2021
Whole-exome Sequencing in Penile Squamous Cell Carcinoma Uncovers Novel Prognostic Categorization and Drug Targets Similar to Head and Neck Squamous Cell CarcinomaClinical Implications of WES in Penile Squamous Carcinoma
Chahoud J, Gleber-Netto FO, McCormick BZ, Rao P, Lu X, Guo M, Morgan MB, Chu RA, Martinez-Ferrer M, Eterovic AK, Pickering CR, Pettaway CA. Whole-exome Sequencing in Penile Squamous Cell Carcinoma Uncovers Novel Prognostic Categorization and Drug Targets Similar to Head and Neck Squamous Cell CarcinomaClinical Implications of WES in Penile Squamous Carcinoma. Clinical Cancer Research 2021, 27: 2560-2570. PMID: 33441293, DOI: 10.1158/1078-0432.ccr-20-4004.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorCase-Control StudiesComputational BiologyDisease ManagementDisease SusceptibilityExome SequencingHumansMaleMiddle AgedMolecular Targeted TherapyMutationNeoplasm GradingNeoplasm StagingPenile NeoplasmsPrognosisSquamous Cell Carcinoma of Head and NeckConceptsPenile squamous cell carcinomaSquamous cell carcinomaCell carcinomaHuman papilloma virus testingNeck squamous cell carcinomaNotch pathway alterationsMutation signaturesTumor mutation burdenWorse overall survivalLimited treatment optionsWhole-exome sequencing analysisPenile squamous carcinomaPotential clinical implicationsMutational signaturesDefective DNA mismatch repairCancer Genome Atlas studyWhole-exome sequencingNovel druggable targetsDistinct mutational signaturesNormal penile tissuesOverall survivalWorse survivalHigh TMBSquamous carcinomaPenile tissue
2020
The mutational landscape of early‐ and typical‐onset oral tongue squamous cell carcinoma
Campbell BR, Chen Z, Faden DL, Agrawal N, Li RJ, Hanna GJ, Iyer NG, Boot A, Rozen SG, Vettore AL, Panda B, Krishnan NM, Pickering CR, Myers JN, Guo X, Kuhs K. The mutational landscape of early‐ and typical‐onset oral tongue squamous cell carcinoma. Cancer 2020, 127: 544-553. PMID: 33146897, PMCID: PMC7891879, DOI: 10.1002/cncr.33309.Peer-Reviewed Original ResearchConceptsOral tongue squamous cell carcinomaTongue squamous cell carcinomaSquamous cell carcinomaTongue cancerYounger patientsCell carcinomaTobacco useDriver genesOral tongue cancerPatient-related factorsCancer driver genesTongue cancer specimensAge of onsetMutational landscapeSomatic mutationsMutation signaturesYounger birth cohortsSomatic mutational burdenOlder patientsCancer Genome AtlasSmoking ratesMutational burdenCancer specimensMulticenter consortiumBirth cohort
2018
The Integrated Genomic Landscape of Thymic Epithelial Tumors
Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, Leiserson MDM, Sethi G, Lu C, Ryan M, Su X, Cherniack AD, Robertson G, Akbani R, Spellman P, Weinstein JN, Hayes DN, Raphael B, Lichtenberg T, Leraas K, Zenklusen JC, Network T, Ally A, Appelbaum E, Auman J, Balasundaram M, Balu S, Behera M, Beroukhim R, Berrios M, Blandino G, Bodenheimer T, Bootwalla M, Bowen J, Brooks D, Carcano F, Carlsen R, Carvalho A, Castro P, Chalabreysse L, Chin L, Cho J, Choe G, Chuah E, Chudamani S, Cibulskis C, Cope L, Cordes M, Crain D, Curley E, Defreitas T, Demchok J, Detterbeck F, Dhalla N, Dienemann H, Edenfield W, Facciolo F, Ferguson M, Frazer S, Fronick C, Fulton L, Fulton R, Gabriel S, Gardner J, Gastier-Foster J, Gehlenborg N, Gerken M, Getz G, Heiman D, Hobensack S, Holbrook A, Holt R, Hoyle A, Hutter C, Ittmann M, Jefferys S, Jones C, Jones S, Kasaian K, Kim J, Kimes P, Lai P, Laird P, Lawrence M, Lin P, Liu J, Lolla L, Lu Y, Ma Y, Maglinte D, Mallery D, Mardis E, Marra M, Martin J, Mayo M, Meier S, Meister M, Meng S, Meyerson M, Mieczkowski P, Miller C, Mills G, Moore R, Morris S, Mose L, Muley T, Mungall A, Mungall K, Naresh R, Newton Y, Noble M, Owonikoko T, Parker J, Paulaskis J, Penny R, Perou C, Perrin C, Pihl T, Radenbaugh A, Ramalingam S, Ramirez N, Rieker R, Roach J, Sadeghi S, Saksena G, Schein J, Schmidt H, Schumacher S, Shelton C, Shelton T, Shi Y, Shih J, Sica G, Silveira H, Simons J, Sipahimalani P, Skelly T, Sofia H, Soloway M, Stuart J, Sun Q, Tam A, Tan D, Tarnuzzer R, Thiessen N, Van Den Berg D, Vasef M, Veluvolu U, Voet D, Walter V, Wan Y, Wang Z, Warth A, Weis C, Weisenberger D, Wilkerson M, Wise L, Wong T, Wu H, Wu Y, Yang L, Zhang J, Zmuda E, Fujimoto J, Scapulatempo-Neto C, Moreira A, Hwang D, Huang J, Marino M, Korst R, Giaccone G, Gokmen-Polar Y, Badve S, Rajan A, Ströbel P, Girard N, Tsao M, Marx A, Tsao A, Loehrer P. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell 2018, 33: 244-258.e10. PMID: 29438696, PMCID: PMC5994906, DOI: 10.1016/j.ccell.2018.01.003.Peer-Reviewed Original ResearchConceptsThymic epithelial tumorsEpithelial tumorsWorld Health Organization (WHO) histological subtypeAutoimmune disease myasthenia gravisDisease myasthenia gravisMuscle autoantigensThymic carcinomaMyasthenia gravisAutoimmune diseasesHistological subtypesAdult malignanciesTumoral overexpressionMarked prevalenceTumorsThymomaSubtypesEnrichment of mutationsGenomic landscapeBiological effectsGenomic hallmarksMolecular linkUnique associationAssociationMulti-platform analysisGravis
2017
Comprehensive Genomic Profiling of Metastatic Squamous Cell Carcinoma of the Anal Canal
Morris V, Rao X, Pickering C, Foo WC, Rashid A, Eterovic K, Kim T, Chen K, Wang J, Shaw K, Eng C. Comprehensive Genomic Profiling of Metastatic Squamous Cell Carcinoma of the Anal Canal. Molecular Cancer Research 2017, 15: 1542-1550. PMID: 28784613, PMCID: PMC5991496, DOI: 10.1158/1541-7786.mcr-17-0060.Peer-Reviewed Original ResearchMeSH KeywordsAgedAged, 80 and overAnimalsAnus NeoplasmsCarcinoma, Squamous CellClass I Phosphatidylinositol 3-KinasesDNA-Binding ProteinsExome SequencingFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMiceMiddle AgedMutationNeoplasm MetastasisNeoplasm ProteinsNeoplasm TransplantationPapillomavirus InfectionsPatient-Specific ModelingTumor Suppressor Protein p53ConceptsMetastatic SCCAHuman papillomavirusMutation burdenPatient-derived xenograft modelsAvailable frozen tissueDistinct tumor subpopulationsAnti-EGFR treatmentTumor mutation burdenRare gastrointestinal malignancySquamous cell carcinomaNovel therapeutic approachesComprehensive molecular profilingLow mutation burdenComprehensive genomic characterizationMajority of casesWhole-exome sequencingGene mutation frequencyGastrointestinal malignanciesAdditional patientsAnal canalAnnual incidenceValidation cohortCell carcinomaStandard treatmentPrior infectionPrevalence of promoter mutations in the TERT gene in oral cavity squamous cell carcinoma
Chang K, Wang C, Pickering CR, Huang Y, Tsai C, Tsang N, Kao H, Cheng M, Myers JN. Prevalence of promoter mutations in the TERT gene in oral cavity squamous cell carcinoma. Head & Neck 2017, 39: 1131-1137. PMID: 28230921, DOI: 10.1002/hed.24728.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overCarcinoma, Squamous CellCohort StudiesDisease ProgressionDisease-Free SurvivalFemaleGene Expression Regulation, NeoplasticHumansKaplan-Meier EstimateMaleMiddle AgedMouth NeoplasmsMutationPrevalencePromoter Regions, GeneticReal-Time Polymerase Chain ReactionRetrospective StudiesRisk AssessmentStatistics, NonparametricSurvival AnalysisTaiwanTelomeraseConceptsOral cavity squamous cell carcinomaSquamous cell carcinomaTERT promoter mutationsAdjacent normal tissuesPromoter mutationsSomatic TERT promoter mutationsNormal tissuesC228T mutationTelomerase reverse transcriptase (TERT) promoterT mutationSCC tumor tissuesHuman telomerase reverse transcriptase (hTERT) promoterC250T mutationsReverse transcriptase promoterCell carcinomaSCC tumorsC228TTumor tissueTERT activityBetel nutTERT promoterTissuePresent studyMutationsSanger method
2013
CT Imaging Correlates of Genomic Expression for Oral Cavity Squamous Cell Carcinoma
Pickering CR, Shah K, Ahmed S, Rao A, Frederick MJ, Zhang J, Unruh AK, Wang J, Ginsberg LE, Kumar AJ, Myers JN, Hamilton JD. CT Imaging Correlates of Genomic Expression for Oral Cavity Squamous Cell Carcinoma. American Journal Of Neuroradiology 2013, 34: 1818-1822. PMID: 23764725, PMCID: PMC7965627, DOI: 10.3174/ajnr.a3635.Peer-Reviewed Original ResearchConceptsOral cavity squamous cell carcinomaSquamous cell carcinomaEpidermal growth factor receptorGrowth factor receptorCell carcinomaGenomic biomarkersFactor receptorPrimary tumorImaging correlatesUntreated oral cavity squamous cell carcinomaRelevant genomic biomarkersVascular endothelial growth factor receptor 1Vascular endothelial growth factor receptorPrimary tumor sizeEndothelial growth factor receptorGrowth factor receptor 1Mass effectPreoperative CT imagingFactor receptor 1Untreated patientsAngiogenesis-related genesCT findingsPerineural invasionTumor sizePredictive biomarkers