2021
Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples
Fu C, Marczyk M, Samuels M, Trevarton AJ, Qu J, Lau R, Du L, Pappas T, Sinn BV, Gould RE, Pusztai L, Hatzis C, Symmans WF. Targeted RNAseq assay incorporating unique molecular identifiers for improved quantification of gene expression signatures and transcribed mutation fraction in fixed tumor samples. BMC Cancer 2021, 21: 114. PMID: 33541297, PMCID: PMC7860187, DOI: 10.1186/s12885-021-07814-8.Peer-Reviewed Original ResearchConceptsPolymerase chain reactionParaffin-embedded tumor tissue samplesConcordance correlation coefficientFresh frozenFFPE samplesPrimary breast cancerMulti-gene signatureTumor tissue samplesActivating point mutationMutant allele fractionReverse transcriptionKey breast cancer genesGene expression signaturesBreast cancer genesPIK3CA mutationsBackgroundOur objectiveBreast cancerWhole transcriptome RNAseqTumor samplesLin's concordance correlation coefficientHormone receptorsFF samplesTissue samplesExpression signaturesChain reaction
2012
Agreement in Risk Prediction Between the 21‐Gene Recurrence Score Assay (Oncotype DX®) and the PAM50 Breast Cancer Intrinsic Classifier™ in Early‐Stage Estrogen Receptor–Positive Breast Cancer
Kelly CM, Bernard PS, Krishnamurthy S, Wang B, Ebbert MT, Bastien RR, Boucher KM, Young E, Iwamoto T, Pusztai L. Agreement in Risk Prediction Between the 21‐Gene Recurrence Score Assay (Oncotype DX®) and the PAM50 Breast Cancer Intrinsic Classifier™ in Early‐Stage Estrogen Receptor–Positive Breast Cancer. The Oncologist 2012, 17: 492-498. PMID: 22418568, PMCID: PMC3336833, DOI: 10.1634/theoncologist.2012-0007.Peer-Reviewed Original ResearchConceptsBreast cancerEstrogen receptorEarly-stage estrogen receptor-positive breast cancerRisk assignmentHuman epidermal growth factor receptor 2 (HER2) expressionEpidermal growth factor receptor 2 expressionEstrogen receptor-positive breast cancerReceptor-positive breast cancerIntermediate RS groupLuminal B cancersReceptor 2 expressionLow-risk categoryQuantitative polymerase chain reactionB cancersMore patientsPolymerase chain reactionIntermediate RSLower riskStage IRS groupCancerPAM50Risk categoriesRisk predictionChain reaction
2009
The HER-2 Receptor and Breast Cancer: Ten Years of Targeted Anti–HER-2 Therapy and Personalized Medicine
Ross JS, Slodkowska EA, Symmans WF, Pusztai L, Ravdin PM, Hortobagyi GN. The HER-2 Receptor and Breast Cancer: Ten Years of Targeted Anti–HER-2 Therapy and Personalized Medicine. The Oncologist 2009, 14: 320-368. PMID: 19346299, DOI: 10.1634/theoncologist.2008-0230.Peer-Reviewed Original ResearchMeSH KeywordsAnthracyclinesAntibodies, MonoclonalAntibodies, Monoclonal, HumanizedAntineoplastic Combined Chemotherapy ProtocolsBevacizumabBiomarkers, TumorBreast NeoplasmsEverolimusEvidence-Based MedicineFemaleGene Expression Regulation, NeoplasticHumansImmunohistochemistryIn Situ HybridizationLapatinibNeoplasm StagingPolymerase Chain ReactionPractice Guidelines as TopicPrognosisPyrazolesPyrimidinesQuinazolinesReceptor, ErbB-2RNA, MessengerSirolimusSurvival AnalysisTaxoidsTrastuzumabTreatment OutcomeUp-RegulationConceptsBreast cancerOverall survivalInsulin-like growth factor receptor pathwayClinical Oncology-CollegeMetastatic breast cancerInvasive breast cancerAmerican Pathologists guidelinesHER-2 receptorTyrosine kinase inhibitorsTarget of therapyGrowth factor receptor pathwayKinase inhibitor lapatinibMean relative riskReal-time polymerase chain reactionTransmembrane tyrosine kinase receptorPrediction of responseChromosome 17 polysomyHormonal therapyTyrosine kinase receptorsTherapy toxicitySitu hybridizationPrognostic significancePolymerase chain reactionPathologists guidelinesRelative risk
2008
Commercialized Multigene Predictors of Clinical Outcome for Breast Cancer
Ross JS, Hatzis C, Symmans WF, Pusztai L, Hortobágyi GN. Commercialized Multigene Predictors of Clinical Outcome for Breast Cancer. The Oncologist 2008, 13: 477-493. PMID: 18515733, DOI: 10.1634/theoncologist.2007-0248.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkers, TumorBreast NeoplasmsCost-Benefit AnalysisDevice ApprovalFemaleGene Expression ProfilingHumansMolecular Diagnostic TechniquesParaffin EmbeddingPredictive Value of TestsPrognosisReceptors, EstrogenReverse Transcriptase Polymerase Chain ReactionUnited StatesUnited States Food and Drug AdministrationConceptsQuantitative multiplex real-time polymerase chain reactionLymph node positiveValidation clinical trialEfficacy of tamoxifenER-positive patientsPredictive testRegulatory approval statusOncotype DX testCurrent clinical utilityReal-time polymerase chain reactionCytochrome P450 CYP2D6High accrual rateMultiplex real-time polymerase chain reactionParaffin-embedded tissuesThird-party payorsProspective trialYounger patientsNode positiveClinical outcomesOncotype DXPatient eligibilityMultigene assaysPolymerase chain reactionClinical trialsBreast cancer
2006
Molecular Classification of Breast Cancer: Limitations and Potential
Pusztai L, Mazouni C, Anderson K, Wu Y, Symmans WF. Molecular Classification of Breast Cancer: Limitations and Potential. The Oncologist 2006, 11: 868-877. PMID: 16951390, DOI: 10.1634/theoncologist.11-8-868.Peer-Reviewed Original ResearchConceptsBreast cancerMolecular classificationNovel risk stratification methodsEstrogen receptor immunohistochemistryBreast cancer patientsRisk stratification methodsRoutine diagnostic workupTranscription-polymerase chain reactionNew molecular classificationReceptor immunohistochemistryCancer patientsDiagnostic workupPolymerase chain reactionBest therapyMolecular subsetsPredictive valueClinical researchCancerDiagnostic testsPredictive testChain reactionMedical decisions
2005
Gene Expression Profiles in Paraffin-Embedded Core Biopsy Tissue Predict Response to Chemotherapy in Women With Locally Advanced Breast Cancer
Gianni L, Zambetti M, Clark K, Baker J, Cronin M, Wu J, Mariani G, Rodriguez J, Carcangiu M, Watson D, Valagussa P, Rouzier R, Symmans WF, Ross JS, Hortobagyi GN, Pusztai L, Shak S. Gene Expression Profiles in Paraffin-Embedded Core Biopsy Tissue Predict Response to Chemotherapy in Women With Locally Advanced Breast Cancer. Journal Of Clinical Oncology 2005, 23: 7265-7277. PMID: 16145055, DOI: 10.1200/jco.2005.02.0818.Peer-Reviewed Original ResearchConceptsPathologic complete responseAdvanced breast cancerBreast cancerNeoadjuvant paclitaxelRecurrence scoreChemotherapy responseRecurrence riskLikelihood of pCRGreater recurrence riskReverse transcriptase-polymerase chain reactionTranscriptase-polymerase chain reactionCore biopsy tissueImmune-related genesNeoadjuvant anthracyclineNeoadjuvant studiesAssessable patientsReceptor-related genesChemotherapy benefitComplete responseCore biopsyPolymerase chain reactionUnivariate analysisProliferation-related genesIndependent patientsBiopsy tissue
2004
Technology Insight: emerging techniques to predict response to preoperative chemotherapy in breast cancer
Pusztai L, Gianni L. Technology Insight: emerging techniques to predict response to preoperative chemotherapy in breast cancer. Nature Reviews Clinical Oncology 2004, 1: 44-50. PMID: 16264799, DOI: 10.1038/ncponc0025.Peer-Reviewed Original ResearchConceptsBreast cancerOptimal chemotherapy regimenHistopathologic predictorsChemotherapy regimenChemotherapy regimensPreoperative chemotherapyPolymerase chain reactionPotential diagnostic toolMultiplex polymerase chain reactionClinical useGene expressionChain reactionDiagnostic toolCancerMeaningful responsesRegimenRegimensChemotherapyPatientsPrognosis