2010
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
Shi L, Campbell G, Jones W, Campagne F, Wen Z, Walker S, Su Z, Chu T, Goodsaid F, Pusztai L, Shaughnessy J, Oberthuer A, Thomas R, Paules R, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas B, Ge X, Megherbi D, Symmans W, Wang M, Zhang J, Bitter H, Brors B, Bushel P, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison T, Delorenzi M, Deng Y, Devanarayan V, Dix D, Dopazo J, Dorff K, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess K, Hong H, Huan J, Irizarry R, Judson R, Juraeva D, Lababidi S, Lambert C, Li L, Li Y, Li Z, Lin S, Liu G, Lobenhofer E, Luo J, Luo W, McCall M, Nikolsky Y, Pennello G, Perkins R, Philip R, Popovici V, Price N, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang S, Wu J, Wu Y, Xie Q, Yousef W, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas A, Berthold F, Brennan R, Buness A, Catalano J, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe J, Gatto L, Ge W, Goldstein D, Guo L, Halbert D, Han J, Harris S, Hatzis C, Herman D, Huang J, Jensen R, Jiang R, Johnson C, Jurman G, Kahlert Y, Khuder S, Kohl M, Li J, Li L, Li M, Li Q, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt R, Montaner D, Mukherjee P, Mulligan G, Neville P, Nikolskaya T, Ning B, Page G, Parker J, Parry R, Peng X, Peterson R, Phan J, Quanz B, Ren Y, Riccadonna S, Roter A, Samuelson F, Schumacher M, Shambaugh J, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes T, Sun Q, Tan P, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega S, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey J, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri R, Scherf U, Tong W, Wolfinger R. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology 2010, 28: 827-838. PMID: 20676074, PMCID: PMC3315840, DOI: 10.1038/nbt.1665.Peer-Reviewed Original Research
2009
Metastatic gene signatures and emerging novel prognostic tests in the management of early stage breast cancer
Tordai A, Liedtke C, Pusztai L. Metastatic gene signatures and emerging novel prognostic tests in the management of early stage breast cancer. Clinical & Experimental Metastasis 2009, 26: 625-632. PMID: 19381845, DOI: 10.1007/s10585-009-9261-z.Peer-Reviewed Original ResearchConceptsMetastatic gene signatureGene expression studiesGene expression profilingDistinct neoplastic diseasesExpression profilingDNA microarraysExpression studiesGene expressionMRNA transcriptsGene signatureSingle experimentNovel diagnostic assaysTranscriptsDiagnostic assaysNovel prognostic testsMicroarrayProfilingExpression
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
2003
Clinical Application of cDNA Microarrays in Oncology
Pusztai L, Ayers M, Stec J, Hortobágyi GN. Clinical Application of cDNA Microarrays in Oncology. The Oncologist 2003, 8: 252-258. PMID: 12773747, DOI: 10.1634/theoncologist.8-3-252.Peer-Reviewed Original ResearchConceptsHundreds of genesGene expression patternsSingle-gene markersIndividual genesTranscriptional profilingCDNA microarrayMRNA speciesDNA microarraysExpression patternsComplex biologyNovel targetImportant new toolMicroarrayClinical outcomesGenesHuman tissuesImportant clinical outcomesDiseased tissuesDrug developmentTrue clinical utilityClinical utilityClinical OncologyNew toolBiologyExciting new technology