AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes.

AmpliconSuite accurately predicts ecDNA and amplification modes in 72 models and reveals ecDNA-mediated oncogene co-amplification in 6,506 pan-cancer samples.

• Why it matters: Understanding mechanisms of focal amplifications like ecDNA is crucial for cancer biology and therapy development. Current tools lack comprehensive analysis and validation across large datasets, limiting insights into amplification formation and oncogene co-amplification.
• What they did: The authors developed AmpliconSuite, a toolkit with modules for identifying extrachromosomal DNA, breakage-fusion-bridges, and other amplification modes, validated with 175 genes in 72 models, and analyzed 6,506 patient samples.
• The result: The platform enables accurate structural categorization and uncovers ecDNA-driven oncogene co-amplification preferences, while AmpliconRepository facilitates community data sharing across over 15,000 samples.