Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background.
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 E...
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2012
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oai:doaj.org-article:83ba9e6c0bd540c49b4769911fdfbdeb2021-11-18T07:30:58ZLarge-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background.1932-620310.1371/journal.pone.0029396https://doaj.org/article/83ba9e6c0bd540c49b4769911fdfbdeb2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22238607/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Pathway 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 I(2) statistic to identify SNPs displaying heterogeneous effects across the five studies. After removing these SNPs, seven pathways ('Aromatic amine metabolism' [P(GSEA) = 0.0100, P(ARTP) = 0.0020], 'NAD biosynthesis' [P(GSEA) = 0.0018, P(ARTP) = 0.0086], 'NAD salvage' [P(ARTP) = 0.0068], 'Clathrin derived vesicle budding' [P(ARTP) = 0.0018], 'Lysosome vesicle biogenesis' [P(GSEA) = 0.0023, P(ARTP)<0.00012], 'Retrograde neurotrophin signaling' [P(GSEA) = 0.00840], and 'Mitotic metaphase/anaphase transition' [P(GSEA) = 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 bladder carcinogenesis.Idan MenasheJonine D FigueroaMontserrat Garcia-ClosasNilanjan ChatterjeeNuria MalatsAntoni PicornellDennis MaederQi YangLudmila Prokunina-OlssonZhaoming WangFrancisco X RealKevin B JacobsDalsu BarisMichael ThunDemetrius AlbanesMark P PurdueManolis KogevinasAmy HutchinsonYi-Ping FuWei TangLaurie BurdetteAdonina TardónConsol SerraAlfredo CarratoReina García-ClosasJosep LloretaAlison JohnsonMolly SchwennAlan SchnedGerald AndrioleAmanda BlackEric J JacobsRyan W DiverSusan M GapsturStephanie J WeinsteinJarmo VirtamoNeil E CaporasoMaria Teresa LandiJoseph F FraumeniStephen J ChanockDebra T SilvermanNathaniel RothmanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 1, p e29396 (2012) |
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Medicine R Science Q |
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Medicine R Science Q Idan Menashe Jonine D Figueroa Montserrat Garcia-Closas Nilanjan Chatterjee Nuria Malats Antoni Picornell Dennis Maeder Qi Yang Ludmila Prokunina-Olsson Zhaoming Wang Francisco X Real Kevin B Jacobs Dalsu Baris Michael Thun Demetrius Albanes Mark P Purdue Manolis Kogevinas Amy Hutchinson Yi-Ping Fu Wei Tang Laurie Burdette Adonina Tardón Consol Serra Alfredo Carrato Reina García-Closas Josep Lloreta Alison Johnson Molly Schwenn Alan Schned Gerald Andriole Amanda Black Eric J Jacobs Ryan W Diver Susan M Gapstur Stephanie J Weinstein Jarmo Virtamo Neil E Caporaso Maria Teresa Landi Joseph F Fraumeni Stephen J Chanock Debra T Silverman Nathaniel Rothman Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background. |
| description |
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 I(2) statistic to identify SNPs displaying heterogeneous effects across the five studies. After removing these SNPs, seven pathways ('Aromatic amine metabolism' [P(GSEA) = 0.0100, P(ARTP) = 0.0020], 'NAD biosynthesis' [P(GSEA) = 0.0018, P(ARTP) = 0.0086], 'NAD salvage' [P(ARTP) = 0.0068], 'Clathrin derived vesicle budding' [P(ARTP) = 0.0018], 'Lysosome vesicle biogenesis' [P(GSEA) = 0.0023, P(ARTP)<0.00012], 'Retrograde neurotrophin signaling' [P(GSEA) = 0.00840], and 'Mitotic metaphase/anaphase transition' [P(GSEA) = 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 bladder carcinogenesis. |
| format |
article |
| author |
Idan Menashe Jonine D Figueroa Montserrat Garcia-Closas Nilanjan Chatterjee Nuria Malats Antoni Picornell Dennis Maeder Qi Yang Ludmila Prokunina-Olsson Zhaoming Wang Francisco X Real Kevin B Jacobs Dalsu Baris Michael Thun Demetrius Albanes Mark P Purdue Manolis Kogevinas Amy Hutchinson Yi-Ping Fu Wei Tang Laurie Burdette Adonina Tardón Consol Serra Alfredo Carrato Reina García-Closas Josep Lloreta Alison Johnson Molly Schwenn Alan Schned Gerald Andriole Amanda Black Eric J Jacobs Ryan W Diver Susan M Gapstur Stephanie J Weinstein Jarmo Virtamo Neil E Caporaso Maria Teresa Landi Joseph F Fraumeni Stephen J Chanock Debra T Silverman Nathaniel Rothman |
| author_facet |
Idan Menashe Jonine D Figueroa Montserrat Garcia-Closas Nilanjan Chatterjee Nuria Malats Antoni Picornell Dennis Maeder Qi Yang Ludmila Prokunina-Olsson Zhaoming Wang Francisco X Real Kevin B Jacobs Dalsu Baris Michael Thun Demetrius Albanes Mark P Purdue Manolis Kogevinas Amy Hutchinson Yi-Ping Fu Wei Tang Laurie Burdette Adonina Tardón Consol Serra Alfredo Carrato Reina García-Closas Josep Lloreta Alison Johnson Molly Schwenn Alan Schned Gerald Andriole Amanda Black Eric J Jacobs Ryan W Diver Susan M Gapstur Stephanie J Weinstein Jarmo Virtamo Neil E Caporaso Maria Teresa Landi Joseph F Fraumeni Stephen J Chanock Debra T Silverman Nathaniel Rothman |
| author_sort |
Idan Menashe |
| title |
Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background. |
| title_short |
Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background. |
| title_full |
Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background. |
| title_fullStr |
Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background. |
| title_full_unstemmed |
Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background. |
| title_sort |
large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of european background. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2012 |
| url |
https://doaj.org/article/83ba9e6c0bd540c49b4769911fdfbdeb |
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