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
2018
Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity
Shi W, Ng CKY, Lim RS, Jiang T, Kumar S, Li X, Wali VB, Piscuoglio S, Gerstein MB, Chagpar AB, Weigelt B, Pusztai L, Reis-Filho JS, Hatzis C. Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity. Cell Reports 2018, 25: 1446-1457. PMID: 30404001, PMCID: PMC6261536, DOI: 10.1016/j.celrep.2018.10.046.Peer-Reviewed Original Research
2017
Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations
Brown D, Smeets D, Székely B, Larsimont D, Szász AM, Adnet PY, Rothé F, Rouas G, Nagy ZI, Faragó Z, Tőkés AM, Dank M, Szentmártoni G, Udvarhelyi N, Zoppoli G, Pusztai L, Piccart M, Kulka J, Lambrechts D, Sotiriou C, Desmedt C. Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations. Nature Communications 2017, 8: 14944. PMID: 28429735, PMCID: PMC5474888, DOI: 10.1038/ncomms14944.Peer-Reviewed Original ResearchConceptsDistant metastasisPrimary tumorClonal frequency analysisMultiple metastatic lesionsBreast cancer disseminationBreast cancer progressionSomatic mutationsWhole-exome sequencingAvailable metastasesMetastatic lesionsMetastatic precursorsPrimary lesionMetastatic tumorsDisease progressionBreast cancerPatterns of disseminationMetastasisMetastatic progressionCancer disseminationPatientsCancer progressionCopy number profilingCopy number aberrationsTumorsMonoclonal originPathway level alterations rather than mutations in single genes predict response to HER2-targeted therapies in the neo-ALTTO trial
Shi W, Jiang T, Nuciforo P, Hatzis C, Holmes E, Harbeck N, Sotiriou C, Peña L, Loi S, Rosa DD, Chia S, Wardley A, Ueno T, Rossari J, Eidtmann H, Armour A, Piccart-Gebhart M, Rimm DL, Baselga J, Pusztai L. Pathway level alterations rather than mutations in single genes predict response to HER2-targeted therapies in the neo-ALTTO trial. Annals Of Oncology 2017, 28: 128-135. PMID: 28177460, PMCID: PMC5834036, DOI: 10.1093/annonc/mdw434.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Combined Chemotherapy ProtocolsBiopsy, Fine-NeedleBreast NeoplasmsClass I Phosphatidylinositol 3-KinasesDNA, NeoplasmExome SequencingFemaleHumansLapatinibMolecular Targeted TherapyMutationProportional Hazards ModelsProtein Kinase InhibitorsQuinazolinesReceptor, ErbB-2RhoA GTP-Binding ProteinTrastuzumabConceptsPathologic complete response