2021
Sequential filtering for clinically relevant variants as a method for clinical interpretation of whole exome sequencing findings in glioma
Ülgen E, Can Ö, Bilguvar K, Akyerli Boylu C, Kılıçturgay Yüksel Ş, Erşen Danyeli A, Sezerman OU, Yakıcıer MC, Pamir MN, Özduman K. Sequential filtering for clinically relevant variants as a method for clinical interpretation of whole exome sequencing findings in glioma. BMC Medical Genomics 2021, 14: 54. PMID: 33622343, PMCID: PMC7903763, DOI: 10.1186/s12920-021-00904-3.Peer-Reviewed Original ResearchConceptsTumor mutational burdenSomatic copy number alterationsWhole-exome sequencing findingsMicrosatellite instabilityGermline variantsClinical interpretationIndividual brain tumorsShort variantRecurrent tumorsMSI incidenceMutational burdenBrain tumorsLoss of heterozygosityPathway enrichment analysisPrimary gliomasClinical settingTumorsWES analysisCopy number alterationsTumor samplesSequencing findingsDiffuse gliomasClinical analysisGliomasChr10 loss
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
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
2014
Spontaneous tumour regression in keratoacanthomas is driven by Wnt/retinoic acid signalling cross-talk
Zito G, Saotome I, Liu Z, Ferro EG, Sun TY, Nguyen DX, Bilguvar K, Ko CJ, Greco V. Spontaneous tumour regression in keratoacanthomas is driven by Wnt/retinoic acid signalling cross-talk. Nature Communications 2014, 5: 3543. PMID: 24667544, PMCID: PMC3974217, DOI: 10.1038/ncomms4543.Peer-Reviewed Original ResearchConceptsTumor regressionRetinoic acidSquamous cell carcinomaSpontaneous tumor regressionMouse model systemCell carcinomaMalignant tumorsTherapeutic strategiesCutaneous keratoacanthomasKeratoacanthomaPhysiological mechanismsTumor growthHuman keratoacanthomaTumorsHair follicle regenerationCancer biologyFollicle regenerationRegressionDifferentiation programWntCarcinomaPathway