-11015. FIS/Spain 98/1274, FIS/Spain 00/0745, PI061614, and G03/174 Fundació Marató TV3, Red Temática Investigación Cooperativa en Cáncer (RTICC), Consolider ONCOBIO, EU-FP7-201663; and RO1- CA089715 and CA34627. NEBCS (Dr. Silverman) - Intramural research program of the National Institutes of Health, National Cancer Institute, Division of Cancer Epidemiology and Genetics and intramural contract number NCI N02-CP-01037 PLCO (Dr. Purdue) - The National Institutes of Health (NIH) Genes, Environment and Health Initiative(GEI) partly funded DNA extraction and statistical analyses (HG-06-033-NCI-01 and RO1HL091172-01), genotyping at the Johns Hopkins University Center for Inherited Disease Research (U01HG004438 and NIH HHSN268200782096C), and study coordination at the GENEVA (Dr. Caporaso)- The NIH Genes, Environment and Health Initiative [GEI] partly funded DNA extraction and statistical analyses (HG-06-033-NCI-01 and RO1HL091172-01), genotyping at the Johns Hopkins University Center for Inherited Disease Research (U01HG004438 and NIH HHSN268200782096C) and study coordination at the GENEVA Coordination Center (U01HG004446) for EAGLE and part of PLCO studies. Genotyping for the remaining part of PLCO and all ATBC and CPS-II samples were supported by the Intramural Research Program of the National Institutes of Health, NCI, Division of Cancer Epidemiology and Genetics. The PLCO is supported by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics and supported by contracts from the Division of Cancer Prevention, National Cancer Institute, National Institutes of Health. ATBC (Dr. Albanes) - This research was supported in part by the Intramural Research Program of the NIH and the National Cancer Institute. Additionally, this research was supported by U.S. Public Health Service contracts N01-CN-45165, N01-RC-45035, and N01-RC-37004 from the National Cancer Institute, Department of Health and Human Servicesen
  • dc.format.mimetype application/pdfca
  • dc.identifier.citation Menashe I, Figueroa JD, García-Closas M, Chatterjee N, Malats N, Picornell A et al. Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background. PLoS ONE. 2012;7(1):e29396. DOI: 10.1371/journal.pone.0029396ca
  • dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0029396
  • dc.identifier.issn 1932-6203ca
  • dc.identifier.uri http://hdl.handle.net/10230/23516
  • dc.language.iso engca
  • dc.publisher Public Library of Science (PLoS)ca
  • dc.relation.ispartof PLoS ONE. 2012;7(1):e29396
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/201663
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/089715
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/34627
  • dc.rights This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise us/ned by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedicationen
  • dc.rights.accessRights info:eu-repo/semantics/openAccessca
  • dc.rights.uri http://creativecommons.org/publicdomain/zero/1.0/
  • dc.subject.other Mitosica
  • dc.subject.other Genoma humàca
  • dc.subject.other Fetge -- Càncerca
  • dc.title Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European backgrounden
  • dc.type info:eu-repo/semantics/articleca
  • dc.type.version info:eu-repo/semantics/publishedVersionca

Col·leccions

Articles (Departament de Medicina i Ciències de la Vida)
Articles (Barcelona Institute for Global Health (ISGlobal) – Campus Mar)
Articles (Hospital del Mar Research Institute)
Documents OpenAIRE (Open Access Infrastructure for Research in Europe)