Featured Publications
Extrachromosomal DNA amplifications in cancer
Yi E, Chamorro González R, Henssen A, Verhaak R. Extrachromosomal DNA amplifications in cancer. Nature Reviews Genetics 2022, 23: 760-771. PMID: 35953594, PMCID: PMC9671848, DOI: 10.1038/s41576-022-00521-5.Peer-Reviewed Original ResearchConceptsExtrachromosomal DNA amplificationsNew therapeutic vulnerabilitiesCopy number heterogeneityEpigenetic architectureDNA amplificationCell divisionNuclear bodiesMost cancer typesNumber heterogeneityRegulatory landscapeTherapeutic vulnerabilitiesFunctional impactCancer typesDriver alterationsCircular structureEcDNAsChromatinizationChromosomesGenesAmplificationEcDNARecent investigationsEnhancerDeregulationCancer
2024
Oncogenic composite mutations can be predicted by co‐mutations and their chromosomal location
Küçükosmanoglu A, van der Borden C, de Boer L, Verhaak R, Noske D, Wurdinger T, Radonic T, Westerman B. Oncogenic composite mutations can be predicted by co‐mutations and their chromosomal location. Molecular Oncology 2024, 18: 2407-2422. PMID: 38757376, PMCID: PMC11459034, DOI: 10.1002/1878-0261.13636.Peer-Reviewed Original ResearchComposite mutationCo-mutationsMutation-specific drugsCell line dataChromosomal locationSub-clonal populationsGenetic heterogeneitySub-clonesTherapy resistanceSelection pressureGenetic eventsStratify patientsKRAS geneResistance-causing mutationsCancer patientsBiopsy samplesMutationsPatientsGenesPrecision medicineTherapyRiskChromosomeBiopsyBRAF
2023
EPCO-34. IMAGE-BASED PHENOTYPIC HIGH-CONTENT CRISPR-CAS9 SCREEN FOR CHARACTERIZING CANCER DRIVERS IN PEDIATRIC HIGH-GRADE GLIOMA
Amin S, Gujar A, Yi E, Kang W, Costa M, Gabriel P, Sjogren G, Maher L, Lee C, Robson P, Dickinson P, Packer R, Courtois E, Verhaak R. EPCO-34. IMAGE-BASED PHENOTYPIC HIGH-CONTENT CRISPR-CAS9 SCREEN FOR CHARACTERIZING CANCER DRIVERS IN PEDIATRIC HIGH-GRADE GLIOMA. Neuro-Oncology 2023, 25: v131-v131. PMCID: PMC10639707, DOI: 10.1093/neuonc/noad179.0497.Peer-Reviewed Original ResearchKnockout phenotypesWhole genome sequencing datasetsPediatric high-grade gliomasCancer Dependency MapCancer aneuploidyCell morphological featuresKnockout screensOntology analysisCancer driversSequencing datasetsHigh-content screening systemTumor suppressorFocal amplificationDriver genesGenomic landscapeHigh-grade glioma cell linesGenesLive cell imagesGlioma cell linesCell membraneDependency MapSingle cellsApoptotic cellsCell linesCRISPR
2012
Studying a Complex Tumor
Zheng S, Chheda M, Verhaak R. Studying a Complex Tumor. The Cancer Journal 2012, 18: 107-114. PMID: 22290264, PMCID: PMC3342695, DOI: 10.1097/ppo.0b013e3182431c57.Peer-Reviewed Original ResearchConceptsGenomic alterationsRecurrent genomic alterationsDNA copy numberGenomic studiesGenomic researchCopy numberExpression signaturesGenomic abnormalitiesGlioblastoma multiforme samplesExpression subtypesNew insightsGenesGlioblastoma multiformeGlioblastoma multiforme therapyHeterogeneous diseaseHigh specificityAlterationsTP53IDH1Identification