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

Le résumé fourni par la source

Focal amplifications in the cancer genome, particularly extrachromosomal DNA (ecDNA) are pivotal in cancer progression yet bioinformatically challenging to identify. We present AmpliconSuite, a collection of tools enabling robust identification of focal amplifications from whole-genome sequencing. AmpliconSuite includes AmpliconSuite-pipeline; utilizing the AmpliconArchitect (AA) method, and AmpliconClassifier (AC) for categorizing amplifications. We assembled a collection of 175 metaphase FISH-validated amplifications across 72 models, demonstrating accurate predictions by AC. We also introduce ecContext for classifying ecDNA formation mechanisms. Analysis of 6,506 patient pan-cancer samples revealed ecDNA-mediated oncogene co-amplification patterns, demonstrating ecDNA is responsible for more than 70% of CDK4-MDM2 co-amplifications, and co-opts neighboring oncogenes and frequently co-opts neighboring chromatin remodeling genes. To democratize data sharing, we created AmpliconRepository.org, a community-editable platform for sharing focal amplification calls featuring interactive visualizations, cross-project batch downloads, and a co-amplification analysis tool, enabling systematic investigation of focal amplification biology across >15,000 hosted samples.

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