2024
Comparative Analysis of Ficoll-Hypaque and CytoLyt® Techniques for Blood Removal in Breast Cancer Malignant Effusions: Effects on RNA Quality and Sequencing Outcomes
Sura G, Tran K, Trevarton A, Marczyk M, Fu C, Du L, Qu J, Lau R, Tasto A, Gould R, Tinnirello A, Sinn B, Pusztai L, Hatzis C, Symmans W. Comparative Analysis of Ficoll-Hypaque and CytoLyt® Techniques for Blood Removal in Breast Cancer Malignant Effusions: Effects on RNA Quality and Sequencing Outcomes. Journal Of The American Society Of Cytopathology 2024 DOI: 10.1016/j.jasc.2024.11.001.Peer-Reviewed Original ResearchRNA integrity numberRNA qualityRNA-seqMeasurement of gene expressionRNA-seq analysisMetastatic breast cancerFicoll-Hypaque methodDensity gradient enrichmentSequence dataRead-basedVariant detectionMalignant effusionsCytospin slidesFresh frozen samplesRNA fragmentsTranscript abundanceSequencing outcomesSequencing methodsBreast cancerRNA sequencingFicoll-HypaqueUMI-basedGene expressionRNAMalignant effusion specimens
2013
Bayesian Mixture Models for Assessment of Gene Differential Behaviour and Prediction of pCR through the Integration of Copy Number and Gene Expression Data
Trentini F, Ji Y, Iwamoto T, Qi Y, Pusztai L, Müller P. Bayesian Mixture Models for Assessment of Gene Differential Behaviour and Prediction of pCR through the Integration of Copy Number and Gene Expression Data. PLOS ONE 2013, 8: e68071. PMID: 23874497, PMCID: PMC3709899, DOI: 10.1371/journal.pone.0068071.Peer-Reviewed Original Research
2006
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
Shi L, Shi L, Reid L, Jones W, Shippy R, Warrington J, Baker S, Collins P, de Longueville F, Kawasaki E, Lee K, Luo Y, Sun Y, Willey J, Setterquist R, Fischer G, Tong W, Dragan Y, Dix D, Frueh F, Goodsaid F, Herman D, Jensen R, Johnson C, Lobenhofer E, Puri R, Scherf U, Thierry-Mieg J, Wang C, Wilson M, Wolber P, Zhang L, Amur S, Bao W, Barbacioru C, Lucas A, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao X, Cebula T, Chen J, Cheng J, Chu T, Chudin E, Corson J, Corton J, Croner L, Davies C, Davison T, Delenstarr G, Deng X, Dorris D, Eklund A, Fan X, Fang H, Fulmer-Smentek S, Fuscoe J, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje P, Han J, Han T, Harbottle H, Harris S, Hatchwell E, Hauser C, Hester S, Hong H, Hurban P, Jackson S, Ji H, Knight C, Kuo W, LeClerc J, Levy S, Li Q, Liu C, Liu Y, Lombardi M, Ma Y, Magnuson S, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr M, Osborn T, Papallo A, Patterson T, Perkins R, Peters E, Peterson R, Philips K, Pine P, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig B, Samaha R, Schena M, Schroth G, Shchegrova S, Smith D, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson K, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker S, Wang S, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology 2006, 24: 1151-1161. PMID: 16964229, PMCID: PMC3272078, DOI: 10.1038/nbt1239.Peer-Reviewed Original ResearchConceptsMicroArray Quality ControlIntroduction of microarray technologyMicroArray Quality Control projectRNA samplesGene expression measurementsGene expression researchMicroarray-basedMicroarray platformExpression dataMicroarray technologyExpression measurementsMicroarrayExpression researchIntraplatformMapping effortsGenesRNAAlternative technology platformsQuality controlData analysis issuesSitesPublication of studiesMultiple test sitesExpression
2005
Pharmacogenomics and Clinical Biomarkers in Drug Discovery and Development
Ross JS, Symmans WF, Pusztai L, Hortobagyi GN. Pharmacogenomics and Clinical Biomarkers in Drug Discovery and Development. American Journal Of Clinical Pathology 2005, 124: s29-s41. PMID: 16468416, DOI: 10.1309/xyqafanapync6x59.Peer-Reviewed Original ResearchConceptsHuman genome sequenceGene expression profilesGenome sequenceEpigenetic eventsExpression profilesProteomics researchDrug discoveryRapid evolutionComputational biologyPharmaceutical industryMolecular diagnosticsDiscoveryFurther understandingBiosensorRNABiologyAnticancerSequenceClinical biomarkersAnti-inflammatory drugsDrug efficacyToxicityPrediction of responseDevelopmentContinuous technological advancements