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
2011
Proposals for uniform collection of biospecimens from neoadjuvant breast cancer clinical trials: timing and specimen types
Loi S, Symmans WF, Bartlett J, Fumagalli D, Veer L, Forbes JF, Bedard P, Denkert C, Zujewski J, Viale G, Pusztai L, Esserman LJ, Leyland-Jones BR. Proposals for uniform collection of biospecimens from neoadjuvant breast cancer clinical trials: timing and specimen types. The Lancet Oncology 2011, 12: 1162-1168. PMID: 21684810, DOI: 10.1016/s1470-2045(11)70117-6.Peer-Reviewed Original ResearchConceptsNorth American Breast Cancer GroupBreast International GroupClinical trialsBiopsy procedureNeoadjuvant breast cancer trialsNeoadjuvant clinical trialsBreast cancer clinical trialsBreast cancer groupBreast cancer trialsStart of treatmentCancer clinical trialsNational Cancer InstituteNeoadjuvant trialsDefinitive surgeryNeoadjuvant treatmentCancer groupStudy protocolCancer trialsBreast cancerCancer InstituteUniform collectionTumor tissueBlood collectionTrialsSpecimen typesEffects of Tissue Handling on RNA Integrity and Microarray Measurements From Resected Breast Cancers
Hatzis C, Sun H, Yao H, Hubbard RE, Meric-Bernstam F, Babiera GV, Wu Y, Pusztai L, Symmans WF. Effects of Tissue Handling on RNA Integrity and Microarray Measurements From Resected Breast Cancers. Journal Of The National Cancer Institute 2011, 103: 1871-1883. PMID: 22034635, PMCID: PMC3243675, DOI: 10.1093/jnci/djr438.Peer-Reviewed Original ResearchAdultAgedAged, 80 and overBiopsyBreast NeoplasmsCarcinoma, Ductal, BreastCarcinoma, LobularCarcinoma, Squamous CellCryopreservationFemaleFreeze DryingGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMastectomyMicroarray AnalysisMiddle AgedRNA, NeoplasmSpecimen HandlingTime Factors