2020
Mutations and Copy Number Alterations in IDH Wild-Type Glioblastomas Are Shaped by Different Oncogenic Mechanisms
Ülgen E, Karacan S, Gerlevik U, Can Ö, Bilguvar K, Oktay Y, Akyerli C, Yüksel Ş, Danyeli A, Tihan T, Sezerman OU, Yakıcıer MC, Pamir MN, Özduman K. Mutations and Copy Number Alterations in IDH Wild-Type Glioblastomas Are Shaped by Different Oncogenic Mechanisms. Biomedicines 2020, 8: 574. PMID: 33297360, PMCID: PMC7762325, DOI: 10.3390/biomedicines8120574.Peer-Reviewed Original ResearchUnderlying oncogenic mechanismsOncogenic mechanismsNumber alterationsDifferent oncogenic mechanismsDiffuse midline gliomaMismatch repair deficiencySingle nucleotide variationsWhole-exome sequencingIDH wild-type glioblastomaWild-type glioblastomaPrimary tumorMolecular subsetsBlood samplesMidline gliomaAdult diffuse gliomasHeterogenous groupWt glioblastomaCopy number alterationsGliomasRecurrenceExome sequencingDiffuse gliomasRepair deficiencyAlteration frequencyGenomic alterations
2019
Whole exome sequencing-based analysis to identify DNA damage repair deficiency as a major contributor to gliomagenesis in adult diffuse gliomas.
Ülgen E, Can Ö, Bilguvar K, Oktay Y, Akyerli CB, Danyeli AE, Yakıcıer MC, Sezerman OU, Pamir MN, Özduman K. Whole exome sequencing-based analysis to identify DNA damage repair deficiency as a major contributor to gliomagenesis in adult diffuse gliomas. Journal Of Neurosurgery 2019, 132: 1435-1446. PMID: 30952131, DOI: 10.3171/2019.1.jns182938.Peer-Reviewed Original ResearchDNA damage repair deficiencyDiffuse gliomasAdult diffuse gliomasMutational signaturesRepair deficiencyMicrosatellite instability statusSignature 1Mutational loadDDR gene mutationsDDR genesHigh mutational loadCancer Genome AtlasMolecular subsetsBlood samplesMSI statusSomatic mutational signaturesInstability statusSignificant associationLarger studyGlioma developmentTumorsGene mutationsGenome AtlasSignature 3TCGA data
2017
Longitudinal analysis of treatment-induced genomic alterations in gliomas
Erson-Omay EZ, Henegariu O, Omay SB, Harmancı AS, Youngblood MW, Mishra-Gorur K, Li J, Özduman K, Carrión-Grant G, Clark VE, Çağlar C, Bakırcıoğlu M, Pamir MN, Tabar V, Vortmeyer AO, Bilguvar K, Yasuno K, DeAngelis LM, Baehring JM, Moliterno J, Günel M. Longitudinal analysis of treatment-induced genomic alterations in gliomas. Genome Medicine 2017, 9: 12. PMID: 28153049, PMCID: PMC5290635, DOI: 10.1186/s13073-017-0401-9.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic AgentsChromosome AberrationsCombined Modality TherapyDisease ProgressionDNA Mismatch RepairDNA Mutational AnalysisDNA, NeoplasmExomeFemaleGeneral SurgeryGenome, HumanGenomicsGlioblastomaHumansImmunotherapyLongitudinal StudiesMiddle AgedMutationNeoplasm Recurrence, LocalPrecision MedicineRadiotherapyTreatment OutcomeConceptsWhole-exome sequencingMismatch repair deficiencyImmune checkpoint inhibitionMalignant brain tumorsMolecular changesLongitudinal analysisMedian survivalCheckpoint inhibitionSubsequent recurrenceMaximal resectionStandard treatmentBackgroundGlioblastoma multiformeBrain tumorsTumor-normal pairsFavorable responsePrimary GBMIndividual tumorsConclusionsOur studyPrecision therapyPersonalized treatmentGenomic profilingRepair deficiencyGenomic alterationsGenomic profilesTherapy
2016
Genomic characterization of sarcomatoid transformation in clear cell renal cell carcinoma
Bi M, Zhao S, Said JW, Merino MJ, Adeniran AJ, Xie Z, Nawaf CB, Choi J, Belldegrun AS, Pantuck AJ, Kluger HM, Bilgüvar K, Lifton RP, Shuch B. Genomic characterization of sarcomatoid transformation in clear cell renal cell carcinoma. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 2170-2175. PMID: 26864202, PMCID: PMC4776463, DOI: 10.1073/pnas.1525735113.Peer-Reviewed Original ResearchMeSH KeywordsAgedCarcinoma, Renal CellCell DedifferentiationDNA Mismatch RepairDNA-Binding ProteinsExomeFemaleGenes, p53HumansKidney NeoplasmsLoss of HeterozygosityMaleMiddle AgedMutationNuclear ProteinsOncogenesPolymorphism, Single NucleotidePrognosisTranscription FactorsTumor Suppressor ProteinsUbiquitin ThiolesteraseConceptsClear cell renal cell carcinomaCell renal cell carcinomaRenal cell carcinomaSarcomatoid elementsCarcinomatous elementsCell carcinomaSomatic single nucleotide variantsVon Hippel-Lindau tumor suppressorPoor-prognosis cancerTreatment of patientsTumor protein p53 (TP53) mutationsMismatch repair deficiencyRich interaction domain 1ASarcomatoid featuresPoor prognosisUnknown pathogenesisPolybromo-1TP53 mutationsP53 mutationsSarcomatoid transformationPan-cancer genesExome sequencingTumorsRepair deficiencyProtein 1