2023
Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing
Marczyk M, Fu C, Lau R, Du L, Trevarton A, Sinn B, Gould R, Pusztai L, Hatzis C, Symmans W. Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing. Cancer Cytopathology 2023, 131: 289-299. PMID: 36650408, PMCID: PMC10614161, DOI: 10.1002/cncy.22679.Peer-Reviewed Original ResearchMeSH KeywordsBreast NeoplasmsFemaleFormaldehydeGene Expression ProfilingHumansParaffin EmbeddingRNASequence Analysis, RNATissue FixationTranscriptomeConceptsCytology smearsBreast cancerConcordance correlation coefficientTumor tissue samplesParaffin-embedded sectionsClinical diagnostic proceduresSurgical resectionRNA sequencingTumor stromaCytologic specimensDiagnostic proceduresLin's concordance correlation coefficientPapanicolaou stainCancerTissue samplesDNA mutation testingSmearsSimilar concordanceTranscriptome RNA-SeqDiagnostic cytologyAllele fractionExpression levelsRNA-seqExpression of genesGene expression levels
2021
Analysis of the Applicability of microRNAs in Peripheral Blood Leukocytes as Biomarkers of Sensitivity and Exposure to Fractionated Radiotherapy towards Breast Cancer
Marczyk M, Polańska J, Wojcik A, Lundholm L. Analysis of the Applicability of microRNAs in Peripheral Blood Leukocytes as Biomarkers of Sensitivity and Exposure to Fractionated Radiotherapy towards Breast Cancer. International Journal Of Molecular Sciences 2021, 22: 8705. PMID: 34445424, PMCID: PMC8395710, DOI: 10.3390/ijms22168705.Peer-Reviewed Original ResearchConceptsBreast cancer patientsExternal beam radiotherapyCourse of radiotherapyPeripheral blood leukocytesBiomarkers of sensitivityLogistic regression modelsMultinomial logistic regression modelsFractionated RadiotherapyInter-individual variabilityCancer patientsUnivariate analysisBreast cancerCombination of miRNAsBeam radiotherapyBlood leukocytesBlood samplesPromising biomarkerTotal doseSensitive biomarkerRadiotherapyPatientsStrong inter-individual variabilityBiomarkersDoseLeukocytesTargeted 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 ResearchMeSH KeywordsBiomarkers, TumorFormaldehydeGene Expression ProfilingHumansMutationNeoplasmsParaffin EmbeddingPrognosisSequence Analysis, RNASpecimen HandlingTissue FixationTranscriptomeConceptsPolymerase 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
2020
Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue
Lau R, Du L, Chen E, Fu C, Gould R, Marczyk M, Sinn BV, Layman R, Bedrosian I, Valero V, Symmans WF. Technical Validity of a Customized Assay of Sensitivity to Endocrine Therapy Using Sections from Fixed Breast Cancer Tissue. Clinical Chemistry 2020, 66: 934-945. PMID: 32613237, DOI: 10.1093/clinchem/hvaa105.Peer-Reviewed Original ResearchConceptsQuantiGene PlexConcordance correlation coefficientBreast cancer tissuesParaffin-embedded tissue sectionsEndocrine therapyResection samplesBreast cancerTumor sectionsCancer tissuesStage IIParaffin blocksLin's concordance correlation coefficientTissue sectionsCustomized assayTherapyAnalytical sensitivityFFPE samplesNanoStringFFPE tissuesExpression indexWeekly testsAssaysTissueTechnical validity
2019
The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues
Marczyk M, Fu C, Lau R, Du L, Trevarton AJ, Sinn BV, Gould RE, Pusztai L, Hatzis C, Symmans WF. The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues. BMC Cancer 2019, 19: 1189. PMID: 31805884, PMCID: PMC6896723, DOI: 10.1186/s12885-019-6363-0.Peer-Reviewed Original ResearchConceptsBreast cancerFresh frozenParaffin-embedded tumor samplesFF samplesFFPE samplesConcordance correlation coefficientMixed-effects model analysisBreast cancer signaturesQiagen RNeasy kitWhole transcriptome RNA sequencingParaffin-embedded tissuesTranscriptome RNA sequencingLinear mixed-effects model analysisGene expression signaturesDifferent kitsClinical trialsGene signatureTumor samplesGene expressionTranslational researchCancerTissue samplesExpression signaturesArchival formalinSimilar concordance
2013
Adaptive filtering of microarray gene expression data based on Gaussian mixture decomposition
Marczyk M, Jaksik R, Polanski A, Polanska J. Adaptive filtering of microarray gene expression data based on Gaussian mixture decomposition. BMC Bioinformatics 2013, 14: 101. PMID: 23510016, PMCID: PMC3637832, DOI: 10.1186/1471-2105-14-101.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsGene Expression ProfilingHumansNormal DistributionOligonucleotide Array Sequence AnalysisConceptsGaussian mixture decompositionFalse discoveriesMicroarray gene expression dataNon-informative genesAdaptive filteringSample meanAdaptive methodSample varianceGaussian componentsMixture decompositionGene filteringEarlier paperGene expression dataFilteringOptimal threshold valuePrevious methodsMicroarray experimentsNew methodTwo-step procedureThreshold valueCorrection methodPower of detectionImportant parametersSecond stepMicroarray data
2011
Association between plasma proteome profiles analysed by mass spectrometry, a lymphocyte-based DNA-break repair assay and radiotherapy-induced acute mucosal reaction in head and neck cancer patients
Pietrowska M, Polańska J, Walaszczyk A, Wygoda A, Rutkowski T, Składowski K, Marczak Ł, Stobiecki M, Marczyk M, Polański A, Widłak P. Association between plasma proteome profiles analysed by mass spectrometry, a lymphocyte-based DNA-break repair assay and radiotherapy-induced acute mucosal reaction in head and neck cancer patients. International Journal Of Radiation Biology 2011, 87: 711-719. PMID: 21351848, DOI: 10.3109/09553002.2011.556174.Peer-Reviewed Original ResearchConceptsAcute mucosal reactionsAcute reactionsMucosal reactionsNeck cancerPlasma proteomeNeck cancer patientsPlasma proteome profilesDefinitive radiotherapyCancer patientsPredictive markerHealthy donorsBlood samplesHealthy individualsPatientsRadiotherapyPlasma samplesComet assayLymphocytesCancerMaximal intensityMarkersProteome profiles