2021
Using Machine Learning Algorithms to Predict Immunotherapy Response in Patients with Advanced Melanoma
Johannet P, Coudray N, Donnelly DM, Jour G, Illa-Bochaca I, Xia Y, Johnson DB, Wheless L, Patrinely JR, Nomikou S, Rimm DL, Pavlick AC, Weber JS, Zhong J, Tsirigos A, Osman I. Using Machine Learning Algorithms to Predict Immunotherapy Response in Patients with Advanced Melanoma. Clinical Cancer Research 2021, 27: 131-140. PMID: 33208341, PMCID: PMC7785656, DOI: 10.1158/1078-0432.ccr-20-2415.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedDisease ProgressionDrug Resistance, NeoplasmFemaleFollow-Up StudiesHumansImage Processing, Computer-AssistedImmune Checkpoint InhibitorsMachine LearningMaleMelanomaMiddle AgedNeoplasm StagingPrognosisProgression-Free SurvivalProspective StudiesRisk AssessmentROC CurveSkinSkin NeoplasmsConceptsProgression-free survivalImmune checkpoint inhibitorsLower riskClinicodemographic characteristicsAdvanced melanomaClinical dataWorse progression-free survivalICI treatment outcomesKaplan-Meier curvesBiomarkers of responseStandard of careCheckpoint inhibitorsICI responseImmunotherapy responseValidation cohortTraining cohortDisease progressionProspective validationTreatment outcomesHigh riskClinical practicePatientsROC curveProgressionRisk
2020
Prospective multi-institutional evaluation of pathologist assessment of PD-L1 assays for patient selection in triple negative breast cancer
Reisenbichler ES, Han G, Bellizzi A, Bossuyt V, Brock J, Cole K, Fadare O, Hameed O, Hanley K, Harrison BT, Kuba MG, Ly A, Miller D, Podoll M, Roden AC, Singh K, Sanders MA, Wei S, Wen H, Pelekanou V, Yaghoobi V, Ahmed F, Pusztai L, Rimm DL. Prospective multi-institutional evaluation of pathologist assessment of PD-L1 assays for patient selection in triple negative breast cancer. Modern Pathology 2020, 33: 1746-1752. PMID: 32300181, PMCID: PMC8366569, DOI: 10.1038/s41379-020-0544-x.Peer-Reviewed Original ResearchConceptsTriple-negative breast cancerNegative breast cancerOverall percent agreementPD-L1Intraclass correlation coefficientBreast cancerAdvanced triple-negative breast cancerPD-L1 positive casesImmune cell stainingMultiple pathologistsPD-L1 scoringMulti-institutional evaluationLung cancer studiesAtezolizumab therapySP142 assaySP263 assaysPatient selectionSP263SP142US FoodDrug AdministrationPathologist's assessmentPositive casesReal-world settingPercent agreement
2014
Quantitative assessment of miR34a as an independent prognostic marker in breast cancer
Agarwal S, Hanna J, Sherman ME, Figueroa J, Rimm DL. Quantitative assessment of miR34a as an independent prognostic marker in breast cancer. British Journal Of Cancer 2014, 112: 61-68. PMID: 25474246, PMCID: PMC4453614, DOI: 10.1038/bjc.2014.573.Peer-Reviewed Original ResearchConceptsDisease-specific survivalBreast cancer cohortPoor disease-specific survivalDisease-specific deathIndependent breast cancer cohortsBreast cancerCancer cohortPoor outcomeCohort 1Multivariate Cox proportional hazards analysisCox proportional hazards analysisNode-positive populationX-tile softwareNode-negative patientsProportional hazards analysisTumor suppressorBreast cancer patientsIndependent prognostic markerExpression of miR34aReceptor statusNode statusPreclinical observationsTumor sizeCancer patientsCohort 2A tissue quality index: an intrinsic control for measurement of effects of preanalytical variables on FFPE tissue
Neumeister VM, Parisi F, England AM, Siddiqui S, Anagnostou V, Zarrella E, Vassilakopolou M, Bai Y, Saylor S, Sapino A, Kluger Y, Hicks DG, Bussolati G, Kwei S, Rimm DL. A tissue quality index: an intrinsic control for measurement of effects of preanalytical variables on FFPE tissue. Laboratory Investigation 2014, 94: 467-474. PMID: 24535259, PMCID: PMC4030875, DOI: 10.1038/labinvest.2014.7.Peer-Reviewed Original ResearchConceptsCold ischemic timeIschemic timeQuantitative immunofluorescenceLevel of expressionTissue qualityER expression levelsBreast cancer casesExpression levelsFormalin fixationInformative epitopesValidation cohortCancer casesBreast cohortProtein statusGlobal assessmentPatient samplesTissue cohortPreanalytical variablesEpitope expressionCohortIntrinsic controlMeasurement of effectsQuality IndexFFPE tissuesEpitopes
2013
A Prospective, Multi-Institutional Diagnostic Trial to Determine Pathologist Accuracy in Estimation of Percentage of Malignant Cells
Viray H, Li K, Long TA, Vasalos P, Bridge JA, Jennings LJ, Halling KC, Hameed M, Rimm DL. A Prospective, Multi-Institutional Diagnostic Trial to Determine Pathologist Accuracy in Estimation of Percentage of Malignant Cells. Archives Of Pathology & Laboratory Medicine 2013, 137: 1545-9. PMID: 24168492, DOI: 10.5858/arpa.2012-0561-cp.Peer-Reviewed Original ResearchConceptsFalse-negative test resultsMalignant cellsMulti-institutional studyColon tissue specimensCriterion standardPatient careTissue specimensTumor tissueDiagnostic trialPathologists' accuracyGenetic alterationsNuclear countsPathologist estimationEstimation of percentageVisual estimationCurrent studyCellsTesting failuresPrediction of Late Disease Recurrence and Extended Adjuvant Letrozole Benefit by the HOXB13/IL17BR Biomarker
Sgroi DC, Carney E, Zarrella E, Steffel L, Binns SN, Finkelstein DM, Szymonifka J, Bhan AK, Shepherd LE, Zhang Y, Schnabel CA, Erlander MG, Ingle JN, Porter P, Muss HB, Pritchard KI, Tu D, Rimm DL, Goss PE. Prediction of Late Disease Recurrence and Extended Adjuvant Letrozole Benefit by the HOXB13/IL17BR Biomarker. Journal Of The National Cancer Institute 2013, 105: 1036-1042. PMID: 23812955, PMCID: PMC3888138, DOI: 10.1093/jnci/djt146.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAntineoplastic AgentsAromatase InhibitorsBiomarkers, TumorBreast NeoplasmsCase-Control StudiesChemotherapy, AdjuvantDisease-Free SurvivalFemaleHomeodomain ProteinsHumansIncidenceLetrozoleLogistic ModelsMiddle AgedMultivariate AnalysisNeoplasm GradingNeoplasm Recurrence, LocalNeoplasm StagingNitrilesPredictive Value of TestsPrognosisProspective StudiesReceptor, ErbB-2Receptors, EstrogenReceptors, InterleukinReceptors, Interleukin-17Receptors, ProgesteroneRetrospective StudiesReverse Transcriptase Polymerase Chain ReactionTriazolesConceptsExtended letrozole therapyStandard clinicopathological factorsLate disease recurrenceLate recurrenceLetrozole therapyEndocrine therapyDisease recurrenceClinicopathological factorsLymph node-negative breast cancer patientsNode-negative breast cancer patientsExtended adjuvant endocrine therapyMultivariable conditional logistic regressionExtended adjuvant letrozolePlacebo-treated patientsAdjuvant endocrine therapyER-positive patientsBreast cancer patientsPositive breast cancerConditional logistic regressionReverse transcription-polymerase chain reactionCase-control designAdjuvant letrozoleLetrozole treatmentAbsolute riskCancer patients
2012
Quantitative Assessment of Effect of Preanalytic Cold Ischemic Time on Protein Expression in Breast Cancer Tissues
Neumeister VM, Anagnostou V, Siddiqui S, England AM, Zarrella ER, Vassilakopoulou M, Parisi F, Kluger Y, Hicks DG, Rimm DL. Quantitative Assessment of Effect of Preanalytic Cold Ischemic Time on Protein Expression in Breast Cancer Tissues. Journal Of The National Cancer Institute 2012, 104: 1815-1824. PMID: 23090068, PMCID: PMC3514166, DOI: 10.1093/jnci/djs438.Peer-Reviewed Original ResearchMeSH KeywordsA Kinase Anchor ProteinsBiomarkers, TumorBiopsy, Large-Core NeedleBreast NeoplasmsCold IschemiaConfounding Factors, EpidemiologicFalse Negative ReactionsFemaleFixativesFluorescent Antibody TechniqueFormaldehydeGene Expression Regulation, NeoplasticHumansHypoxia-Inducible Factor 1, alpha SubunitKi-67 AntigenMastectomy, SegmentalMatched-Pair AnalysisMinor Histocompatibility AntigensProspective StudiesProto-Oncogene ProteinsReceptor, ErbB-2Receptors, EstrogenReceptors, ProgesteroneResearch DesignTime FactorsConceptsCold ischemic timeIschemic timeBreast cancer tissuesEstrogen receptorCancer tissuesLoss of antigenicityBreast cancer resectionProtein expressionCore needle biopsyCompanion diagnostic testsConditions of hypoxiaFalse-negative resultsBreast cancer biomarkersCancer resectionProgesterone receptorNeedle biopsyRecent guidelinesCold ischemiaBreast cancerTissue microarrayEvidence of lossQuantitative immunofluorescenceDiagnostic testsAntigenicityAQUA method
2011
Lymph Node Ratio Should Be Considered for Incorporation into Staging for Breast Cancer
Chagpar AB, Camp RL, Rimm DL. Lymph Node Ratio Should Be Considered for Incorporation into Staging for Breast Cancer. Annals Of Surgical Oncology 2011, 18: 3143. PMID: 21847696, DOI: 10.1245/s10434-011-2012-9.Peer-Reviewed Original ResearchConceptsNode-positive breast cancer patientsDifferent OS ratesOverall survivalBreast cancer patientsOS independentClinicopathologic factorsOS ratesCancer patientsBreast cancer staging systemCurrent American Joint CommitteeLymph node ratioAdditional prognostic informationAmerican Joint CommitteeCancer (AJCC) staging systemTraditional clinicopathologic factorsPN statusIntermediate riskNodal statusStaging systemPrognostic informationBreast cancerHigh riskLower riskJoint CommitteeNode ratio
2010
Multiplexed Assessment of the Southwest Oncology Group-Directed Intergroup Breast Cancer Trial S9313 by AQUA Shows that Both High and Low Levels of HER2 Are Associated with Poor Outcome
Harigopal M, Barlow WE, Tedeschi G, Porter PL, Yeh IT, Haskell C, Livingston R, Hortobagyi GN, Sledge G, Shapiro C, Ingle JN, Rimm DL, Hayes DF. Multiplexed Assessment of the Southwest Oncology Group-Directed Intergroup Breast Cancer Trial S9313 by AQUA Shows that Both High and Low Levels of HER2 Are Associated with Poor Outcome. American Journal Of Pathology 2010, 176: 1639-1647. PMID: 20150438, PMCID: PMC2843456, DOI: 10.2353/ajpath.2010.090711.Peer-Reviewed Original ResearchConceptsDisease-free survivalEstrogen receptorContinuous variablesSouthwest Oncology GroupAQUA methodAC chemotherapyMenopausal statusNegative patientsOncology GroupNode statusSequential doxorubicinPoor outcomeTumor sizeProgesterone receptorPrognostic informationWorse outcomesTissue biomarkersTissue microarrayBiphasic effectP53 expressionPatientsHER2Low expressersDiagnostic approachMultiplexed assessment