2019
Longitudinal molecular trajectories of diffuse glioma in adults
Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW. Longitudinal molecular trajectories of diffuse glioma in adults. Nature 2019, 576: 112-120. PMID: 31748746, PMCID: PMC6897368, DOI: 10.1038/s41586-019-1775-1.Peer-Reviewed Original ResearchMeSH KeywordsAdultChromosomes, Human, Pair 1Chromosomes, Human, Pair 19Disease ProgressionGliomaHumansIsocitrate DehydrogenaseMutationPolymorphism, Single NucleotideRecurrenceConceptsAdult patientsDiffuse gliomasRecurrent gliomaOverall survivalPoor outcomeCurrent therapiesChromosome arms 1p/19qAcquired alterationsMajor subtypesTherapeutic resistanceGliomasGlioma developmentGene alterationsIDH mutationsGlioma subtypesPatientsHypermutator phenotypeDriver genesSubtypesClinical annotationSurvivalSubclonal selectionCell cycleAlterationsLittle evidence
2017
TumorFusions: an integrative resource for cancer-associated transcript fusions
Hu X, Wang Q, Tang M, Barthel F, Amin S, Yoshihara K, Lang F, Martinez-Ledesma E, Lee S, Zheng S, Verhaak R. TumorFusions: an integrative resource for cancer-associated transcript fusions. Nucleic Acids Research 2017, 46: gkx1018-. PMID: 29099951, PMCID: PMC5753333, DOI: 10.1093/nar/gkx1018.Peer-Reviewed Original ResearchConceptsTranscript fusionsGene fusionsWhole-genome sequencing dataSomatic DNA rearrangementsTranscript-level expressionGenome sequencing dataGene annotationCopy number levelsCancer samplesCancer Genome AtlasDNA rearrangementsUniform pipelineFunctional fusionSequencing dataIntegrative resourceLevel expressionPartner genesGenome AtlasChromosomal alterationsMutational patternsCancer typesFusion transcriptsNon-neoplastic samplesMolecular aberrationsNumber levels
2011
The dChip survival analysis module for microarray data
Amin S, Shah P, Yan A, Adamia S, Minvielle S, Avet-Loiseau H, Munshi N, Li C. The dChip survival analysis module for microarray data. BMC Bioinformatics 2011, 12: 72. PMID: 21388547, PMCID: PMC3068974, DOI: 10.1186/1471-2105-12-72.Peer-Reviewed Original ResearchMeSH KeywordsBreast NeoplasmsCluster AnalysisGene Expression ProfilingHumansKaplan-Meier EstimateOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideProportional Hazards ModelsSoftwareConceptsAnalysis moduleUser-friendly wayDemonstration dataMicroarray data analysisAnalysis functionsFast computationSoftware packageSoftwareSignificant chromosome regionsMicroarray dataMinimal learning curveGene expressionDChip softwareModuleGenome-wide copy number alterationsData analysisSNP array dataSurvival gene signaturesCopy number dataChromosome displayContext of genesUsersCopy number alterationsChromosome regionsClustering