2024
Detection of hepatocellular carcinoma methylation markers in salivary DNA
Mezzacappa C, Wang Z, Lu L, Risch H, Taddei T, Yu H. Detection of hepatocellular carcinoma methylation markers in salivary DNA. Bioscience Reports 2024, 44: bsr20232063. PMID: 38457142, PMCID: PMC10958141, DOI: 10.1042/bsr20232063.Peer-Reviewed Original ResearchHepatocellular carcinoma screeningCase patientsHepatocellular carcinomaControl subjectsDiagnosis of hepatocellular carcinomaAssociated with hepatocellular carcinomaScreening testSalivary DNASaliva-based testCpG sitesStudy of risk factorsSalivary DNA methylationDNA methylationViral hepatitisCirculating DNAAlterations to DNA methylationRisk factorsMethylation markersPatientsRegulation of cell cycle progressionBlood samplesCell cycle progressionAffected individualsAlternative to blood samplingMultiple comparisons
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
2013
Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer
Shen H, Fridley BL, Song H, Lawrenson K, Cunningham JM, Ramus SJ, Cicek MS, Tyrer J, Stram D, Larson MC, Köbel M, Ziogas A, Zheng W, Yang H, Wu A, Wozniak E, Ling Woo Y, Winterhoff B, Wik E, Whittemore A, Wentzensen N, Palmieri Weber R, Vitonis A, Vincent D, Vierkant R, Vergote I, Van Den Berg D, Van Altena A, Tworoger S, Thompson P, Tessier D, Terry K, Teo S, Templeman C, Stram D, Southey M, Sieh W, Siddiqui N, Shvetsov Y, Shu X, Shridhar V, Wang-Gohrke S, Severi G, Schwaab I, Salvesen H, Rzepecka I, Runnebaum I, Anne Rossing M, Rodriguez-Rodriguez L, Risch H, Renner S, Poole E, Pike M, Phelan C, Pelttari L, Pejovic T, Paul J, Orlow I, Zawiah Omar S, Olson S, Odunsi K, Nickels S, Nevanlinna H, Ness R, Narod S, Nakanishi T, Moysich K, Monteiro A, Moes-Sosnowska J, Modugno F, Menon U, McLaughlin J, McGuire V, Matsuo K, Mat Adenan N, Massuger L, Lurie G, Lundvall L, Lubiński J, Lissowska J, Levine D, Leminen A, Lee A, Le N, Lambrechts S, Lambrechts D, Kupryjanczyk J, Krakstad C, Konecny G, Krüger Kjaer S, Kiemeney L, Kelemen L, Keeney G, Karlan B, Karevan R, Kalli K, Kajiyama H, Ji B, Jensen A, Jakubowska A, Iversen E, Hosono S, Høgdall C, Høgdall E, Hoatlin M, Hillemanns P, Heitz F, Hein R, Harter P, Halle M, Hall P, Gronwald J, Gore M, Goodman M, Giles G, Gentry-Maharaj A, Garcia-Closas M, Flanagan J, Fasching P, Ekici A, Edwards R, Eccles D, Easton D, Dürst M, du Bois A, Dörk T, Doherty J, Despierre E, Dansonka-Mieszkowska A, Cybulski C, Cramer D, Cook L, Chen X, Charbonneau B, Chang-Claude J, Campbell I, Butzow R, Bunker C, Brueggmann D, Brown R, Brooks-Wilson A, Brinton L, Bogdanova N, Block M, Benjamin E, Beesley J, Beckmann M, Bandera E, Baglietto L, Bacot F, Armasu S, Antonenkova N, Anton-Culver H, Aben K, Liang D, Wu X, Lu K, Hildebrandt M, Schildkraut J, Sellers T, Huntsman D, Berchuck A, Chenevix-Trench G, Gayther S, Pharoah P, Laird P, Goode E, Leigh Pearce C. Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer. Nature Communications 2013, 4: 1628. PMID: 23535649, PMCID: PMC3848248, DOI: 10.1038/ncomms2629.Peer-Reviewed Original ResearchConceptsDNA methylationAnalyse DNA methylationClear cell epithelial ovarian cancerSingle nucleotide polymorphismsEpigenetic analysisExpression patternsExpression profilesDifferent single nucleotide polymorphismsCpG island methylator phenotypeSusceptibility genesMethylationDistinct mechanismsGenesMethylator phenotypeHNF1BOvarian cancerRisk allelesSerous epithelial ovarian cancerEpithelial ovarian cancerAssociatesEpithelial ovarian cancer riskGenomePromoterPhenotypeAlleles
2012
Association of large noncoding RNA HOTAIR expression and its downstream intergenic CpG island methylation with survival in breast cancer
Lu L, Zhu G, Zhang C, Deng Q, Katsaros D, Mayne ST, Risch HA, Mu L, Canuto EM, Gregori G, Benedetto C, Yu H. Association of large noncoding RNA HOTAIR expression and its downstream intergenic CpG island methylation with survival in breast cancer. Breast Cancer Research And Treatment 2012, 136: 875-883. PMID: 23124417, DOI: 10.1007/s10549-012-2314-z.Peer-Reviewed Original ResearchConceptsPrimary breast cancerBreast cancerHOTAIR expressionPathologic featuresCox proportional hazards regression modelProportional hazards regression modelsLow HOTAIR expressionUnfavorable disease characteristicsHazards regression modelsIndependent prognostic markerHigh HOTAIR expressionBreast cancer progressionQuantitative RT-PCRPatient survivalDisease characteristicsMethylation-specific PCRPrognostic markerLower riskSignificant associationRNA HOTAIRCancerCancer progressionBiologic relevanceRT-PCRDNA methylation