2021
Automated digital TIL analysis (ADTA) adds prognostic value to standard assessment of depth and ulceration in primary melanoma
Moore MR, Friesner ID, Rizk EM, Fullerton BT, Mondal M, Trager MH, Mendelson K, Chikeka I, Kurc T, Gupta R, Rohr BR, Robinson EJ, Acs B, Chang R, Kluger H, Taback B, Geskin LJ, Horst B, Gardner K, Niedt G, Celebi JT, Gartrell-Corrado RD, Messina J, Ferringer T, Rimm DL, Saltz J, Wang J, Vanguri R, Saenger YM. Automated digital TIL analysis (ADTA) adds prognostic value to standard assessment of depth and ulceration in primary melanoma. Scientific Reports 2021, 11: 2809. PMID: 33531581, PMCID: PMC7854647, DOI: 10.1038/s41598-021-82305-1.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiopsyChemotherapy, AdjuvantClinical Decision-MakingDeep LearningFemaleFollow-Up StudiesHumansImage Processing, Computer-AssistedKaplan-Meier EstimateLymphocytes, Tumor-InfiltratingMaleMelanomaMiddle AgedNeoplasm StagingPatient SelectionPrognosisRetrospective StudiesRisk AssessmentROC CurveSkinSkin NeoplasmsYoung AdultConceptsTumor-infiltrating lymphocytesDisease-specific survivalEarly-stage melanomaOpen-source deep learningCutoff valueMultivariable Cox proportional hazards analysisCox proportional hazards analysisDeep learningLow-risk patientsProportional hazards analysisKaplan-Meier analysisAccurate prognostic biomarkersEosin imagesAccuracy of predictionAdjuvant therapyRisk patientsSpecific survivalPrognostic valueValidation cohortReceiver operating curvesTraining cohortTIL analysisClinical trialsPrimary melanomaPrognostic biomarker
2019
Deep Learning Based on Standard H&E Images of Primary Melanoma Tumors Identifies Patients at Risk for Visceral Recurrence and Death
Kulkarni PM, Robinson EJ, Pradhan J, Gartrell-Corrado RD, Rohr BR, Trager MH, Geskin LJ, Kluger HM, Wong PF, Acs B, Rizk EM, Yang C, Mondal M, Moore MR, Osman I, Phelps R, Horst BA, Chen ZS, Ferringer T, Rimm DL, Wang J, Saenger YM. Deep Learning Based on Standard H&E Images of Primary Melanoma Tumors Identifies Patients at Risk for Visceral Recurrence and Death. Clinical Cancer Research 2019, 26: 1126-1134. PMID: 31636101, PMCID: PMC8142811, DOI: 10.1158/1078-0432.ccr-19-1495.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAlgorithmsArea Under CurveBiopsyDeep LearningDisease ProgressionFemaleFollow-Up StudiesHumansImage Processing, Computer-AssistedMaleMelanomaMiddle AgedNeoplasm Recurrence, LocalNeural Networks, ComputerRetrospective StudiesRisk FactorsStaining and LabelingSurvival RateYoung AdultConceptsDeep neural network architectureNeural network architectureDeep learningNetwork architectureComputational modelImage sequencesDigital imagesVote aggregationDisease-specific survivalDSS predictionPractical advancesComputational methodsIHC-based methodsImagesGeisinger Health SystemNovel methodGHS patientsArchitectureLearningKaplan-Meier analysisPrimary melanoma tumorsEarly-stage melanomaClinical trial designModelAdjuvant immunotherapyPhenotyping tumor infiltrating lymphocytes (PhenoTIL) on H&E tissue images: predicting recurrence in lung cancer
Barrera C, Corredor G, Wang X, Schalper K, Rimm D, Velcheti V, Madabhushi A, Castro E. Phenotyping tumor infiltrating lymphocytes (PhenoTIL) on H&E tissue images: predicting recurrence in lung cancer. Progress In Biomedical Optics And Imaging 2019, 10956: 1095607-1095607-8. DOI: 10.1117/12.2513048.Peer-Reviewed Original ResearchTumor-infiltrating lymphocytesTIL densityLung cancerEarly stage non-small cell lung cancer patientsNon-small cell lung cancer patientsCell lung cancer patientsEarly-stage lung cancerKaplan-Meier analysisLung cancer patientsStage lung cancerLikelihood of recurrenceBetter prognosisLate recurrenceCancer patientsDifferent cancer typesDisease outcomeRecurrenceDifferent subtypesCancer typesLymphocytesCancerPatientsPrognosisIndependent validation
2014
Markers of Epithelial to Mesenchymal Transition in Association with Survival in Head and Neck Squamous Cell Carcinoma (HNSCC)
Pectasides E, Rampias T, Sasaki C, Perisanidis C, Kouloulias V, Burtness B, Zaramboukas T, Rimm D, Fountzilas G, Psyrri A. Markers of Epithelial to Mesenchymal Transition in Association with Survival in Head and Neck Squamous Cell Carcinoma (HNSCC). PLOS ONE 2014, 9: e94273. PMID: 24722213, PMCID: PMC3983114, DOI: 10.1371/journal.pone.0094273.Peer-Reviewed Original ResearchMeSH KeywordsAutomationBiomarkers, TumorCarcinoma, Squamous CellCohort StudiesEpithelial-Mesenchymal TransitionFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHead and Neck NeoplasmsHumansImage Processing, Computer-AssistedImmunohistochemistryKaplan-Meier EstimateMaleMultivariate AnalysisNeoplasm MetastasisPhenotypePrognosisProportional Hazards ModelsSquamous Cell Carcinoma of Head and NeckTreatment OutcomeConceptsProgression-free survivalSquamous cell carcinomaOverall survivalCell carcinomaE-cadherinPrimary squamous cell carcinomaNeck squamous cell carcinomaHigh-risk HNSCCKaplan-Meier analysisNovel therapeutic approachesMesenchymal transition phenotypeHigh metastatic potentialLow E-cadherinImproved OSInferior OSIndependent predictorsPoor prognosisCarcinoma prognosisClinicopathological parametersInclusion criteriaTherapeutic approachesTransition phenotypeMetastatic potentialMesenchymal transitionProtein expression analysis
2012
In situ quantitative measurement of mRNA to predict response to trastuzumab in a cohort of metastatic breast cancer patients.
Vassilakopoulou M, Bordeaux J, Neumeister V, Cheng H, Schalper K, Skarlos D, Pectasides D, Pavlidis N, Koutras A, Linardou H, Razis E, Bobos M, Kotoula V, Rimm D, Fountzilas G, Psyrri A. In situ quantitative measurement of mRNA to predict response to trastuzumab in a cohort of metastatic breast cancer patients. Journal Of Clinical Oncology 2012, 30: 573-573. DOI: 10.1200/jco.2012.30.15_suppl.573.Peer-Reviewed Original ResearchBreast cancer patientsMetastatic breast cancer patientsCancer patientsHER2 mRNA levelsHER2 mRNAHistological gradeTrastuzumab-treated metastatic breast cancer patientsMultivariate analysisCox proportional hazards modelHormone receptor statusMetastatic breast cancerKaplan-Meier analysisOverall survival timeMRNA levelsProportional hazards modelHER2 extracellular domainAssessment of HER2Extracellular domainTrastuzumab initiationChemotherapy regimensPrimary endpointReceptor statusTrastuzumab therapyMetastatic cohortTrastuzumab treatmentEvaluation of the pattern of SOX2 expression in non-small cell lung cancer (NSCLC) and correlation with clinicopathologic (CP) features and prognosis.
Velcheti V, Cheng H, Yao X, Deng Y, Gettinger S, Rimm D. Evaluation of the pattern of SOX2 expression in non-small cell lung cancer (NSCLC) and correlation with clinicopathologic (CP) features and prognosis. Journal Of Clinical Oncology 2012, 30: e21106-e21106. DOI: 10.1200/jco.2012.30.15_suppl.e21106.Peer-Reviewed Original ResearchNon-small cell lung cancerSquamous cell carcinomaSOX2 expressionWorse median overall survivalYale-New Haven HospitalMedian overall survivalMore stage IIIPatras University HospitalKaplan-Meier analysisCell lung cancerLog-rank testHigh SOX2 expressionNew Haven HospitalMore effective markersSOX2 expression levelsOverall survivalCell carcinomaLung cancerUniversity HospitalIndependent cohortKruskal-Wallis testStage IIIBetter outcomesStem cell transcription factorsSurvival analysis
2011
Evaluation of prognostic and predictive value of microtubule associated protein tau in two independent cohorts
Baquero MT, Lostritto K, Gustavson MD, Bassi KA, Appia F, Camp RL, Molinaro AM, Harris LN, Rimm DL. Evaluation of prognostic and predictive value of microtubule associated protein tau in two independent cohorts. Breast Cancer Research 2011, 13: r85. PMID: 21888627, PMCID: PMC3262195, DOI: 10.1186/bcr2937.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAntineoplastic Combined Chemotherapy ProtocolsBiomarkers, TumorBreast NeoplasmsCohort StudiesCyclophosphamideCytoplasmDocetaxelDoxorubicinEpithelial CellsFemaleFluorouracilHumansKaplan-Meier EstimateMiddle AgedPredictive Value of TestsPrognosisRandomized Controlled Trials as TopicRetrospective StudiesSurvival RateTau ProteinsTaxoidsConceptsOverall survivalBreast cancer cohortTreatment armsPredictive markerCancer cohortPredictive valueResponse rateConventional whole tissue sectionsMAP-tauImproved overall survivalHigh expressionMicrotubule associated protein tauTaxane-based chemotherapyKaplan-Meier analysisLonger median timeUseful predictive markerCox univariate analysisIndependent breast cancer cohortsWhole tissue sectionsFAC chemotherapyLonger TTPMedian timeMeier analysisPrognostic valueClinicopathologic variables
2005
β-Catenin Functions Mainly as an Adhesion Molecule in Patients with Squamous Cell Cancer of the Head and Neck
Yu Z, Weinberger PM, Provost E, Haffty BG, Sasaki C, Joe J, Camp RL, Rimm DL, Psyrri A. β-Catenin Functions Mainly as an Adhesion Molecule in Patients with Squamous Cell Cancer of the Head and Neck. Clinical Cancer Research 2005, 11: 2471-2477. PMID: 15814622, DOI: 10.1158/1078-0432.ccr-04-2199.Peer-Reviewed Original ResearchConceptsSquamous cell cancerCyclin D1 levelsCell cancerNeck squamous cell cancerAdhesion moleculesD1 levelsDisease-free survivalIndependent prognostic factorLocal recurrence rateKaplan-Meier analysisMembranous expression patternLow cyclin D1Cancer tissue microarrayIncidence of mutationsProtein expression levelsMean followHazard ratioPrognostic factorsLocal recurrencePathologic dataCox regressionRecurrence rateMetastasis stageTissue microarrayBeta-catenin expression