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 ResearchConceptsCytology 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
2022
Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencing
Sura G, Tran K, Fu C, Du L, Marczyk M, Martinez Y, Tinnirello A, Gould R, Lau R, Symmans W. Molecular testing opportunities on cytology effusion specimens: the pre-analytic effects of various body fluid cytology preparation methods on RNA extraction quality and targeted sequencing. Journal Of The American Society Of Cytopathology 2022, 12: 10-19. PMID: 36270909, PMCID: PMC10644714, DOI: 10.1016/j.jasc.2022.09.003.Peer-Reviewed Original ResearchConceptsCell blocksCarnoy's solutionDiff-QuikFF samplesCytology laboratoryFFPE cell blocksMultigene expression signaturesConcordance correlation coefficientCell block sectionsParaffin-embedded sectionsMalignant effusionsEffusion specimensMolecular subtypesSurePath samplesCytospin preparationsCytologic methodsCytologic samplesSurePath preparationsDiagnostic approachClinical researchRNA sequencing analysisExpression signaturesHigh concordanceBlock sectionsFrozen cell pellets
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
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