References
- Tumor Analysis Best Practices Working GroupExpression profiling – best practices for data generation and interpretation in clinical trialsNat Rev Genet20045322923714970825
- AuerHNewsomDLKornackerKExpression profiling using Affymetrix GeneChip microarraysMethods Mol Biol2009509354619212713
- FuscoeJCTongWShiLQA/QC issues to aid regulatory acceptance of microarray gene expression dataEnviron Mol Mutagen200748534935317567852
- HackettJLGutmanSIIntroduction to the Food and Drug Administration (FDA) regulatory processJ Proteome Res2005441110111316083260
- ImbeaudSAuffrayCThe ‘39 steps’ in gene expression profiling: Critical issues and proposed best practices for microarray experimentsDrug Discov Today200510171175118216182210
- National Cancer InstituteNCI Best Practices for Biospecimen ResourcesBethesda, MDUnited States National Cancer Institute2010 Available from: http://www.allirelandnci.com/pdf/NCI_Best_Practices_060507.pdf. Accessed August 18, 2011.
- FoxPHendlerJChanging the equation on scientific data visualizationScience2011331601870570821311008
- JenningsLVan DeerlinVMGulleyMLRecommended principles and practices for validating clinical molecular pathology testsArch Pathol Lab Med2009133574375519415949
- BurdEMValidation of laboratory-developed molecular assays for infectious diseasesClin Microbiol Rev201023355057620610823
- KohlMDevelopment and validation of predictive molecular signaturesCurr Mol Med201010217317920196729
- ArcherKJMasVRO’BrienTRPfeifferRLumNLFisherRAQuality assessment of microarray data in a multicenter studyDiagn Mol Pathol2009181344319214110
- BammlerTBeyerRPBhattacharyaSStandardizing global gene expression analysis between laboratories and across platformsNat Methods20052535135615846362
- CoyleVMJohnstonPGGenomic markers for decision making: What is preventing us from using markers?Nat Rev Clin Oncol201072909720010899
- ShackSGene expression profiling of tissues and cell lines: A dual-color microarray methodMethods Mol Biol201170012514321204031
- OberthuerAJuraevaDLiLComparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patientsPharmacogenomics J201010425826620676065
- PattersonTALobenhoferEKFulmer-SmentekSBPerformance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) projectNat Biotechnol20062491140115016964228
- HollandNTSmithMTEskenaziBBastakiMBiological sample collection and processing for molecular epidemiological studiesMutat Res2003543321723412787814
- De CeccoLMusellaVVeneroniSImpact of biospecimens handling on biomarker research in breast cancerBMC Cancer2009940919930681
- LippiGChanceJJChurchSPreanalytical quality improvement: From dream to realityClin Chem Lab Med20114971113112621517699
- PlebaniMErrors in clinical laboratories or errors in laboratory medicine?Clin Chem Lab Med200644675075916729864
- SchmittMMengeleKSchuerenEEuropean Organisation for Research and Treatment of Cancer (EORTC) Pathobiology Group standard operating procedure for the preparation of human tumour tissue extracts suited for the quantitative analysis of tissue-associated biomarkersEur J Cancer200743583584417321128
- DrubinDSmithJSLiuWZhaoWChaseGAClawsonGAComparison of cryopreservation and standard needle biopsy for gene expression profiling of human breast cancer specimensBreast Cancer Res Treat2005901939615770532
- JochumsenKMTanQDahlgaardJKruseTAMogensenORNA quality and gene expression analysis of ovarian tumor tissue undergoing repeated thaw-freezingExp Mol Pathol20078219510216842777
- VartanianKSlottkeRJohnstoneTGene expression profiling of whole blood: Comparison of target preparation methods for accurate and reproducible microarray analysisBMC Genomics2009101219123946
- RainenLArbiqueJCAsthanaDClinical Laboratory Standards Institute Document MM13-A: Collection, transport, preparation, and storage of specimens for molecular methods approved guidelineWayne, PAClinical and Laboratory Standards Institute2005
- Leyland-JonesBRAmbrosoneCBBartlettJRecommendations for collection and handling of specimens from group breast cancer clinical trialsJ Clin Oncol200826345638564418955459
- MooreHMKellyABJewellSDBiospecimen Reporting for Improved Study Quality (BRISQ)J Proteome Res20111083429343821574648
- WilliamsMAStabilizing the code-methods to preserve RNA prove their worthBiomark Insights2010513914321151590
- AsareALKolchinskySAGaoZDifferential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolationBMC Genomics2008947418847473
- MathesonLADuongTTRosenbergAMYeungRSAssessment of sample collection and storage methods for multicenter immunologic research in childrenJ Immunol Methods20083391828918771669
- DebeySZanderTBrorsBPopovAEilsRSchultzeJLA highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trialsGenomics200687565366416387473
- ShouJDotsonCQianHROptimized blood cell profiling method for genomic biomarker discovery using high-density microarrayBiomarkers200510431032016191486
- WeberDGCasjensSRozynekPAssessment of mRNA and microRNA stabilization in peripheral human blood for multicenter studies and biobanksBiomark Insights201059510220981139
- HewittSMLewisFACaoYTissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissueArch Pathol Lab Med2008132121929193519061293
- DashAMaineIPVaramballySShenRChinnaiyanAMRubinMAChanges in differential gene expression because of warm ischemia time of radical prostatectomy specimensAm J Pathol200216151743174812414521
- FerrueloAEl-AssarMLorenteJATranscriptional profiling and genotyping of degraded nucleic acids from autopsy tissue samples after prolonged formalin fixation timesInt J Clin Exp Pathol20114215616121326810
- RoepmanPde KoningEvan LeenenDDissection of a metastatic gene expression signature into distinct componentsGenome Biol2006712R11717156469
- Macabeo-OngMGinzingerDGDekkerNEffect of duration of fixation on quantitative reverse transcription polymerase chain reaction analysesMod Pathol200215997998712218216
- ChungJYHewittSMAn optimized RNA extraction method from archival formalin-fixed paraffin-embedded tissueMethods Mol Biol2010611192719960319
- BudcziesJWeichertWNoskeAGenome-wide gene expression profiling of formalin-fixed paraffin-embedded breast cancer core biopsies using microarraysJ Histochem Cytochem201159214615721339180
- SalehAZainRBHussainiHTranscriptional profiling of oral squamous cell carcinoma using formalin-fixed paraffin-embedded samplesOral Oncol201046537938620371203
- TonCCVartanianNChaiXGene expression array testing of FFPE archival breast tumor samples: An optimized protocol for WG-DASL sample preparationBreast Cancer Res Treat2011125387988320842525
- ChungJYBraunschweigTWilliamsRFactors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissueJ Histochem Cytochem200856111033104218711211
- ParkerJSMullinsMCheangMCSupervised risk predictor of breast cancer based on intrinsic subtypesJ Clin Oncol20092781160116719204204
- AbduevaDWingMSchaubBTricheTDavicioniEQuantitative expression profiling in formalin-fixed paraffin-embedded samples by Affymetrix microarraysJ Mol Diagn201012440941720522636
- DuenwaldSZhouMWangYDevelopment of a microarray platform for FFPET profiling: Application to the classification of human tumorsJ Transl Med200976519638234
- MittempergherLde RondeJJNieuwlandMGene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissuePLoS One201162e1716321347257
- RobertsLBowersJSensingerKLisowskiAGettsRAndersonMGIdentification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profilingGenomics200994534134819660539
- CoxMLSchrayCLLusterCNAssessment of fixatives, fixation, and tissue processing on morphology and RNA integrityExp Mol Pathol200680218319116332367
- CoxMLEddySMStewartZSInvestigating fixative-induced changes in RNA quality and utility by microarray analysisExp Mol Pathol200884215617218291364
- LawsonMHRasslDMCummingsNMTissue banking of diagnostic lung cancer biopsies for extraction of high quality RNAJ Thorac Oncol20105795696320512072
- MedeirosFRiglCTAndersonGGBeckerSHHallingKCTissue handling for genome-wide expression analysis: A review of the issues, evidence, and opportunitiesArch Pathol Lab Med2007131121805181618081440
- HessCDenkersFOssenkoppeleGGene expression profiling of minimal residual disease in acute myeloid leukaemia by novel multiplex-PCR-based methodLeukemia200418121981198815470488
- WangSWangLZhuTImprovement of tissue preparation for laser capture microdissection: Application for cell type-specific miRNA expression profiling in colorectal tumorsBMC Genomics20101116320219115
- LuttgesJHahnSAHeidenblutAMManual microdissection combined with antisense RNA-longSAGE for the analysis of limited cell numbersMethods Mol Biol201057613515419882261
- MojicaWDSykesDEConroyJGaileDFangXNowakNA comparative analysis of two tissue procurement approaches for the genomic profiling of clinical colorectal cancer samplesInt J Colorectal Dis200823111089109818629512
- MojicaWDSteinLHawthornLUniversal Reference RNA is not a representative normal sample for oligonucleotide microarray studiesPathol Oncol Res20081432435118553159
- MojicaWDSteinLHawthornLAn exfoliation and enrichment strategy results in improved transcriptional profiles when compared to matched formalin fixed samplesBMC Clin Pathol20077717683544
- BurgemeisterRNucleic acids extraction from laser microdissected FFPE tissue sectionsMethods Mol Biol201172411712921370010
- ShiLPerkinsRGFangHTongWReproducible and reliable microarray results through quality control: Good laboratory proficiency and appropriate data analysis practices are essentialCurr Opin Biotechnol2008191101818155896
- ShiLReidLHJonesWDThe MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurementsNat Biotechnol20062491151116116964229
- NovoradovskayaNWhitfieldMLBasehoreLSUniversal reference RNA as a standard for microarray experimentsBMC Genomics2004512015113400
- AuerHLyianarachchiSNewsomDKlisovicMIMarcucciGKornackerKChipping away at the chip bias: RNA degradation in microarray analysisNat Genet200335429229314647279
- VandesompeleJDe PreterKPattynFAccurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genesGenome Biol200237 RESEARCH0034
- HellemansJMortierGDe PaepeASpelemanFVandesompeleJqBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR dataGenome Biol200782R1917291332
- BeckerCHammerle-FickingerARiedmaierIPfafflMWmRNA and microRNA quality control for RT-qPCR analysisMethods201050423724320079844
- DevonshireASElaswarapuRFoyCAEvaluation of external RNA controls for the standardisation of gene expression biomarker measurementsBMC Genomics20101166221106083
- BakerSCBauerSRBeyerRPThe external RNA controls consortium: A progress reportNat Methods200521073173416179916
- Invitrogen. Available from: www.invitrogen.com. Accessed May 7, 2011.
- VWR International Available from: https://ca.vwr.com. Accessed August 25, 2011.
- FanXFangHHongHPerkinsRShiLTongWCorrelation analysis of external RNA controls reveals its utility for assessment of microarray assayAnal Biochem2009385220320719059192
- WalterMHoneggerASchweizerRPothsSBoninMUtilization of AFFX spike-in control probes to monitor sample identity throughout Affymetrix GeneChip Array processingBiotechniques201048537137820569210
- StaalFJCarioGCazzanigaGConsensus guidelines for microarray gene expression analyses in leukemia from three European leukemia networksLeukemia20062081385139216761018
- RudloffUBhanotUGeraldWBiobanking of human pancreas cancer tissue: Impact of ex-vivo procurement times on RNA qualityAnn Surg Oncol20101782229223620162455
- BotlingJMickePBiobanking of fresh frozen tissue from clinical surgical specimens: Transport logistics, sample selection, and histologic characterizationMethods Mol Biol201167529930620949397
- BotlingJMickePFresh frozen tissue: RNA extraction and quality controlMethods Mol Biol201167540541320949406
- BotlingJEdlundKSegerstenUImpact of thawing on RNA integrity and gene expression analysis in fresh frozen tissueDiagn Mol Pathol2009181445219214109
- VermeulenJDerveauxSLefeverSRNA pre-amplification enables large-scale RT-qPCR gene-expression studies on limiting sample amountsBMC Res Notes2009223519930725
- Gonzalez-RocaEGarcia-AlbenizXRodriguez-MuleroSGomisRRKornackerKAuerHAccurate expression profiling of very small cell populationsPLoS One2010512e1441821203435
- CorbiFCInaokaRJFelixRSComparative expression of a set of genes to an internal housekeeping control in CDNA amplified and not amplified by PolyAPCR in non-Hodgkin’s lymphoma samples obtained from fine-needle aspiration cytologyDiagn Mol Pathol2010191404420186011
- FerreiraENMaschiettoMSilvaSDBrentaniHCarraroDMEvaluation of quantitative rt-PCR using nonamplified and amplified RNADiagn Mol Pathol2010191455320186012
- SpurgeonSLJonesRCRamakrishnanRHigh throughput gene expression measurement with real time PCR in a microfluidic dynamic arrayPLoS One200832e166218301740
- GlavesPDTugwoodJDGeneration and analysis of transcriptomics dataMethods Mol Biol201169116718520972753
- LippaKADuewerDLSalitMLGameLCaustonHCExploring the use of internal and external controls for assessing microarray technical performanceBMC Res Notes2010334921189145
- FengLLiuHLiuYPower of deep sequencing and agilent microarray for gene expression profiling studyMol Biotechnol201045210111020432071
- CanalesRDLuoYWilleyJCEvaluation of DNA microarray results with quantitative gene expression platformsNat Biotechnol20062491115112216964225
- CoppéeJYDo DNA microarrays have their future behind them?Microbes Infect20081091067107118662797
- Anonymous.Quality System (QS) Regulation/Medical Device Good Manufacturing PracticesSilver Spring, MDFood and Drug Administration2011 Available from: www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/PostmarketRequirements/QualitySystemsRegulations. Accessed May 7, 2011.
- International Organization for StandardizationISO 900 EssentialsGeneva, Switzerland Available from: www.iso.org/iso/iso_9000_essentials. Accessed May 7, 2011.
- BengtssonMStåhlbergARorsmanPKubistaMGene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levelsGenome Res200515101388139216204192
- RitchieMESilverJOshlackAA comparison of background correction methods for two-colour microarraysBioinformatics200723202700270717720982
- DurbinBPRockeDMVariance-stabilizing transformations for two-color microarraysBioinformatics200420566066715033873
- FanJNiuYSelection and validation of normalization methods for c-DNA microarrays using within-array replicationsBioinformatics200723182391239817660210
- McMullenPDMorimotoRIAmaralLANPhysically grounded approach for estimating gene expression from microarray dataProc Natl Acad Sci U S A201010731136901369520643961
- ShiLCampbellGJonesWDThe MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive modelsNat Biotechnol201028882783820676074
- HackettJLArcherJKGaigalasAKLaboratory Standards Institute Document MM12-A: Diagnostic nucleic acid microarrays approved guidelineWayne, PAClinical and Laboratory Standards Institute2006 Available from: http://www.clsi.org/source/orders/free/mm12AF.pdf. Accessed August 18, 2011.
- HubbleJDemeterJJinHImplementation of GenePattern within the Stanford Microarray DatabaseNucleic Acids Res.200937Database issueD89890118953035
- SimonRAnalysis of DNA microarray expression dataBest Pract Res Clin Haematol200922227128219698933
- ParryRMJonesWStokesTHk-Nearest neighbor models for microarray gene expression analysis and clinical outcome predictionPharmacogenomics J201010429230920676068
- MonzonFAMedeirosFLyons-WeilerMHennerWDIdentification of tissue of origin in carcinoma of unknown primary with a microarray-based gene expression testDiagn Pathol20105320205775
- SchultzKRBowmanWPAledoAImproved early event-free survival with imatinib in Philadelphia chromosome-positive acute lymphoblastic leukemia: A Children’s Oncology Group studyJ Clin Oncol200927315175518119805687
- IzraeliSApplication of genomics for risk stratification of childhood acute lymphoblastic leukaemia: From bench to bedside?Br J Haematol2010151211913120678159
- JelierRGoemanJJHettneKMSchuemieMJden DunnenJTt’HoenPALiterature-aided interpretation of gene expression data with the weighted global testBrief Bioinform292011 [Epub ahead of print.]
- GudgeonJMMcClainMRPalomakiGEWilliamsMSRapid ACCE: Experience with a rapid and structured approach for evaluating gene-based testingGenet Med20079747347817666894
- GulleyMLBrazielRMHallingKCClinical laboratory reports in molecular pathologyArch Pathol Lab Med2007131685286317550311
- SchiffGDHasanOKimSDiagnostic error in medicine: Analysis of 583 physician-reported errorsArch Intern Med2009169201881188719901140
- SotiriouCPiccartMJTaking gene-expression profiling to the clinic: When will molecular signatures become relevant to patient care?Nat Rev Cancer20077754555317585334
- Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working GroupRecommendations from the EGAPP Working Group: Can tumor gene expression profiling improve outcomes in patients with breast cancer?Genet Med2009111667319125125
- MookSBonnefoiHPruneriGDaily clinical practice of fresh tumour tissue freezing and gene expression profiling: Logistics pilot study preceding the MINDACT trialEur J Cancer20094571201120819232484
- National Comprehensive Cancer NetworkNCCN Chronic Myelogenous Leukemia Clinical Practice Guidelines in Oncology (Version 2.2011)2011 Available from: www.nccn.org. Accessed June 7, 2011.
- HarrisLFritscheHMennelRAmerican Society of Clinical Oncology 2007 update of recommendations for the use of tumor markers in breast cancerJ Clin Oncol200725335287521217954709
- National Comprehensive Cancer NetworkNCCN Breast Cancer Clinical Practice Guidelines in Oncology (Version 2.2011) Available from: www.nccn.org. Accessed June 7, 2011.
- RiversPADobalianAGerminarioFAA review and analysis of the clinical laboratory improvement amendment of 1988: Compliance plans and enforcement policyHealth Care Manage Rev20053029310215923911
- United States Food and Drug AdministrationUnited States Food and Drug Administration MicroArray Quality Control (MAQC) project Available from: http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/default.htm. Accessed June 7, 2011.
- FanXLobenhoferEKChenMConsistency of predictive signature genes and classifiers generated using different microarray platformsPharmacogenomics J201010424725720676064
- ShiWBessarabovaMDosymbekovDFunctional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genesPharmacogenomics J201010431032320676069
- TillinghastGWMicroarrays in the clinicNat Biotechnol201028881081220697405
- BustinSABeaulieuJFHuggettJMIQE precis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experimentsBMC Mol Biol2010117420858237
- College of American Pathologists Available from: www.cap.org. Accessed May 7, 2011.
- WarringtonJACorbisierPFeilotterHClinical Laboratory Standards Institute Document MM16-A: Use of external RNA controls in gene expression assays approved guidelineWayne, PAClinical and Laboratory Standards Institute2006
- WilsonJAZoccoliMAJacobsonJWClinical Laboratory Standards Institute Document MM17-A: Verification and validation of multiplex nucleic acid assays approved guidelineWayne, PAClinical and Laboratory Standards Institute2008
- ValdesRPayneDLinderMWGuidelines and recommendations for laboratory analysis and application of pharmacogenetics to clinical practiceWashington, DCNational Academy of Clinical Biochemistry2007
- SzecsiPBOdumLError tracking in a clinical biochemistry laboratoryClin Chem Lab Med200947101253125719663542
- FabbrettiGRisk management: Correct patient and specimen identification in a surgical pathology laboratory. The experience of Infermi Hospital, Rimini, ItalyPathologica201010239610121171512
- ValensteinPNAlpernGAKerenDFResponding to large-scale testing errorsAm J Clin Pathol2010133344044620154282
- StainesHGarcia-FernandezLPogothataRWallacePMacKayWVan LoonAMonitoring performance of nucleic acid-based diagnostic measurement system users by EQAAccreditation and Quality Assurance: Journal for Quality, Comparability and Reliability in Chemical Measurement2009145243252
- TholenDWBLBooneDJCooperWGClinical Laboratory Standards Institute document GP27-A2: Using proficiency testing to improve the clinical laboratory approved guideline2nd ed.Wayne, PAClinical and Laboratory Standards Institute2007
- MadejRMCaoZDolingerDLHallLNeuwaldPWilliamsLOClinical and Laboratory Standards Institute Document MM14-A: Proficiency testing (external quality assessment) for molecular methods approved guidelineWayne, PAClinical and Laboratory Standards Institute2005
- Quality Control for Molecular Diagnostics Available from: www.qcmd.org. Accessed May 7, 2011.
- SarewitzSJGeorgeHMillerWGTholenDWValensteinPNClinical Laboratory Standards Institute Document GP29-A2: Assessment of laboratory tests when proficiency testing is not available approved guideline2nd ed.Wayne, PAClinical and Laboratory Standards Institute2008
- Association for Molecular PathologyAMP Test Directory Available from: www.amptestdirectory.org. Accessed May 7, 2011.
- National Center for Biotechnology InformationGeneTests Available from: www.genetests.org. Accessed May 7, 2011.
- BildAHParkerJSGustafsonAMAn integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancerBreast Cancer Res2009114R5519638211
- HuZFanCLivasyCA compact VEGF signature associated with distant metastases and poor outcomesBMC Med20097919291283
- HuangJShiWZhangJGenomic indicators in the blood predict drug-induced liver injuryPharmacogenomics J201010426727720676066