2015
Mechanisms for the Generation of Two Quadruplications Associated with Split‐Hand Malformation
Gu S, Posey JE, Yuan B, Carvalho CM, Luk HM, Erikson K, Lo IF, Leung GK, Pickering CR, Chung BH, Lupski JR. Mechanisms for the Generation of Two Quadruplications Associated with Split‐Hand Malformation. Human Mutation 2015, 37: 160-164. PMID: 26549411, PMCID: PMC4718869, DOI: 10.1002/humu.22929.Peer-Reviewed Original ResearchMeSH Keywords14-3-3 ProteinsAdultAgedAlu ElementsBase SequenceBasic Helix-Loop-Helix Transcription FactorsChromosome DuplicationChromosomes, Human, Pair 17DNA Copy Number VariationsFemaleGenetic LociGenome, HumanHand Deformities, CongenitalHumansInfantMaleMolecular Sequence DataPedigreeSequence AlignmentSequence Analysis, DNAComprehensive genomic characterization of head and neck squamous cell carcinomas
Lawrence M, Sougnez C, Lichtenstein L, Cibulskis K, Lander E, Gabriel S, Getz G, Ally A, Balasundaram M, Birol I, Bowlby R, Brooks D, Butterfield Y, Carlsen R, Cheng D, Chu A, Dhalla N, Guin R, Holt R, Jones S, Lee D, Li H, Marra M, Mayo M, Moore R, Mungall A, Gordon Robertson A, Schein J, Sipahimalani P, Tam A, Thiessen N, Wong T, Protopopov A, Santoso N, Lee S, Parfenov M, Zhang J, Mahadeshwar H, Tang J, Ren X, Seth S, Haseley P, Zeng D, Yang L, Xu A, Song X, Pantazi A, Bristow C, Hadjipanayis A, Seidman J, Chin L, Park P, Kucherlapati R, Akbani R, Casasent T, Liu W, Lu Y, Mills G, Motter T, Weinstein J, Diao L, Wang J, Hong Fan Y, Liu J, Wang K, Todd Auman J, Balu S, Bodenheimer T, Buda E, Neil Hayes D, Hoadley K, Hoyle A, Jefferys S, Jones C, Kimes P, Liu Y, Marron J, Meng S, Mieczkowski P, Mose L, Parker J, Perou C, Prins J, Roach J, Shi Y, Simons J, Singh D, Soloway M, Tan D, Veluvolu U, Walter V, Waring S, Wilkerson M, Wu J, Zhao N, Cherniack A, Hammerman P, Tward A, Sekhar Pedamallu C, Saksena G, Jung J, Ojesina A, Carter S, Zack T, Schumacher S, Beroukhim R, Freeman S, Meyerson M, Cho J, Chin L, Getz G, Noble M, DiCara D, Zhang H, Heiman D, Gehlenborg N, Voet D, Lin P, Frazer S, Stojanov P, Liu Y, Zou L, Kim J, Sougnez C, Gabriel S, Lawrence M, Muzny D, Doddapaneni H, Kovar C, Reid J, Morton D, Han Y, Hale W, Chao H, Chang K, Drummond J, Gibbs R, Kakkar N, Wheeler D, Xi L, Ciriello G, Ladanyi M, Lee W, Ramirez R, Sander C, Shen R, Sinha R, Weinhold N, Taylor B, Arman Aksoy B, Dresdner G, Gao J, Gross B, Jacobsen A, Reva B, Schultz N, Onur Sumer S, Sun Y, Chan T, Morris L, Stuart J, Benz S, Ng S, Benz C, Yau C, Baylin S, Cope L, Danilova L, Herman J, Bootwalla M, Maglinte D, Laird P, Triche T, Weisenberger D, Van Den Berg D, Agrawal N, Bishop J, Boutros P, Bruce J, Averett Byers L, Califano J, Carey T, Chen Z, Cheng H, Chiosea S, Cohen E, Diergaarde B, Marie Egloff A, El-Naggar A, Ferris R, Frederick M, Grandis J, Guo Y, Haddad R, Hammerman P, Harris T, Neil Hayes D, Hui A, Jack Lee J, Lippman S, Liu F, McHugh J, Myers J, Kwok Shing Ng P, Perez-Ordonez B, Pickering C, Prystowsky M, Romkes M, Saleh A, Sartor M, Seethala R, Seiwert T, Si H, Tward A, Van Waes C, Waggott D, Wiznerowicz M, Yarbrough W, Zhang J, Zuo Z, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton C, Shelton T, Sherman M, Yena P, Black A, Bowen J, Frick J, Gastier-Foster J, Harper H, Leraas K, Lichtenberg T, Ramirez N, Wise L, Zmuda E, Baboud J, Jensen M, Kahn A, Pihl T, Pot D, Srinivasan D, Walton J, Wan Y, Burton R, Davidsen T, Demchok J, Eley G, Ferguson M, Mills Shaw K, Ozenberger B, Sheth M, Sofia H, Tarnuzzer R, Wang Z, Yang L, Claude Zenklusen J, Saller C, Tarvin K, Chen C, Bollag R, Weinberger P, Golusiński W, Golusiński P, Ibbs M, Korski K, Mackiewicz A, Suchorska W, Szybiak B, Wiznerowicz M, Burnett K, Curley E, Gardner J, Mallery D, Penny R, Shelton T, Yena P, Beard C, Mitchell C, Sandusky G, Agrawal N, Ahn J, Bishop J, Califano J, Khan Z, Bruce J, Hui A, Irish J, Liu F, Perez-Ordonez B, Waldron J, Boutros P, Waggott D, Myers J, William W, Lippman S, Egea S, Gomez-Fernandez C, Herbert L, Bradford C, Carey T, Chepeha D, Haddad A, Jones T, Komarck C, Malakh M, McHugh J, Moyer J, Nguyen A, Peterson L, Prince M, Rozek L, Sartor M, Taylor E, Walline H, Wolf G, Boice L, Chera B, Funkhouser W, Gulley M, Hackman T, Neil Hayes D, Hayward M, Huang M, Kimryn Rathmell W, Salazar A, Shockley W, Shores C, Thorne L, Weissler M, Wrenn S, Zanation A, Chiosea S, Diergaarde B, Marie Egloff A, Ferris R, Romkes M, Seethala R, Brown B, Guo Y, Pham M, Yarbrough W. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 2015, 517: 576-582. PMID: 25631445, PMCID: PMC4311405, DOI: 10.1038/nature14129.Peer-Reviewed Original ResearchMeSH KeywordsCarcinoma, Squamous CellDNA Copy Number VariationsDNA, NeoplasmFemaleGene Expression Regulation, NeoplasticGenome, HumanGenomicsHead and Neck NeoplasmsHumansMaleMolecular Targeted TherapyMutationOncogenesRNA, NeoplasmSignal TransductionSquamous Cell Carcinoma of Head and NeckTranscription FactorsConceptsNeck squamous cell carcinomaSquamous cell carcinomaCell carcinomaCopy number alterationsMutations of HRASFavorable clinical outcomeFrequent copy number alterationsComprehensive genomic characterizationNumber alterationsFunction TP53 mutationsCancer Genome AtlasSomatic genomic alterationsClinical outcomesLaryngeal tumorsOral cavityFunction alterationsTP53 mutationsCandidate alterationsOncogene PIK3CALoss of TRAF3Novel alterationsCDKN2A inactivationGenome AtlasGenomic alterationsDomain mutations
2014
Mutational Landscape of Aggressive Cutaneous Squamous Cell Carcinoma
Pickering CR, Zhou JH, Lee JJ, Drummond JA, Peng SA, Saade RE, Tsai KY, Curry JL, Tetzlaff MT, Lai SY, Yu J, Muzny DM, Doddapaneni H, Shinbrot E, Covington KR, Zhang J, Seth S, Caulin C, Clayman GL, El-Naggar AK, Gibbs RA, Weber RS, Myers JN, Wheeler DA, Frederick MJ. Mutational Landscape of Aggressive Cutaneous Squamous Cell Carcinoma. Clinical Cancer Research 2014, 20: 6582-6592. PMID: 25303977, PMCID: PMC4367811, DOI: 10.1158/1078-0432.ccr-14-1768.Peer-Reviewed Original ResearchConceptsAggressive cutaneous squamous cell carcinomaCutaneous squamous cell carcinomaSquamous cell carcinomaCell carcinomaCandidate tumor suppressorNeck squamous cell carcinomaNovel therapeutic targetNovel candidate tumor suppressorTumor suppressorWhole-exome sequencingBone invasionPoor outcomeTherapeutic targetLethal diseaseTumor suppressor geneCarcinomaKMT2C mutationsHigh mutational backgroundGene TP53Mutational landscapePutative linkDriver genesDiseaseMutational spectrumUV exposureSquamous Cell Carcinoma of the Oral Tongue in Young Non-Smokers Is Genomically Similar to Tumors in Older Smokers
Pickering CR, Zhang J, Neskey DM, Zhao M, Jasser SA, Wang J, Ward A, Tsai CJ, Alves M, Zhou JH, Drummond J, El-Naggar AK, Gibbs R, Weinstein JN, Wheeler DA, Wang J, Frederick MJ, Myers JN. Squamous Cell Carcinoma of the Oral Tongue in Young Non-Smokers Is Genomically Similar to Tumors in Older Smokers. Clinical Cancer Research 2014, 20: 3842-3848. PMID: 24874835, PMCID: PMC4102633, DOI: 10.1158/1078-0432.ccr-14-0565.Peer-Reviewed Original ResearchMeSH KeywordsAdultAge FactorsCarcinoma, Squamous CellDNA Copy Number VariationsDNA Mutational AnalysisFemaleHumansMaleMiddle AgedMutationPrognosisSmokingTongue NeoplasmsConceptsSquamous cell carcinomaOlder patientsOral tongueYounger patientsCell carcinomaWhole-exome sequencingOlder smokersSimilar patientsTongue tumorsNon smokersIncreasing incidenceEpidemiologic studiesIndependent cohortPatientsSCCOTSmokingTumorsCohortAlteration frequencyGenomic effectsTCGA dataCopy number analysisGene-specific mutationsOlder cohortTypes of mutations
2013
Integrative Genomic Characterization of Oral Squamous Cell Carcinoma Identifies Frequent Somatic Drivers
Pickering CR, Zhang J, Yoo SY, Bengtsson L, Moorthy S, Neskey DM, Zhao M, Alves M, Chang K, Drummond J, Cortez E, Xie TX, Zhang D, Chung W, Issa JP, Zweidler-McKay PA, Wu X, El-Naggar AK, Weinstein JN, Wang J, Muzny DM, Gibbs RA, Wheeler DA, Myers JN, Frederick MJ. Integrative Genomic Characterization of Oral Squamous Cell Carcinoma Identifies Frequent Somatic Drivers. Cancer Discovery 2013, 3: 770-781. PMID: 23619168, PMCID: PMC3858325, DOI: 10.1158/2159-8290.cd-12-0537.Peer-Reviewed Original ResearchConceptsOral squamous cell carcinomaCaspase-8Integrative Genomic CharacterizationGenomic alterationsSquamous cell carcinomaComprehensive genomic analysisTumor suppressor geneCopy number changesSomatic driversKey genesGenomic analysisCell carcinomaGene expressionNotch pathwayGenomic characterizationSuppressor geneDriver pathwaysCopy numberPoint mutationsGenesSomatic eventsNumber changesSurvival of patientsOSCC cell linesSubset of head