2022
Double knockout CRISPR screen for cancer resistance to T cell cytotoxicity
Park J, Codina A, Ye L, Lam S, Guo J, Clark P, Zhou X, Peng L, Chen S. Double knockout CRISPR screen for cancer resistance to T cell cytotoxicity. Journal Of Hematology & Oncology 2022, 15: 172. PMID: 36456981, PMCID: PMC9716677, DOI: 10.1186/s13045-022-01389-y.Peer-Reviewed Original ResearchConceptsT cell cytotoxicityCell cytotoxicityT cell killingTumor suppressorCancer patientsImmune responseAvailable agentsSurvival analysisClinical patientsCancer treatmentCancer cellsCancer resistanceDirect targetingPotential new conceptCancer mutationsPatientsCell killingNormal samplesResistance pathwaysCellular responsesSuch resistanceCytotoxicityResistance genes
2021
OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers
Zhang Y, Yao X, Zhou H, Wu X, Tian J, Zeng J, Yan L, Duan C, Liu H, Li H, Chen K, Hu Z, Ye Z, Xu H. OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers. Nucleic Acids Research 2021, 50: d1340-d1347. PMID: 34554251, PMCID: PMC8728274, DOI: 10.1093/nar/gkab851.Peer-Reviewed Original ResearchConceptsAlternative splicingCancer-specific splicing eventsDifferential alternative splicingHuman cancersTCGA tumor samplesSplicing differencesSplicing eventsProtein complexityAdjacent normal samplesSplicingGene expressionSplicing dataNormal samplesAbnormal splicingIntegrative viewMRNA levelsDifferential analysisTumor samplesTranscripts
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
2017
RNA‐seq Based Transcription Characterization of Fusion Breakpoints as a Potential Estimator for Its Oncogenic Potential
Gu J, Chukhman M, Lu Y, Liu C, Liu S, Lu H. RNA‐seq Based Transcription Characterization of Fusion Breakpoints as a Potential Estimator for Its Oncogenic Potential. BioMed Research International 2017, 2017: 9829175. PMID: 29181411, PMCID: PMC5664375, DOI: 10.1155/2017/9829175.Peer-Reviewed Original ResearchConceptsOncogenic potentialFusion mutationsFusion geneHigh-throughput sequencing technologyClonal evolution theoryTranscriptome sequencing datasetsLarger clonal sizeSequencing technologiesSequencing datasetsGene fusionsClone ratioGenesFusion breakpointsGenomic alterationsMutationsFunctional featuresNeoplastic cellsTMPRSS2-ERGNormal samplesClonal sizeTumor samplesRecent studiesCellsEvolution theoryBreakpoints
2016
Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival – Evidence from TCGA Pan-Cancer Data
Huang X, Stern DF, Zhao H. Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival – Evidence from TCGA Pan-Cancer Data. Scientific Reports 2016, 6: 20567. PMID: 26837275, PMCID: PMC4738355, DOI: 10.1038/srep20567.Peer-Reviewed Original ResearchConceptsPatient survivalTumor cell contaminationField cancerization effectNormal samplesCancer patient survivalNormal tissue samplesSitu immunizationCancer Genome AtlasCancer patientsPatient progressionNormal controlsTumorsNormal tissuesPan-cancer dataTissue samplesGenome AtlasCancer studiesDisease etiologyCell contaminationPatientsPathway analysisTCGA pan-cancer dataSurvivalTranscriptional profilesPotential benefits
2014
Whole-Exome Sequencing Characterizes the Landscape of Somatic Mutations and Copy Number Alterations in Adrenocortical Carcinoma
Juhlin CC, Goh G, Healy JM, Fonseca AL, Scholl UI, Stenman A, Kunstman JW, Brown TC, Overton JD, Mane SM, Nelson-Williams C, Bäckdahl M, Suttorp AC, Haase M, Choi M, Schlessinger J, Rimm DL, Höög A, Prasad ML, Korah R, Larsson C, Lifton RP, Carling T. Whole-Exome Sequencing Characterizes the Landscape of Somatic Mutations and Copy Number Alterations in Adrenocortical Carcinoma. The Journal Of Clinical Endocrinology & Metabolism 2014, 100: e493-e502. PMID: 25490274, PMCID: PMC5393505, DOI: 10.1210/jc.2014-3282.Peer-Reviewed Original ResearchConceptsAdrenocortical carcinomaSomatic mutationsCopy number alterationsNumber alterationsNonsynonymous somatic mutationsWnt pathway dysregulationHomozygous deletionMajority of casesPotential disease-causing mutationsWhole-exome sequencingUnderlying somatic mutationsLethal malignancyPathway dysregulationTumorsExome sequencingFocal CNAsDisease-causing mutationsCarcinomaTERT locusZNRF3Recurrent CNAsAlterationsNormal samplesTP53Unknown rolePomalidomide Modulates Transcription Networks Regulating Human Erythropoiesis and Globin Switching: Implications for Treatment of Hemoglobinopathies
Dulmovits B, Appiah-Kubi A, Papoin J, Gould M, An X, Mohandas N, Gallagher P, Lipton J, Liu J, Blanc L. Pomalidomide Modulates Transcription Networks Regulating Human Erythropoiesis and Globin Switching: Implications for Treatment of Hemoglobinopathies. Blood 2014, 124: 1375. DOI: 10.1182/blood.v124.21.1375.1375.Peer-Reviewed Original ResearchSickle cell diseaseWestern blot analysisΓ-globin productionSide effectsDay 6Painful vaso-occlusive crisesSecond-generation immunomodulatory drugMay-Grunwald Giemsa stainingVaso-occlusive crisisSignificant side effectsQRT-PCRCurrent treatment approachesHbF productionErythroid differentiationBlot analysisFlow cytometric analysisRed cell sicklingMechanism of actionImmunomodulatory drugsNormal samplesPeripheral bloodPharmacologic interventionsCulture systemCell diseaseSimilar dose
2012
Molecular diagnostic testing for Klinefelter syndrome and other male sex chromosome aneuploidies
Hager K, Jennings K, Hosono S, Howell S, Gruen JR, Rivkees SA, Tartaglia NR, Rinder HM. Molecular diagnostic testing for Klinefelter syndrome and other male sex chromosome aneuploidies. International Journal Of Pediatric Endocrinology 2012, 2012: 8. PMID: 22524164, PMCID: PMC3411476, DOI: 10.1186/1687-9856-2012-8.Peer-Reviewed Original ResearchSex chromosome aneuploidyChromosome aneuploidyEarly mitotic divisionsHigh-throughput potentialAutosome ratiosDNA sequencing methodsBiallelic SNPsX chromosomeMolecular diagnostic assaysMitotic divisionGenomic DNASequencing methodsMarker dataDiagnostic assaysBuccal swab samplesPCR productsPyrosequencingKaryotypeAneuploidyDNANormal samplesMolecular diagnostic testingAssaysChromosomesMarkers
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