2015
Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments
Qi Y, Liu X, Liu CG, Wang B, Hess KR, Symmans WF, Shi W, Pusztai L. Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments. PLOS ONE 2015, 10: e0119230. PMID: 26136146, PMCID: PMC4489803, DOI: 10.1371/journal.pone.0119230.Peer-Reviewed Original ResearchConceptsSingle nucleotide variantsEuropean Genome-phenome ArchiveProtein kinase geneMillions of nucleotidesSame genomic DNANext-generation sequencing experimentsVariant callsGenomic locationNext-generation sequencingSequence dataSNV callsKinase geneGenomic DNANucleotide substitutionsSequencing experimentsHigh stringencyVariant allele frequencyNucleotide variantsTrue biological changeNucleotide alterationsGeneration sequencingAllele countsSequencing errorsBreast cancer samplesAllele frequencies
2012
Prognostic evaluation of the B cell/IL-8 metagene in different intrinsic breast cancer subtypes
Hanker LC, Rody A, Holtrich U, Pusztai L, Ruckhaeberle E, Liedtke C, Ahr A, Heinrich TM, Sänger N, Becker S, Karn T. Prognostic evaluation of the B cell/IL-8 metagene in different intrinsic breast cancer subtypes. Breast Cancer Research And Treatment 2012, 137: 407-416. PMID: 23242614, DOI: 10.1007/s10549-012-2356-2.Peer-Reviewed Original ResearchMeSH KeywordsB-LymphocytesBreast NeoplasmsDisease-Free SurvivalFemaleFollow-Up StudiesGene Expression Regulation, NeoplasticHumansInterleukin-8Middle AgedOligonucleotide Array Sequence AnalysisPredictive Value of TestsPrognosisProportional Hazards ModelsReceptor, ErbB-2Receptors, EstrogenReceptors, ProgesteroneConceptsTriple-negative breast cancerCell/ILNegative breast cancerBreast cancer subtypesPrognostic valueBreast cancerBetter prognosisB cellsCancer subtypesIntrinsic breast cancer subtypesPrimary breast cancer samplesER-negative subtypesEvent-free survivalB cell signaturesHigher B cellsSignificant prognostic valueTriple-negative samplesBreast cancer samplesRoutine clinicopathological variablesOnly significant predictorSubtype-specific analysesTNBC subtypesClinicopathological variablesOutcome predictorsPrognostic evaluation
2010
Genomic Index of Sensitivity to Endocrine Therapy for Breast Cancer
Symmans WF, Hatzis C, Sotiriou C, Andre F, Peintinger F, Regitnig P, Daxenbichler G, Desmedt C, Domont J, Marth C, Delaloge S, Bauernhofer T, Valero V, Booser DJ, Hortobagyi GN, Pusztai L. Genomic Index of Sensitivity to Endocrine Therapy for Breast Cancer. Journal Of Clinical Oncology 2010, 28: 4111-4119. PMID: 20697068, PMCID: PMC2953969, DOI: 10.1200/jco.2010.28.4273.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Agents, HormonalAromatase InhibitorsBiomarkers, TumorBreast NeoplasmsChemotherapy, AdjuvantChi-Square DistributionDisease-Free SurvivalEstrogen Receptor alphaFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticGenomicsHumansMiddle AgedNeoplasm StagingOligonucleotide Array Sequence AnalysisPatient SelectionProportional Hazards ModelsRisk AssessmentRisk FactorsSurvival AnalysisTamoxifenTime FactorsTranscription, GeneticTreatment OutcomeConceptsAdjuvant endocrine therapyEndocrine therapyBreast cancerDistant relapseER-positive breast cancerChemo-endocrine therapyDistant relapse riskYears of tamoxifenAdjuvant systemic therapyEstrogen receptor αBreast cancer samplesPrior chemotherapyNeoadjuvant chemotherapyPathologic responseSurvival benefitSystemic therapyUntreated cohortRelapse riskDeath riskTherapy indexAromatase inhibitionESR1 levelsReceptor αTamoxifenTherapy
2009
T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers
Rody A, Holtrich U, Pusztai L, Liedtke C, Gaetje R, Ruckhaeberle E, Solbach C, Hanker L, Ahr A, Metzler D, Engels K, Karn T, Kaufmann M. T-cell metagene predicts a favorable prognosis in estrogen receptor-negative and HER2-positive breast cancers. Breast Cancer Research 2009, 11: r15. PMID: 19272155, PMCID: PMC2688939, DOI: 10.1186/bcr2234.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkers, TumorBreast NeoplasmsFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansImmunoenzyme TechniquesLymphocyte Specific Protein Tyrosine Kinase p56(lck)Neoplasm StagingOligonucleotide Array Sequence AnalysisPrognosisReceptor, ErbB-2Receptors, EstrogenT-LymphocytesConceptsER-negative tumorsImmune cellsBreast cancer samplesSurrogate markerPrognostic valueBreast cancerHuman epidermal growth factor receptor 2 (HER2) amplificationHER2-positive breast cancerDifferent immune cell typesCancer samplesPrimary breast cancer samplesER-negative groupER-positive tumorsDifferent immune cellsSignificant prognostic valuePositive prognostic valueImmune cell typesSubgroup of tumorsPrognostic gene signatureNeoadjuvant chemotherapyFavorable prognosisCytokine milieuClinical parametersNegative tumorsWorse prognosis
2005
The Nuclear Transcription Factor κB/bcl-2 Pathway Correlates with Pathologic Complete Response to Doxorubicin-Based Neoadjuvant Chemotherapy in Human Breast Cancer
Buchholz TA, Garg AK, Chakravarti N, Aggarwal BB, Esteva FJ, Kuerer HM, Singletary SE, Hortobagyi GN, Pusztai L, Cristofanilli M, Sahin AA. The Nuclear Transcription Factor κB/bcl-2 Pathway Correlates with Pathologic Complete Response to Doxorubicin-Based Neoadjuvant Chemotherapy in Human Breast Cancer. Clinical Cancer Research 2005, 11: 8398-8402. PMID: 16322301, DOI: 10.1158/1078-0432.ccr-05-0885.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic AgentsAntineoplastic Combined Chemotherapy ProtocolsBcl-2-Associated X ProteinBreast NeoplasmsCell NucleusChemotherapy, AdjuvantCyclophosphamideCytoplasmDoxorubicinFemaleFluorouracilHumansMiddle AgedNeoadjuvant TherapyNeoplasm StagingNF-kappa BProto-Oncogene Proteins c-bcl-2Signal TransductionSurvival RateTreatment OutcomeConceptsPathologic complete responseHuman breast cancerNF-kappaBNeoadjuvant chemotherapyComplete responseNeoadjuvant doxorubicinBcl-2Poor responseBreast cancerAnthracycline-based neoadjuvant chemotherapyNF-kappaB.Bcl-2-positive tumorsHuman breast cancer samplesBreast cancer responseClinical outcome dataTranscription factor NF-kappaBBreast cancer pathologistNuclear factor-kappaBBreast cancer samplesPCR ratePositive tumorsChemotherapy responseTumor stainingImmunohistochemical stainingCancer response