2011
Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies
Parisi F, Ariyan S, Narayan D, Bacchiocchi A, Hoyt K, Cheng E, Xu F, Li P, Halaban R, Kluger Y. Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies. BMC Genomics 2011, 12: 230. PMID: 21569352, PMCID: PMC3114747, DOI: 10.1186/1471-2164-12-230.Peer-Reviewed Original ResearchConceptsCopy number statusMelanoma samplesSingle nucleotide polymorphism arrayHigh-throughput technologiesNext-generation sequencing dataHigh-throughput techniquesCopy number profilesHigh-throughput assaysNucleotide polymorphism arrayNumber statusCopy number alterationsTranscriptome sequencingNext-generation sequencingRNA-seqSingle exonSNP arraySequencing dataMelanoma cell linesNumerous aberrationsPolymorphism arrayNovel aberrationsNumber alterationsSubclonal heterogeneitySitu hybridizationAllelic imbalancePlasma Markers for Identifying Patients with Metastatic Melanoma
Kluger HM, Hoyt K, Bacchiocchi A, Mayer T, Kirsch J, Kluger Y, Sznol M, Ariyan S, Molinaro A, Halaban R. Plasma Markers for Identifying Patients with Metastatic Melanoma. Clinical Cancer Research 2011, 17: 2417-2425. PMID: 21487066, PMCID: PMC3415234, DOI: 10.1158/1078-0432.ccr-10-2402.Peer-Reviewed Original ResearchMeSH KeywordsAgedAntigens, CDBiomarkers, TumorCell Adhesion MoleculesEnzyme-Linked Immunosorbent AssayExtracellular Matrix ProteinsFemaleGlycoproteinsGrowth Differentiation Factor 15HumansIntercellular Adhesion Molecule-1L-Lactate DehydrogenaseMaleMelanomaMiddle AgedNeoplasm MetastasisNeoplasm ProteinsNeoplasm Recurrence, LocalNeoplasm StagingNerve Growth FactorsPrognosisReproducibility of ResultsS100 Calcium Binding Protein beta SubunitS100 ProteinsSensitivity and SpecificityTissue Inhibitor of Metalloproteinase-1ConceptsGenome-wide gene expression dataGene expression dataHigh expression levelsLevels of proteinExpression dataExpression levelsProteinMelanoma cellsStage I/II diseaseEqual-sized trainingMarkersGenesDisease recurrencePlasma markersMetastatic melanomaTIMP-1Lactate dehydrogenaseCEACAMsStage I/II patientsDehydrogenaseOsteopontinStage IV diseaseStage IV patientsMetastatic melanoma patientsGender-matched patients
2009
Genome-wide screen of promoter methylation identifies novel markers in melanoma
Koga Y, Pelizzola M, Cheng E, Krauthammer M, Sznol M, Ariyan S, Narayan D, Molinaro AM, Halaban R, Weissman SM. Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Research 2009, 19: 1462-1470. PMID: 19491193, PMCID: PMC2720187, DOI: 10.1101/gr.091447.109.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAdultAgedBiomarkers, TumorCells, CulturedCluster AnalysisCollagenCollagen Type IDNA MethylationFemaleGene Expression ProfilingGenome, HumanGenome-Wide Association StudyHSP20 Heat-Shock ProteinsHumansInfant, NewbornMaleMelanomaMetallothioneinMiddle AgedMolecular ChaperonesNuclear ProteinsNucleoplasminsOligonucleotide Array Sequence AnalysisPhosphoproteinsPromoter Regions, GeneticProteinsReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionSequence Analysis, DNATumor Cells, CulturedConceptsDifferential gene expressionGene expressionPromoter methylationGenome-wide promoter methylationGenome-wide integrative analysisPromoter CpG contentMethylation markersGenome-wide screenSequencing of bisulfiteTranscription start siteMelanoma cell strainsCell strainsTranscriptional machineryNovel genesEpigenetic modificationsDNA methylationIdentifies novel markersStart siteSnap-frozen tissuesCpG contentAdult melanocytesIntegrative analysisReal-time reverse transcriptase PCRHuman diseasesMethylation
2004
Automated Quantitative Analysis of HDM2 Expression in Malignant Melanoma Shows Association with Early-Stage Disease and Improved Outcome
Berger AJ, Camp RL, DiVito KA, Kluger HM, Halaban R, Rimm DL. Automated Quantitative Analysis of HDM2 Expression in Malignant Melanoma Shows Association with Early-Stage Disease and Improved Outcome. Cancer Research 2004, 64: 8767-8772. PMID: 15574789, DOI: 10.1158/0008-5472.can-04-1384.Peer-Reviewed Original ResearchConceptsMurine double minute 2Double minute 2Protein expressionMalignant melanomaMinute 2Early-stage diseaseTissue microarray cohortPotential tissue biomarkersCutaneous malignant melanomaValuable prognostic toolNormal skin samplesSkin cancer deathsMicroarray cohortAdvanced melanomaMetastatic lesionsCancer deathPrimary melanomaImproved outcomesExpression of HDM2Tissue biomarkersPrognostic toolBetter outcomesMelanoma lesionsAggressive natureMelanoma