2022
How often is each gene mutated within the cancer patient population?
Mendiratta G, Jones M, Stites E. How often is each gene mutated within the cancer patient population? Molecular & Cellular Oncology 2022, 9: 2065176. PMID: 35529901, PMCID: PMC9067461, DOI: 10.1080/23723556.2022.2065176.Peer-Reviewed Original Research
2020
Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries
Pinoli P, Stamoulakatou E, Nguyen A, Martínez M, Ceri S. Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries. PLOS ONE 2020, 15: e0227180. PMID: 31945090, PMCID: PMC6964824, DOI: 10.1371/journal.pone.0227180.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsBinding SitesCCCTC-Binding FactorChromosomes, Human, Pair 11DNA Copy Number VariationsDNA MethylationDNA Mutational AnalysisEpigenesis, GeneticExonsFemaleGene Expression Regulation, NeoplasticGenome, HumanHumansInsulator ElementsMutation RateNeoplasmsPoint MutationPromoter Regions, GeneticConceptsCTCF motifsCopy number alterationsSomatic mutationsAbnormal methylationCTCF binding sitesCopy number alteration eventsAnalysis of somatic mutationsMatched normal samplesCancer typesCTCF bindingOncogene dysregulationMutation enrichmentPan-cancer analysisPositive selectionEpigenetic alterationsIn-boundaryGenomic alterationsMotifMutational signaturesBinding sitesMutationsCTCFPan-CancerCopyNormal samples
2019
Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker
Dong S, Li W, Wang L, Hu J, Song Y, Zhang B, Ren X, Ji S, Li J, Xu P, Liang Y, Chen G, Lou J, Yu W. Histone-Related Genes Are Hypermethylated in Lung Cancer and Hypermethylated HIST1H4F Could Serve as a Pan-Cancer Biomarker. Cancer Research 2019, 79: 6101-6112. PMID: 31575549, DOI: 10.1158/0008-5472.can-19-1019.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorBronchoalveolar Lavage FluidCell Line, TumorCpG IslandsDatasets as TopicDNA MethylationEarly Detection of CancerFemaleGene Expression Regulation, NeoplasticGenetic LociHistonesHumansLung NeoplasmsMaleMiddle AgedPromoter Regions, GeneticWhole Genome SequencingConceptsHistone-related genesWhole-genome DNA methylation analysisDNA methylation analysisHistone genesCancer Genome AtlasMethylation signaturesMethylation analysisGenesGenome AtlasPan-CancerBronchoalveolar lavage fluid samplesHypermethylationLavage fluid samplesEarly cancer diagnosisTCGA datasetPan-cancer biomarkerLung cancerTCGACancer-related deathsLung cancer cohortMethylationCancer cohortTumor typesTumorigenesisCancer diagnosis
2017
Reliable Pan-Cancer Microsatellite Instability Assessment by Using Targeted Next-Generation Sequencing Data
Middha S, Zhang L, Nafa K, Jayakumaran G, Wong D, Kim H, Sadowska J, Berger M, Delair D, Shia J, Stadler Z, Klimstra D, Ladanyi M, Zehir A, Hechtman J. Reliable Pan-Cancer Microsatellite Instability Assessment by Using Targeted Next-Generation Sequencing Data. JCO Precision Oncology 2017, 2017: 1-17. PMID: 30211344, PMCID: PMC6130812, DOI: 10.1200/po.17.00084.Peer-Reviewed Original ResearchPolymerase chain reactionMicrosatellite instability statusColorectal cancerMicrosatellite instabilityResponse to immune checkpoint inhibitorsMSI-HImmune checkpoint inhibitorsMMR immunohistochemistryAdvanced solid cancersManagement of patientsSolid cancer typesTargeted NGS dataCheckpoint inhibitorsClinical NGS assayEndometrioid cancerMutational burdenSolid cancersNGS assayMSI polymerase chain reactionCancer typesCancerMSI-H tumorsPan-CancerNGS dataChain reaction
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