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-37. DISSECTING GBM EVOLUTION FOLLOWING STANDARD-OF-CARE BY LARGE-SCALE LONGITUDINAL SINGLE NUCLEUS RNA-SEQUENCING
Nomura M, Spitzer A, Johnson K, Garofano L, Nehar-Belaid D, Oh Y, Anderson K, Najac R, Bussema L, Varn F, D’Angelo F, Chowdhury T, Migliozzi S, Park J, Ermini L, Golebiewska A, Niclou S, Das S, Paek S, Moon H, Mathon B, Di Stefano A, Bielle F, Laurenge A, Sanson M, Tanaka S, Saito N, Keir S, Ashley D, Huse J, Yung W, Lasorella A, Iavarone A, Verhaak R, Suva M, Tirosh I. EPCO-37. DISSECTING GBM EVOLUTION FOLLOWING STANDARD-OF-CARE BY LARGE-SCALE LONGITUDINAL SINGLE NUCLEUS RNA-SEQUENCING. Neuro-Oncology 2023, 25: v132-v132. PMCID: PMC10639295, DOI: 10.1093/neuonc/noad179.0499.Peer-Reviewed Original ResearchSingle-nucleus RNA sequencingLarge-scale longitudinal cohortTME compositionRecurrent samplesGood clinical courseInitial tumor resectionMajority of patientsTumor microenvironment cellsPrimary tumor samplesMGMT methylation statusTME changesClinical courseRNA sequencingTherapy failureLikely respondersTumor resectionDisease progressionNucleus RNA sequencingLongitudinal cohortReciprocal increaseTumor samplesMicroenvironment cellsMalignant cell fractionGlioblastomaRecurrence