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
2021
Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription
Zhu Y, Gujar A, Wong C, Tjong H, Ngan C, Gong L, Chen Y, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho A, Ruan Y, Verhaak R, Wei C. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell 2021, 39: 694-707.e7. PMID: 33836152, PMCID: PMC8119378, DOI: 10.1016/j.ccell.2021.03.006.Peer-Reviewed Original ResearchConceptsGenome-wide activationSingle-molecule resolutionMobile enhancerChromatin interactionsChromosomal interactionsChromatin contactsTranscription controlChromosomal transcriptionChromosomal targetsTranscriptional programsTranscriptional enhancersChromosomal genesChIA-PETGene transcriptionCancer genomesInteraction networksDNA functionH3K27ac signalProstate cancer cellsCircular DNAEcDNAsExpression levelsCancer cellsOncogenic alterationsTranscription