2020
A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer
Zhong J, Jermusyk A, Wu L, Hoskins JW, Collins I, Mocci E, Zhang M, Song L, Chung CC, Zhang T, Xiao W, Albanes D, Andreotti G, Arslan AA, Babic A, Bamlet WR, Beane-Freeman L, Berndt S, Borgida A, Bracci PM, Brais L, Brennan P, Bueno-de-Mesquita B, Buring J, Canzian F, Childs EJ, Cotterchio M, Du M, Duell EJ, Fuchs C, Gallinger S, Gaziano JM, Giles GG, Giovannucci E, Goggins M, Goodman GE, Goodman PJ, Haiman C, Hartge P, Hasan M, Helzlsouer KJ, Holly EA, Klein EA, Kogevinas M, Kurtz RJ, LeMarchand L, Malats N, Männistö S, Milne R, Neale RE, Ng K, Obazee O, Oberg AL, Orlow I, Patel AV, Peters U, Porta M, Rothman N, Scelo G, Sesso HD, Severi G, Sieri S, Silverman D, Sund M, Tjønneland A, Thornquist MD, Tobias GS, Trichopoulou A, Van Den Eeden SK, Visvanathan K, Wactawski-Wende J, Wentzensen N, White E, Yu H, Yuan C, Zeleniuch-Jacquotte A, Hoover R, Brown K, Kooperberg C, Risch HA, Jacobs EJ, Li D, Yu K, Shu XO, Chanock SJ, Wolpin BM, Stolzenberg-Solomon RZ, Chatterjee N, Klein AP, Smith JP, Kraft P, Shi J, Petersen GM, Zheng W, Amundadottir LT. A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer. Journal Of The National Cancer Institute 2020, 112: 1003-1012. PMID: 31917448, PMCID: PMC7566474, DOI: 10.1093/jnci/djz246.Peer-Reviewed Original ResearchConceptsTranscriptome-wide association studyCancer risk lociRisk lociAssociation studiesPancreatic cancer susceptibility lociGene expression prediction modelsNovel candidate susceptibility genesPossible causal genesGenome-wide association studiesGenome-wide associationCancer susceptibility lociCandidate susceptibility genesNormal pancreatic tissue samplesFunctional genesTranscriptome dataCausal genesNovel lociCandidate genesGene expressionSusceptibility lociGenesGenotype dataLociSusceptibility genesDifferent tissuesFine-mapping of 150 breast cancer risk regions identifies 191 likely target genes
Fachal L, Aschard H, Beesley J, Barnes DR, Allen J, Kar S, Pooley KA, Dennis J, Michailidou K, Turman C, Soucy P, Lemaçon A, Lush M, Tyrer JP, Ghoussaini M, Moradi Marjaneh M, Jiang X, Agata S, Aittomäki K, Alonso MR, Andrulis IL, Anton-Culver H, Antonenkova NN, Arason A, Arndt V, Aronson KJ, Arun BK, Auber B, Auer PL, Azzollini J, Balmaña J, Barkardottir RB, Barrowdale D, Beeghly-Fadiel A, Benitez J, Bermisheva M, Białkowska K, Blanco AM, Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borg A, Bosse K, Brauch H, Brenner H, Briceno I, Brock IW, Brooks-Wilson A, Brüning T, Burwinkel B, Buys SS, Cai Q, Caldés T, Caligo MA, Camp NJ, Campbell I, Canzian F, Carroll JS, Carter BD, Castelao JE, Chiquette J, Christiansen H, Chung WK, Claes KBM, Clarke CL, Collée J, Cornelissen S, Couch F, Cox A, Cross S, Cybulski C, Czene K, Daly M, de la Hoya M, Devilee P, Diez O, Ding Y, Dite G, Domchek S, Dörk T, dos-Santos-Silva I, Droit A, Dubois S, Dumont M, Duran M, Durcan L, Dwek M, Eccles D, Engel C, Eriksson M, Evans D, Fasching P, Fletcher O, Floris G, Flyger H, Foretova L, Foulkes W, Friedman E, Fritschi L, Frost D, Gabrielson M, Gago-Dominguez M, Gambino G, Ganz P, Gapstur S, Garber J, García-Sáenz J, Gaudet M, Georgoulias V, Giles G, Glendon G, Godwin A, Goldberg M, Goldgar D, González-Neira A, Tibiletti M, Greene M, Grip M, Gronwald J, Grundy A, Guénel P, Hahnen E, Haiman C, Håkansson N, Hall P, Hamann U, Harrington P, Hartikainen J, Hartman M, He W, Healey C, Heemskerk-Gerritsen B, Heyworth J, Hillemanns P, Hogervorst F, Hollestelle A, Hooning M, Hopper J, Howell A, Huang G, Hulick P, Imyanitov E, Isaacs C, Iwasaki M, Jager A, Jakimovska M, Jakubowska A, James P, Janavicius R, Jankowitz R, John E, Johnson N, Jones M, Jukkola-Vuorinen A, Jung A, Kaaks R, Kang D, Kapoor P, Karlan B, Keeman R, Kerin M, Khusnutdinova E, Kiiski J, Kirk J, Kitahara C, Ko Y, Konstantopoulou I, Kosma V, Koutros S, Kubelka-Sabit K, Kwong A, Kyriacou K, Laitman Y, Lambrechts D, Lee E, Leslie G, Lester J, Lesueur F, Lindblom A, Lo W, Long J, Lophatananon A, Loud J, Lubiński J, MacInnis R, Maishman T, Makalic E, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez M, Matsuo K, Maurer T, Mavroudis D, Mayes R, McGuffog L, McLean C, Mebirouk N, Meindl A, Miller A, Miller N, Montagna M, Moreno F, Muir K, Mulligan A, Muñoz-Garzon V, Muranen T, Narod S, Nassir R, Nathanson K, Neuhausen S, Nevanlinna H, Neven P, Nielsen F, Nikitina-Zake L, Norman A, Offit K, Olah E, Olopade O, Olsson H, Orr N, Osorio A, Pankratz V, Papp J, Park S, Park-Simon T, Parsons M, Paul J, Pedersen I, Peissel B, Peshkin B, Peterlongo P, Peto J, Plaseska-Karanfilska D, Prajzendanc K, Prentice R, Presneau N, Prokofyeva D, Pujana M, Pylkäs K, Radice P, Ramus S, Rantala J, Rau-Murthy R, Rennert G, Risch H, Robson M, Romero A, Rossing M, Saloustros E, Sánchez-Herrero E, Sandler D, Santamariña M, Saunders C, Sawyer E, Scheuner M, Schmidt D, Schmutzler R, Schneeweiss A, Schoemaker M, Schöttker B, Schürmann P, Scott C, Scott R, Senter L, Seynaeve C, Shah M, Sharma P, Shen C, Shu X, Singer C, Slavin T, Smichkoska S, Southey M, Spinelli J, Spurdle A, Stone J, Stoppa-Lyonnet D, Sutter C, Swerdlow A, Tamimi R, Tan Y, Tapper W, Taylor J, Teixeira M, Tengström M, Teo S, Terry M, Teulé A, Thomassen M, Thull D, Tischkowitz M, Toland A, Tollenaar R, Tomlinson I, Torres D, Torres-Mejía G, Troester M, Truong T, Tung N, Tzardi M, Ulmer H, Vachon C, van Asperen C, van der Kolk L, van Rensburg E, Vega A, Viel A, Vijai J, Vogel M, Wang Q, Wappenschmidt B, Weinberg C, Weitzel J, Wendt C, Wildiers H, Winqvist R, Wolk A, Wu A, Yannoukakos D, Zhang Y, Zheng W, Hunter D, Pharoah P, Chang-Claude J, García-Closas M, Schmidt M, Milne R, Kristensen V, French J, Edwards S, Antoniou A, Chenevix-Trench G, Simard J, Easton D, Kraft P, Dunning A. Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. Nature Genetics 2020, 52: 56-73. PMID: 31911677, PMCID: PMC6974400, DOI: 10.1038/s41588-019-0537-1.Peer-Reviewed Original ResearchConceptsCausal variantsTranscription factorsTarget genesActive gene regulatory regionsHigh-confidence target genesGenomic feature annotationsGenome-wide association studiesBreast cancer risk variantsGene regulatory regionsCredible causal variantsGene ontology pathwaysChromatin interactionsFunctional annotationGenomic regionsOntology pathwaysRegulatory regionsGenomic featuresCancer driversGene expressionAssociation studiesAssociation analysisGenesLinkage disequilibriumRisk variantsHigh posterior probability
2019
Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer
Ferreira MA, Gamazon ER, Al-Ejeh F, Aittomäki K, Andrulis IL, Anton-Culver H, Arason A, Arndt V, Aronson KJ, Arun BK, Asseryanis E, Azzollini J, Balmaña J, Barnes DR, Barrowdale D, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Białkowska K, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Borg A, Brauch H, Brenner H, Broeks A, Burwinkel B, Caldés T, Caligo MA, Campa D, Campbell I, Canzian F, Carter J, Carter BD, Castelao JE, Chang-Claude J, Chanock SJ, Christiansen H, Chung WK, Claes KBM, Clarke CL, Couch F, Cox A, Cross S, Czene K, Daly M, de la Hoya M, Dennis J, Devilee P, Diez O, Dörk T, Dunning A, Dwek M, Eccles D, Ejlertsen B, Ellberg C, Engel C, Eriksson M, Fasching P, Fletcher O, Flyger H, Friedman E, Frost D, Gabrielson M, Gago-Dominguez M, Ganz P, Gapstur S, Garber J, García-Closas M, García-Sáenz J, Gaudet M, Giles G, Glendon G, Godwin A, Goldberg M, Goldgar D, González-Neira A, Greene M, Gronwald J, Guénel P, Haiman C, Hall P, Hamann U, He W, Heyworth J, Hogervorst F, Hollestelle A, Hoover R, Hopper J, Hulick P, Humphreys K, Imyanitov E, Isaacs C, Jakimovska M, Jakubowska A, James P, Janavicius R, Jankowitz R, John E, Johnson N, Joseph V, Karlan B, Khusnutdinova E, Kiiski J, Ko Y, Jones M, Konstantopoulou I, Kristensen V, Laitman Y, Lambrechts D, Lazaro C, Leslie G, Lester J, Lesueur F, Lindström S, Long J, Loud J, Lubiński J, Makalic E, Mannermaa A, Manoochehri M, Margolin S, Maurer T, Mavroudis D, McGuffog L, Meindl A, Menon U, Michailidou K, Miller A, Montagna M, Moreno F, Moserle L, Mulligan A, Nathanson K, Neuhausen S, Nevanlinna H, Nevelsteen I, Nielsen F, Nikitina-Zake L, Nussbaum R, Offit K, Olah E, Olopade O, Olsson H, Osorio A, Papp J, Park-Simon T, Parsons M, Pedersen I, Peixoto A, Peterlongo P, Pharoah P, Plaseska-Karanfilska D, Poppe B, Presneau N, Radice P, Rantala J, Rennert G, Risch H, Saloustros E, Sanden K, Sawyer E, Schmidt M, Schmutzler R, Sharma P, Shu X, Simard J, Singer C, Soucy P, Southey M, Spinelli J, Spurdle A, Stone J, Swerdlow A, Tapper W, Taylor J, Teixeira M, Terry M, Teulé A, Thomassen M, Thöne K, Thull D, Tischkowitz M, Toland A, Torres D, Truong T, Tung N, Vachon C, van Asperen C, van den Ouweland A, van Rensburg E, Vega A, Viel A, Wang Q, Wappenschmidt B, Weitzel J, Wendt C, Winqvist R, Yang X, Yannoukakos D, Ziogas A, Kraft P, Antoniou A, Zheng W, Easton D, Milne R, Beesley J, Chenevix-Trench G. Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer. Nature Communications 2019, 10: 1741. PMID: 30988301, PMCID: PMC6465407, DOI: 10.1038/s41467-018-08053-5.Peer-Reviewed Original ResearchConceptsExpression quantitative trait lociGenome-wide association studiesTarget genesMultiple expression quantitative trait lociBreast cancer risk variantsPrevious genome-wide association studyQuantitative trait lociGenome-wide associationGene-based testsBreast cancerBreast cancer susceptibility lociCancer susceptibility lociRisk-associated variantsImmune cellsTrait lociTranscriptome studiesRisk lociGene expressionAssociation studiesOverall breast cancer riskSusceptibility lociMultiple tissuesBreast cancer riskNegative breast cancerRisk variants
2018
A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk
Lu Y, Beeghly-Fadiel A, Wu L, Guo X, Li B, Schildkraut JM, Im HK, Chen YA, Permuth JB, Reid BM, Teer JK, Moysich KB, Andrulis IL, Anton-Culver H, Arun BK, Bandera EV, Barkardottir RB, Barnes DR, Benitez J, Bjorge L, Brenton J, Butzow R, Caldes T, Caligo MA, Campbell I, Chang-Claude J, Claes KBM, Couch FJ, Cramer DW, Daly MB, deFazio A, Dennis J, Diez O, Domchek SM, Dörk T, Easton DF, Eccles DM, Fasching PA, Fortner RT, Fountzilas G, Friedman E, Ganz PA, Garber J, Giles GG, Godwin AK, Goldgar DE, Goodman MT, Greene MH, Gronwald J, Hamann U, Heitz F, Hildebrandt MAT, Høgdall CK, Hollestelle A, Hulick PJ, Huntsman DG, Imyanitov EN, Isaacs C, Jakubowska A, James P, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Kwong A, Le ND, Leslie G, Lesueur F, Levine DA, Mattiello A, May T, McGuffog L, McNeish IA, Merritt MA, Modugno F, Montagna M, Neuhausen SL, Nevanlinna H, Nielsen FC, Nikitina-Zake L, Nussbaum RL, Offit K, Olah E, Olopade OI, Olson SH, Olsson H, Osorio A, Park SK, Parsons MT, Peeters PHM, Pejovic T, Peterlongo P, Phelan CM, Pujana MA, Ramus SJ, Rennert G, Risch H, Rodriguez GC, Rodríguez-Antona C, Romieu I, Rookus MA, Rossing MA, Rzepecka IK, Sandler DP, Schmutzler RK, Setiawan VW, Sharma P, Sieh W, Simard J, Singer CF, Song H, Southey MC, Spurdle AB, Sutphen R, Swerdlow AJ, Teixeira MR, Teo SH, Thomassen M, Tischkowitz M, Toland AE, Trichopoulou A, Tung N, Tworoger SS, van Rensburg EJ, Vanderstichele A, Vega A, Edwards DV, Webb PM, Weitzel JN, Wentzensen N, White E, Wolk A, Wu AH, Yannoukakos D, Zorn KK, Gayther SA, Antoniou AC, Berchuck A, Goode EL, Chenevix-Trench G, Sellers TA, Pharoah PDP, Zheng W, Long J. A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk. Cancer Research 2018, 78: 5419-5430. PMID: 30054336, PMCID: PMC6139053, DOI: 10.1158/0008-5472.can-18-0951.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesNovel lociGWAS lociCausal genesMajority of GWASTranscriptome-wide association studyAssociation studiesGenotype-Tissue Expression (GTEx) projectLarge-scale genome-wide association studiesHigh-density genotyping dataPlausible causal genesPotential novel lociNovel genetic lociGWAS-identified variantsRNA sequencing dataDisease susceptibility variantsBonferroni-corrected significance levelTranscriptomic analysisExpression projectGenetic lociSummary statistics dataRisk lociGene expressionSequencing dataGenes
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
2016
Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility: results from a large-scale collaboration
Permuth JB, Reid B, Earp M, Chen YA, Monteiro AN, Chen Z, Group A, Chenevix-Trench G, Fasching PA, Beckmann MW, Lambrechts D, Vanderstichele A, Van Niewenhuyse E, Vergote I, Rossing MA, Doherty JA, Chang-Claude J, Moysich K, Odunsi K, Goodman MT, Shvetsov YB, Wilkens LR, Thompson PJ, Dörk T, Bogdanova N, Butzow R, Nevanlinna H, Pelttari L, Leminen A, Modugno F, Edwards RP, Ness RB, Kelley J, Heitz F, Karlan B, Lester J, Kjaer SK, Jensen A, Giles G, Hildebrandt M, Liang D, Lu KH, Wu X, Levine DA, Bisogna M, Berchuck A, Cramer DW, Terry KL, Tworoger SS, Poole EM, Bandera EV, Fridley B, Cunningham J, Winham SJ, Olson SH, Orlow I, Bjorge L, Kiemeney LA, Massuger L, Pejovic T, Moffitt M, Le N, Cook LS, Brooks-Wilson A, Kelemen LE, Gronwald J, Lubinski J, Wentzensen N, Brinton LA, Lissowska J, Yang H, Hogdall E, Hogdall C, Lundvall L, Pharoah PD, Song H, Campbell I, Eccles D, McNeish I, Whittemore A, McGuire V, Sieh W, Rothstein J, Phelan CM, Risch H, Narod S, McLaughlin J, Anton-Culver H, Ziogas A, Menon U, Gayther S, Ramus SJ, Gentry-Maharaj A, Pearce CL, Wu AH, Kupryjanczyk J, Dansonka-Mieszkowska A, Schildkraut JM, Cheng JQ, Goode EL, Sellers TA. Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility: results from a large-scale collaboration. Oncotarget 2016, 5: 72381-72394. PMID: 27911851, PMCID: PMC5340123, DOI: 10.18632/oncotarget.10546.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsGene-level analysisRNA editingEOC susceptibilityADAR expressionExpression quantitative trait loci (eQTL) analysisQuantitative trait locus (QTL) analysisPost-transcriptional modificationsSequence kernel association testAdmixture maximum likelihood testInvasive EOC casesADAR genesRNA familiesLocus analysisUntranslated regionGene expressionAssociation analysisOvarian cancer susceptibilityADARGermline variationNucleotide polymorphismsTissue gene expressionMaximum likelihood testADAR3European ancestry
2015
Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC)
Jim HS, Lin HY, Tyrer JP, Lawrenson K, Dennis J, Chornokur G, Chen Z, Chen AY, Permuth-Wey J, Aben KK, Anton-Culver H, Antonenkova N, Bruinsma F, Bandera EV, Bean YT, Beckmann MW, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bunker CH, Butzow R, Campbell IG, Carty K, Chang-Claude J, Cook LS, Cramer DW, Cunningham JM, Cybulski C, Dansonka-Mieszkowska A, du Bois A, Despierre E, Sieh W, Doherty JA, Dörk T, Dürst M, Easton DF, Eccles DM, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Goodman MT, Gronwald J, Harter P, Hasmad HN, Hein A, Heitz F, Hildebrandt MA, Hillemanns P, Hogdall CK, Hogdall E, Hosono S, Iversen ES, Jakubowska A, Jensen A, Ji BT, Karlan BY, Kellar M, Kiemeney LA, Krakstad C, Kjaer SK, Kupryjanczyk J, Vierkant RA, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lim BK, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger LF, Matsuo K, McGuire V, McLaughlin JR, McNeish I, Menon U, Milne RL, Modugno F, Thomsen L, Moysich KB, Ness RB, Nevanlinna H, Eilber U, Odunsi K, Olson SH, Orlow I, Orsulic S, Palmieri Weber R, Paul J, Pearce CL, Pejovic T, Pelttari LM, Pike MC, Poole EM, Schernhammer E, Risch HA, Rosen B, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schwaab I, Shu XO, Shvetsov YB, Siddiqui N, Song H, Southey MC, Spiewankiewicz B, Sucheston-Campbell L, Teo SH, Terry KL, Thompson PJ, Tangen IL, Tworoger SS, van Altena AM, Vergote I, Walsh CS, Wang-Gohrke S, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Wu AH, Wu X, Woo YL, Yang H, Zheng W, Ziogas A, Amankwah E, Berchuck A, , Schildkraut JM, Kelemen LE, Ramus SJ, Monteiro AN, Goode EL, Narod SA, Gayther SA, Pharoah PD, Sellers TA, Phelan CM. Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC). Journal Of Genetics And Genome Research 2015, 2: 017. PMID: 26807442, PMCID: PMC4722961, DOI: 10.23937/2378-3648/1410017.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsCircadian genesGenetic variationDownstream transcription factorsCircadian gene expressionCommon genetic variationGenotyped single nucleotide polymorphismsCircadian rhythm genesOvarian surface epithelial cellsAlternative splicingTranscription factorsGene expressionFunctional analysisHormonal pathwaysOvarian Cancer Association ConsortiumRhythm genesGenesGenotype dataNucleotide polymorphismsSurface epithelial cellsEpithelial cellsEnvironmental factorsGranulosa cellsOvarian cancerEpithelial ovarian cancerNetwork-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk
Kar SP, Tyrer JP, Li Q, Lawrenson K, Aben KK, Anton-Culver H, Antonenkova N, Chenevix-Trench G, Study O, Group A, Baker H, Bandera EV, Bean YT, Beckmann MW, Berchuck A, Bisogna M, Bjørge L, Bogdanova N, Brinton L, Brooks-Wilson A, Butzow R, Campbell I, Carty K, Chang-Claude J, Chen YA, Chen Z, Cook LS, Cramer D, Cunningham JM, Cybulski C, Dansonka-Mieszkowska A, Dennis J, Dicks E, Doherty JA, Dörk T, du Bois A, Dürst M, Eccles D, Easton DF, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Goode EL, Goodman MT, Grownwald J, Harrington P, Harter P, Hein A, Heitz F, Hildebrandt MA, Hillemanns P, Hogdall E, Hogdall CK, Hosono S, Iversen ES, Jakubowska A, Paul J, Jensen A, Ji BT, Karlan BY, Kjaer SK, Kelemen LE, Kellar M, Kelley J, Kiemeney LA, Krakstad C, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger L, Matsuo K, McGuire V, McLaughlin JR, McNeish IA, Menon U, Modugno F, Moysich KB, Narod SA, Nedergaard L, Ness RB, Nevanlinna H, Odunsi K, Olson SH, Orlow I, Orsulic S, Weber RP, Pearce CL, Pejovic T, Pelttari LM, Permuth-Wey J, Phelan CM, Pike MC, Poole EM, Ramus SJ, Risch HA, Rosen B, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schildkraut JM, Schwaab I, Shu XO, Shvetsov YB, Siddiqui N, Sieh W, Song H, Southey MC, Sucheston-Campbell LE, Tangen IL, Teo SH, Terry KL, Thompson PJ, Timorek A, Tsai YY, Tworoger SS, van Altena AM, Van Nieuwenhuysen E, Vergote I, Vierkant RA, Wang-Gohrke S, Walsh C, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Woo YL, Wu X, Wu A, Yang H, Zheng W, Ziogas A, Sellers TA, Monteiro AN, Freedman ML, Gayther SA, Pharoah PD. Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk. Cancer Epidemiology Biomarkers & Prevention 2015, 24: 1574-1584. PMID: 26209509, PMCID: PMC4592449, DOI: 10.1158/1055-9965.epi-14-1270.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesTF genesGenome-wide significant risk lociAssociation studiesTranscription factor genesNetwork of genesPutative target genesSignificant risk lociGene-level testsIndependent association studiesContext-specific datasetsSerous ovarian cancer riskCancer Genome AtlasLocus functionsTarget genesFactor genesEnrichment analysisRisk lociGene expressionTop signalsGenesMicroarray datasetsNetworks AssociatedEOC tumorsGenome AtlasCommon variants at the CHEK2 gene locus and risk of epithelial ovarian cancer
Lawrenson K, Iversen ES, Tyrer J, Weber RP, Concannon P, Hazelett DJ, Li Q, Marks JR, Berchuck A, Lee JM, Aben KK, Anton-Culver H, Antonenkova N, Bandera E, Bean Y, Beckmann M, Bisogna M, Bjorge L, Bogdanova N, Brinton L, Brooks-Wilson A, Bruinsma F, Butzow R, Campbell I, Carty K, Chang-Claude J, Chenevix-Trench G, Chen A, Chen Z, Cook L, Cramer D, Cunningham J, Cybulski C, Plisiecka-Halasa J, Dennis J, Dicks E, Doherty J, Dörk T, du Bois A, Eccles D, Easton D, Edwards R, Eilber U, Ekici A, Fasching P, Fridley B, Gao Y, Gentry-Maharaj A, Giles G, Glasspool R, Goode E, Goodman M, Gronwald J, Harter P, Hasmad H, Hein A, Heitz F, Hildebrandt M, Hillemanns P, Hogdall E, Hogdall C, Hosono S, Jakubowska A, Paul J, Jensen A, Karlan B, Kjaer S, Kelemen L, Kellar M, Kelley J, Kiemeney L, Krakstad C, Lambrechts D, Lambrechts S, Le N, Lee A, Cannioto R, Leminen A, Lester J, Levine D, Liang D, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger L, Matsuo K, McGuire V, McLaughlin J, Nevanlinna H, McNeish I, Menon U, Modugno F, Moysich K, Narod S, Nedergaard L, Ness R, Azmi M, Odunsi K, Olson S, Orlow I, Orsulic S, Pearce C, Pejovic T, Pelttari L, Permuth-Wey J, Phelan C, Pike M, Poole E, Ramus S, Risch H, Rosen B, Rossing M, Rothstein J, Rudolph A, Runnebaum I, Rzepecka I, Salvesen H, Budzilowska A, Sellers T, Shu X, Shvetsov Y, Siddiqui N, Sieh W, Song H, Southey M, Sucheston L, Tangen I, Teo S, Terry K, Thompson P, Timorek A, Tworoger S, Van Nieuwenhuysen E, Vergote I, Vierkant R, Wang-Gohrke S, Walsh C, Wentzensen N, Whittemore A, Wicklund K, Wilkens L, Woo Y, Wu X, Wu A, Yang H, Zheng W, Ziogas A, Coetzee G, Freedman M, Monteiro A, Moes-Sosnowska J, Kupryjanczyk J, Pharoah P, Gayther S, Schildkraut J. Common variants at the CHEK2 gene locus and risk of epithelial ovarian cancer. Carcinogenesis 2015, 36: 1341-1353. PMID: 26424751, PMCID: PMC4635670, DOI: 10.1093/carcin/bgv138.Peer-Reviewed Original ResearchConceptsGene locusCommon variantsGenome-wide association studiesAdditional risk variantsDNA repair genesCommon genetic variantsImputation of genotypesCancer Genome Atlas (TCGA) datasetFunctional annotationGenomic regionsTranscription factorsRegulatory elementsNormal fallopian tube tissuesGenome ProjectCausal variantsPrecursor tissueGene expressionSerous epithelial ovarian cancerCandidate SNPsAssociation studiesAdditional genotypingRepair genesSusceptibility genesRisk variantsGenetic variants
2014
Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
Wang Z, Zhu B, Zhang M, Parikh H, Jia J, Chung CC, Sampson JN, Hoskins JW, Hutchinson A, Burdette L, Ibrahim A, Hautman C, Raj PS, Abnet CC, Adjei AA, Ahlbom A, Albanes D, Allen NE, Ambrosone CB, Aldrich M, Amiano P, Amos C, Andersson U, Andriole G, Andrulis IL, Arici C, Arslan AA, Austin MA, Baris D, Barkauskas DA, Bassig BA, Beane Freeman LE, Berg CD, Berndt SI, Bertazzi PA, Biritwum RB, Black A, Blot W, Boeing H, Boffetta P, Bolton K, Boutron-Ruault MC, Bracci PM, Brennan P, Brinton LA, Brotzman M, Bueno-de-Mesquita HB, Buring JE, Butler MA, Cai Q, Cancel-Tassin G, Canzian F, Cao G, Caporaso NE, Carrato A, Carreon T, Carta A, Chang GC, Chang IS, Chang-Claude J, Che X, Chen CJ, Chen CY, Chen CH, Chen C, Chen KY, Chen YM, Chokkalingam AP, Chu LW, Clavel-Chapelon F, Colditz GA, Colt JS, Conti D, Cook MB, Cortessis VK, Crawford ED, Cussenot O, Davis FG, De Vivo I, Deng X, Ding T, Dinney CP, Di Stefano AL, Diver WR, Duell EJ, Elena JW, Fan JH, Feigelson HS, Feychting M, Figueroa JD, Flanagan AM, Fraumeni JF, Freedman ND, Fridley BL, Fuchs CS, Gago-Dominguez M, Gallinger S, Gao YT, Gapstur SM, Garcia-Closas M, Garcia-Closas R, Gastier-Foster JM, Gaziano JM, Gerhard DS, Giffen CA, Giles GG, Gillanders EM, Giovannucci EL, Goggins M, Gokgoz N, Goldstein AM, Gonzalez C, Gorlick R, Greene MH, Gross M, Grossman HB, Grubb R, Gu J, Guan P, Haiman CA, Hallmans G, Hankinson SE, Harris CC, Hartge P, Hattinger C, Hayes RB, He Q, Helman L, Henderson BE, Henriksson R, Hoffman-Bolton J, Hohensee C, Holly EA, Hong YC, Hoover RN, Hosgood HD, Hsiao CF, Hsing AW, Hsiung CA, Hu N, Hu W, Hu Z, Huang MS, Hunter DJ, Inskip PD, Ito H, Jacobs EJ, Jacobs KB, Jenab M, Ji BT, Johansen C, Johansson M, Johnson A, Kaaks R, Kamat AM, Kamineni A, Karagas M, Khanna C, Khaw KT, Kim C, Kim IS, Kim JH, Kim YH, Kim YC, Kim YT, Kang CH, Jung YJ, Kitahara CM, Klein AP, Klein R, Kogevinas M, Koh WP, Kohno T, Kolonel LN, Kooperberg C, Kratz CP, Krogh V, Kunitoh H, Kurtz RC, Kurucu N, Lan Q, Lathrop M, Lau CC, Lecanda F, Lee KM, Lee MP, Le Marchand L, Lerner SP, Li D, Liao LM, Lim WY, Lin D, Lin J, Lindstrom S, Linet MS, Lissowska J, Liu J, Ljungberg B, Lloreta J, Lu D, Ma J, Malats N, Mannisto S, Marina N, Mastrangelo G, Matsuo K, McGlynn KA, McKean-Cowdin R, McNeill LH, McWilliams RR, Melin BS, Meltzer PS, Mensah JE, Miao X, Michaud DS, Mondul AM, Moore LE, Muir K, Niwa S, Olson SH, Orr N, Panico S, Park JY, Patel AV, Patino-Garcia A, Pavanello S, Peeters PH, Peplonska B, Peters U, Petersen GM, Picci P, Pike MC, Porru S, Prescott J, Pu X, Purdue MP, Qiao YL, Rajaraman P, Riboli E, Risch HA, Rodabough RJ, Rothman N, Ruder AM, Ryu JS, Sanson M, Schned A, Schumacher FR, Schwartz AG, Schwartz KL, Schwenn M, Scotlandi K, Seow A, Serra C, Serra M, Sesso HD, Severi G, Shen H, Shen M, Shete S, Shiraishi K, Shu XO, Siddiq A, Sierrasesumaga L, Sierri S, Loon Sihoe AD, Silverman DT, Simon M, Southey MC, Spector L, Spitz M, Stampfer M, Stattin P, Stern MC, Stevens VL, Stolzenberg-Solomon RZ, Stram DO, Strom SS, Su WC, Sund M, Sung SW, Swerdlow A, Tan W, Tanaka H, Tang W, Tang ZZ, Tardon A, Tay E, Taylor PR, Tettey Y, Thomas DM, Tirabosco R, Tjonneland A, Tobias GS, Toro JR, Travis RC, Trichopoulos D, Troisi R, Truelove A, Tsai YH, Tucker MA, Tumino R, Van Den Berg D, Van Den Eeden SK, Vermeulen R, Vineis P, Visvanathan K, Vogel U, Wang C, Wang C, Wang J, Wang SS, Weiderpass E, Weinstein SJ, Wentzensen N, Wheeler W, White E, Wiencke JK, Wolk A, Wolpin BM, Wong MP, Wrensch M, Wu C, Wu T, Wu X, Wu YL, Wunder JS, Xiang YB, Xu J, Yang HP, Yang PC, Yatabe Y, Ye Y, Yeboah ED, Yin Z, Ying C, Yu CJ, Yu K, Yuan JM, Zanetti KA, Zeleniuch-Jacquotte A, Zheng W, Zhou B, Mirabello L, Savage SA, Kraft P, Chanock SJ, Yeager M, Landi MT, Shi J, Chatterjee N, Amundadottir LT. Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33. Human Molecular Genetics 2014, 23: 6616-6633. PMID: 25027329, PMCID: PMC4240198, DOI: 10.1093/hmg/ddu363.Peer-Reviewed Original ResearchMeSH KeywordsAllelesChromosomes, Human, Pair 5Computational BiologyDNA MethylationEpigenesis, GeneticFemaleGene Expression Regulation, NeoplasticGene FrequencyGenetic LociGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansMaleMembrane ProteinsNeoplasm ProteinsNeoplasmsOdds RatioPolymorphism, Single NucleotideRiskTelomeraseConceptsGenome-wide association studiesIndependent risk lociRisk lociCLPTM1L geneSequential conditional analysesTERT-CLPTM1L regionAllele-specific effectsDistinct cancersCommon susceptibility allelesCancer susceptibility lociTelomerase reverse transcriptaseCommon single nucleotide polymorphismsGenetic architectureCatalytic subunitSingle nucleotide polymorphismsDNA methylationIndependent lociExtensive pleiotropyGene expressionAssociation studiesAssociation analysisSusceptibility lociDifferent cancer typesLociTERT gene
2011
Physical activity and breast cancer survival: an epigenetic link through reduced methylation of a tumor suppressor gene L3MBTL1
Zeng H, Irwin ML, Lu L, Risch H, Mayne S, Mu L, Deng Q, Scarampi L, Mitidieri M, Katsaros D, Yu H. Physical activity and breast cancer survival: an epigenetic link through reduced methylation of a tumor suppressor gene L3MBTL1. Breast Cancer Research And Treatment 2011, 133: 127-135. PMID: 21837478, DOI: 10.1007/s10549-011-1716-7.Peer-Reviewed Original ResearchMeSH KeywordsBreast NeoplasmsCarcinoma, Ductal, BreastCarcinoma, LobularChromosomal Proteins, Non-HistoneDNA MethylationEpigenesis, GeneticFemaleGene ExpressionGene Expression ProfilingGene Expression Regulation, NeoplasticGenes, Tumor SuppressorHumansKaplan-Meier EstimateMotor ActivityRepressor ProteinsTumor Suppressor ProteinsConceptsBreast cancer patientsBreast cancer survivalCancer patientsPhysical activityOverall survivalSurvival outcomesTumor suppressor geneCancer survivalHormone receptor-positive tumorsModerate-intensity aerobic exerciseHigh expressionBreast cancer deathsReceptor-positive tumorsRandomized clinical trialsExercise-related changesSuppressor genePeripheral blood leukocytesBreast cancer diagnosisGene expressionDisease recurrenceAerobic exerciseCancer deathClinical trialsTumor featuresBlood leukocytes