2013
Extraction and processing of circulating DNA from large sample volumes using methylation on beads for the detection of rare epigenetic events
Keeley B, Stark A, Pisanic TR, Kwak R, Zhang Y, Wrangle J, Baylin S, Herman J, Ahuja N, Brock MV, Wang TH. Extraction and processing of circulating DNA from large sample volumes using methylation on beads for the detection of rare epigenetic events. Clinica Chimica Acta 2013, 425: 169-175. PMID: 23911908, PMCID: PMC3963364, DOI: 10.1016/j.cca.2013.07.023.Peer-Reviewed Original ResearchDNA Methylation Biomarkers of Stool and Blood for Early Detection of Colon Cancer
Hong L, Ahuja N. DNA Methylation Biomarkers of Stool and Blood for Early Detection of Colon Cancer. Genetic Testing And Molecular Biomarkers 2013, 17: 401-406. PMID: 23406208, DOI: 10.1089/gtmb.2012.0478.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkersColonic NeoplasmsDNA MethylationEarly Detection of CancerFecesGenetic MarkersHumansPolymerase Chain ReactionConceptsColon cancerDNA methylation markersEarly detectionMethylation markersStool-based testsCurrent screening testsScreening complianceColorectal cancerGeneral populationDNA methylation biomarkersClinical availabilityScreening testCancerClinical researchHigh efficacyBloodMethylation biomarkersStoolMarkersMore investigationEarly stagesColonoscopyPatientsMortalityDiseaseKRAS G>A mutation favors poor tumor differentiation but may not be associated with prognosis in patients with curatively resected duodenal adenocarcinoma
Fu T, Guzzetta AA, Jeschke J, Vatapalli R, Dave P, Hooker CM, Morgan R, Iacobuzio‐Donahue C, Liu B, Ahuja N. KRAS G>A mutation favors poor tumor differentiation but may not be associated with prognosis in patients with curatively resected duodenal adenocarcinoma. International Journal Of Cancer 2013, 132: 2502-2509. PMID: 23065691, PMCID: PMC3579006, DOI: 10.1002/ijc.27910.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaBiomarkers, TumorCell DifferentiationDNA, NeoplasmDuodenal NeoplasmsFemaleHumansMaleMicrosatellite RepeatsMiddle AgedMutationNeoplasm Recurrence, LocalNeoplasm StagingPolymerase Chain ReactionPrognosisProto-Oncogene ProteinsProto-Oncogene Proteins p21(ras)Ras ProteinsSurvival RateConceptsPoor tumor differentiationKRAS GPositive lymph nodesDuodenal adenocarcinomaKRAS mutationsTumor differentiationMutation carriersDistant relapseLymph nodesMultivariate logistic regression analysisShorter relapse-free survivalFuture staging systemsRelapse-free survivalShorter overall survivalPossible prognostic roleLogistic regression analysisCurative resectionPoor OSOverall survivalPrognostic roleTumor characteristicsClinical outcomesClinicopathological characteristicsPoor prognosisPrognostic significance
2012
A pressure cooking-based DNA extraction from archival formalin-fixed, paraffin-embedded tissue
Chung JY, Yi JM, Xie R, Brown V, Lee O, Ahuja N, Braunschweig T, Hewitt SM. A pressure cooking-based DNA extraction from archival formalin-fixed, paraffin-embedded tissue. Analytical Biochemistry 2012, 425: 128-134. PMID: 22449494, PMCID: PMC3358925, DOI: 10.1016/j.ab.2012.03.012.Peer-Reviewed Original Research
2008
Epigenetic Inactivation of the Canonical Wnt Antagonist SRY-Box Containing Gene 17 in Colorectal Cancer
Zhang W, Glöckner S, Guo M, Machida EO, Wang DH, Easwaran H, Van Neste L, Herman JG, Schuebel KE, Watkins DN, Ahuja N, Baylin SB. Epigenetic Inactivation of the Canonical Wnt Antagonist SRY-Box Containing Gene 17 in Colorectal Cancer. Cancer Research 2008, 68: 2764-2772. PMID: 18413743, PMCID: PMC2823123, DOI: 10.1158/0008-5472.can-07-6349.Peer-Reviewed Original ResearchConceptsGene 17T-cell factor-dependent transcriptionHigh-mobility group transcription factorsFactor-dependent transcriptionMethylation-dependent silencingRegulation of developmentOverexpression of Sox17Cell linesCpG island hypermethylationWnt pathway activityPrecursor cell functionRepression domainHMG boxTranscription factorsDeletion analysisCpG islandsGene silencingDNA hypermethylationGene expressionPromoter regionEpigenetic inactivationCanonical WntGenetic changesIsland hypermethylationSOX17
2002
DNA Methylation and Environmental Exposures in Human Hepatocellular Carcinoma
Shen L, Ahuja N, Shen Y, Habib NA, Toyota M, Rashid A, Issa JP. DNA Methylation and Environmental Exposures in Human Hepatocellular Carcinoma. Journal Of The National Cancer Institute 2002, 94: 755-761. PMID: 12011226, DOI: 10.1093/jnci/94.10.755.Peer-Reviewed Original Research
1999
Aberrant methylation in gastric cancer associated with the CpG island methylator phenotype.
Toyota M, Ahuja N, Suzuki H, Itoh F, Ohe-Toyota M, Imai K, Baylin SB, Issa JP. Aberrant methylation in gastric cancer associated with the CpG island methylator phenotype. Cancer Research 1999, 59: 5438-42. PMID: 10554013.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAllelesCarrier ProteinsCpG IslandsCyclin-Dependent Kinase Inhibitor p16Gene Expression Regulation, NeoplasticHumansMethylationModels, GeneticMucous MembraneMutL Protein Homolog 1Neoplasm ProteinsNuclear ProteinsPhenotypePolymerase Chain ReactionStomach NeoplasmsCpG island methylator phenotype in colorectal cancer
Toyota M, Ahuja N, Ohe-Toyota M, Herman J, Baylin S, Issa J. CpG island methylator phenotype in colorectal cancer. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 8681-8686. PMID: 10411935, PMCID: PMC17576, DOI: 10.1073/pnas.96.15.8681.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAge FactorsCarrier ProteinsCloning, MolecularColorectal NeoplasmsCpG IslandsDNA MethylationDNA RepairGenes, p16Genes, Tumor SuppressorHumansMicrosatellite RepeatsMutL Protein Homolog 1Neoplasm ProteinsNuclear ProteinsPhenotypePolymerase Chain ReactionSulfitesTumor Cells, CulturedConceptsCpG island methylator phenotypeColorectal cancerMethylator phenotypeSporadic colorectal cancerMismatch repair deficiencyCpG islandsAge-dependent mannerNormal colonic cellsCpG island amplificationHigh incidenceColon cancerTHBS1 methylationNormal colonPromoter region CpG islandsSporadic tumorsCancerMicrosatellite instabilityColonic cellsTumor suppressor geneCpG island methylationRepair deficiencyCancer-specific mannerHMLH1 methylationCell linesTranscriptional inactivationIdentification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification.
Toyota M, Ho C, Ahuja N, Jair KW, Li Q, Ohe-Toyota M, Baylin SB, Issa JP. Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification. Cancer Research 1999, 59: 2307-12. PMID: 10344734.Peer-Reviewed Original Research5-MethylcytosineAdenocarcinomaChondroitin Sulfate ProteoglycansCloning, MolecularColorectal NeoplasmsCpG IslandsCytosineDNA MethylationDNA, NeoplasmDNA, RibosomalDNA-Binding ProteinsExonsEye ProteinsGenes, p16Homeobox Protein Nkx-2.5Homeodomain ProteinsHumansLectins, C-TypePaired Box Transcription FactorsPAX6 Transcription FactorPolymerase Chain ReactionRepressor ProteinsRNA, RibosomalSubtraction TechniqueTranscription FactorsTubulinVersicans