2024
13. AmpliconSuite: Analyzing focal amplifications in cancer genomes
Luebeck J, Huang E, Dameracharla B, Kim F, Liefeld T, Ahuja R, Prasad D, Prasad G, Kim S, Kim H, Bailey P, Verhaak R, Deshpande V, Reich M, Mischel P, Mesirov J, Bafna V. 13. AmpliconSuite: Analyzing focal amplifications in cancer genomes. Cancer Genetics 2024, 286: s5. DOI: 10.1016/j.cancergen.2024.08.015.Peer-Reviewed Original ResearchWhole-genome sequencingWhole-genome sequencing dataFocal amplificationCancer genomesStructural variationsAmplification of oncogenesExtrachromosomal DNACopy numberEcDNAGenomeOncogene amplificationAmpliconArchitectCancer progressionAmplificationAmplification typeTumor samplesBiocondaNextflowPCAWGGenePatternRobust identificationDNACCLESequenceOncogene
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