2018
Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer
Walsh N, Zhang H, Hyland PL, Yang Q, Mocci E, Zhang M, Childs EJ, Collins I, Wang Z, Arslan AA, Beane-Freeman L, Bracci PM, Brennan P, Canzian F, Duell EJ, Gallinger S, Giles GG, Goggins M, Goodman GE, Goodman PJ, Hung RJ, Kooperberg C, Kurtz RC, Malats N, LeMarchand L, Neale RE, Olson SH, Scelo G, Shu XO, Van Den Eeden SK, Visvanathan K, White E, Zheng W, consortia P, Albanes D, Andreotti G, Babic A, Bamlet W, Berndt S, Borgida A, Boutron-Ruault M, Brais L, Brennan P, Bueno-de-Mesquita B, Buring J, Chaffee K, Chanock S, Cleary S, Cotterchio M, Foretova L, Fuchs C, Gaziano J, Giovannucci E, Goggins M, Hackert T, Haiman C, Hartge P, Hasan M, Helzlsouer K, Herman J, Holcatova I, Holly E, Hoover R, Hung R, Janout V, Klein E, Kurtz R, Laheru D, Lee I, Lu L, Malats N, Mannisto S, Milne R, Oberg A, Orlow I, Patel A, Peters U, Porta M, Real F, Rothman N, Sesso H, Severi G, Silverman D, Strobel O, Sund M, Thornquist M, Tobias G, Wactawski-Wende J, Wareham N, Weiderpass E, Wentzensen N, Wheeler W, Yu H, Zeleniuch-Jacquotte A, Kraft P, Li D, Jacobs E, Petersen G, Wolpin B, Risch H, Amundadottir L, Yu K, Klein A, Stolzenberg-Solomon R. Agnostic Pathway/Gene Set Analysis of Genome-Wide Association Data Identifies Associations for Pancreatic Cancer. Journal Of The National Cancer Institute 2018, 111: 557-567. PMID: 30541042, PMCID: PMC6579744, DOI: 10.1093/jnci/djy155.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGene setsSingle nucleotide polymorphismsFunctional annotationEpidermal growth factor receptor transactivationExpression quantitative trait loci (eQTL) analysisQuantitative trait locus (QTL) analysisGrowth factor receptor transactivationTop single nucleotide polymorphismsG protein-coupled receptorsGene-set analysisProtein-coupled receptorsIndividual single nucleotide polymorphismsBeta-cell developmentEQTL analysisGWAS dataPCC genesPancreatic ductal adenocarcinomaReceptor transactivationLocus analysisPathway analysisAssociation studiesGenesSusceptibility genesIdentifies associations
2017
Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci
Kar SP, Adler E, Tyrer J, Hazelett D, Anton-Culver H, Bandera EV, Beckmann MW, Berchuck A, Bogdanova N, Brinton L, Butzow R, Campbell I, Carty K, Chang-Claude J, Cook LS, Cramer DW, Cunningham JM, Dansonka-Mieszkowska A, Doherty JA, Dörk T, Dürst M, Eccles D, Fasching PA, Flanagan J, Gentry-Maharaj A, Glasspool R, Goode EL, Goodman MT, Gronwald J, Heitz F, Hildebrandt MA, Høgdall E, Høgdall CK, Huntsman DG, Jensen A, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Kupryjanczyk J, Lambrechts D, Levine DA, Li Q, Lissowska J, Lu KH, Lubiński J, Massuger LF, McGuire V, McNeish I, Menon U, Modugno F, Monteiro AN, Moysich KB, Ness RB, Nevanlinna H, Paul J, Pearce CL, Pejovic T, Permuth JB, Phelan C, Pike MC, Poole EM, Ramus SJ, Risch HA, Rossing MA, Salvesen HB, Schildkraut JM, Sellers TA, Sherman M, Siddiqui N, Sieh W, Song H, Southey M, Terry KL, Tworoger SS, Walsh C, Wentzensen N, Whittemore AS, Wu AH, Yang H, Zheng W, Ziogas A, Freedman ML, Gayther SA, Pharoah PD, Lawrenson K. Enrichment of putative PAX8 target genes at serous epithelial ovarian cancer susceptibility loci. British Journal Of Cancer 2017, 116: 524-535. PMID: 28103614, PMCID: PMC5318969, DOI: 10.1038/bjc.2016.426.Peer-Reviewed Original ResearchMeSH KeywordsCarcinoma, Ovarian EpithelialCase-Control StudiesCell Line, TumorCell Transformation, NeoplasticCystadenocarcinoma, SerousFemaleGene AmplificationGene Expression ProfilingGene Expression Regulation, NeoplasticGenetic LociGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMeta-Analysis as TopicMicroarray AnalysisNeoplasms, Glandular and EpithelialOvarian NeoplasmsPolymorphism, Single NucleotideConceptsGenome-wide association studiesTarget genesTranscription factorsRisk lociOvarian cancer susceptibility lociCancer risk lociDifferential gene expressionCancer susceptibility lociMolecular Signatures DatabaseShRNA-mediated silencingGene setsEnrichment analysisGene expressionTranscriptomic perturbationsAssociation studiesSusceptibility lociGenesLociOvarian cancer susceptibilityRisk variantsAgnostic evaluationCell of originCancer susceptibilityBiological mechanismsPathway
2014
Axonal guidance signaling pathway interacting with smoking in modifying the risk of pancreatic cancer: a gene- and pathway-based interaction analysis of GWAS data
Tang H, Wei P, Duell EJ, Risch HA, Olson SH, Bueno-de-Mesquita HB, Gallinger S, Holly EA, Petersen G, Bracci PM, McWilliams RR, Jenab M, Riboli E, Tjønneland A, Boutron-Ruault MC, Kaaks R, Trichopoulos D, Panico S, Sund M, Peeters PH, Khaw KT, Amos CI, Li D. Axonal guidance signaling pathway interacting with smoking in modifying the risk of pancreatic cancer: a gene- and pathway-based interaction analysis of GWAS data. Carcinogenesis 2014, 35: 1039-1045. PMID: 24419231, PMCID: PMC4004205, DOI: 10.1093/carcin/bgu010.Peer-Reviewed Original ResearchConceptsIngenuity Pathway AnalysisKEGG pathwaysSingle nucleotide polymorphism (SNP) levelAxonal guidanceGenome-wide levelGene ontology pathwaysSalivary secretion pathwaysSlit/RoboGenes/SNPsOntology pathwaysPolymorphism levelSecretion pathwayGWAS dataGene setsPancreatic Cancer Case-Control ConsortiumCanonical pathwaysPathway analysisAxon guidanceGenesSNPsRegion SNPsPathwayIPA analysisPancreatic cancerDiscovery studies