2024
Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions
Dareng E, Coetzee S, Tyrer J, Peng P, Rosenow W, Chen S, Davis B, Dezem F, Seo J, Nameki R, Reyes A, Aben K, Anton-Culver H, Antonenkova N, Aravantinos G, Bandera E, Freeman L, Beckmann M, Beeghly-Fadiel A, Benitez J, Bernardini M, Bjorge L, Black A, Bogdanova N, Bolton K, Brenton J, Budzilowska A, Butzow R, Cai H, Campbell I, Cannioto R, Chang-Claude J, Chanock S, Chen K, Chenevix-Trench G, Group A, Chiew Y, Cook L, DeFazio A, Dennis J, Doherty J, Dörk T, du Bois A, Dürst M, Eccles D, Ene G, Fasching P, Flanagan J, Fortner R, Fostira F, Gentry-Maharaj A, Giles G, Goodman M, Gronwald J, Haiman C, Håkansson N, Heitz F, Hildebrandt M, Høgdall E, Høgdall C, Huang R, Jensen A, Jones M, Kang D, Karlan B, Karnezis A, Kelemen L, Kennedy C, Khusnutdinova E, Kiemeney L, Kjaer S, Kupryjanczyk J, Labrie M, Lambrechts D, Larson M, Le N, Lester J, Li L, Lubiński J, Lush M, Marks J, Matsuo K, May T, McLaughlin J, McNeish I, Menon U, Missmer S, Modugno F, Moffitt M, Monteiro A, Moysich K, Narod S, Nguyen-Dumont T, Odunsi K, Olsson H, Onland-Moret N, Park S, Pejovic T, Permuth J, Piskorz A, Prokofyeva D, Riggan M, Risch H, Rodríguez-Antona C, Rossing M, Sandler D, Setiawan V, Shan K, Song H, Southey M, Steed H, Sutphen R, Swerdlow A, Teo S, Terry K, Thompson P, Thomsen L, Titus L, Trabert B, Travis R, Tworoger S, Valen E, Van Nieuwenhuysen E, Edwards D, Vierkant R, Webb P, Group O, Weinberg C, Weise R, Wentzensen N, White E, Winham S, Wolk A, Woo Y, Wu A, Yan L, Yannoukakos D, Zeinomar N, Zheng W, Ziogas A, Berchuck A, Goode E, Huntsman D, Pearce C, Ramus S, Sellers T, Consortium T, Freedman M, Lawrenson K, Schildkraut J, Hazelett D, Plummer J, Kar S, Jones M, Pharoah P, Gayther S. Integrative multi-omics analyses to identify the genetic and functional mechanisms underlying ovarian cancer risk regions. American Journal Of Human Genetics 2024, 111: 1061-1083. PMID: 38723632, PMCID: PMC11179261, DOI: 10.1016/j.ajhg.2024.04.011.Peer-Reviewed Original ResearchTranscriptome-wide association studyRisk lociAssociation studiesTranscription factor ChIP-seqSusceptibility genesGenome-wide association analysisGenome-wide association studiesCausal risk variantsControls of European originTranscriptome-wide associationEpithelial ovarian cancerVariant Effect PredictorIntegrative multi-omics analysisMulti-omics analysisChIP-seqChromatin marksGenomic regionsFine-mappingSusceptibility lociInteractome analysisAssociation analysisEpithelial ovarian cancer histotypesRisk variantsTissue-specificLoci
2020
Fine-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
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
MiRNA-Related SNPs and Risk of Esophageal Adenocarcinoma and Barrett’s Esophagus: Post Genome-Wide Association Analysis in the BEACON Consortium
Buas MF, Onstad L, Levine DM, Risch HA, Chow WH, Liu G, Fitzgerald RC, Bernstein L, Ye W, Bird NC, Romero Y, Casson AG, Corley DA, Shaheen NJ, Wu AH, Gammon MD, Reid BJ, Hardie LJ, Peters U, Whiteman DC, Vaughan TL. MiRNA-Related SNPs and Risk of Esophageal Adenocarcinoma and Barrett’s Esophagus: Post Genome-Wide Association Analysis in the BEACON Consortium. PLOS ONE 2015, 10: e0128617. PMID: 26039359, PMCID: PMC4454432, DOI: 10.1371/journal.pone.0128617.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaAgedBarrett EsophagusCase-Control StudiesEsophageal NeoplasmsEsophagusFemaleGastroesophageal RefluxGene Expression RegulationGenetic LociGenome-Wide Association StudyHumansMaleMicroRNAsMiddle AgedObesityPolymorphism, Single NucleotideRisk FactorsSex FactorsSmokingWhite PeopleConceptsGenome-wide association studiesSingle nucleotide polymorphismsPost-transcriptional gene regulationGenome-wide association analysisMiRNA-related single nucleotide polymorphismsMiRNA gene lociSmall non-coding RNAsClasses of genesMiRNA-targeted mRNAsMiRNA biogenesis genesGenetic variantsNon-coding RNAsCommon genetic variantsGermline genetic variantsMiRNA genesBiogenesis genesGene regulationCore pathwaysGene locusAssociation studiesAssociation analysisGenesNucleotide polymorphismsNominal associationEuropean ancestry
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