AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes
Abstract
Abstract Here we present AmpliconSuite, a toolkit for focal amplification analysis from cancer whole-genome sequencing that identifies extrachromosomal DNA (ecDNA), breakage–fusion–bridges and other amplification modes. Its ecContext module categorizes ecDNA structures to understand formation mechanisms. Validation across 175 metaphase fluorescence in situ hybridization-probed genes in 72 models demonstrated accurate predictions. Analysis of 6,506 patient pan-cancer samples revealed ecDNA-mediated oncogene co-amplification preferences. To democratize data sharing, we created AmpliconRepository, a community-contributable platform, enabling investigation of results across >15,000 publicly hosted samples.
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Authors: Jens Luebeck, Ted Liefeld, Ivy Tsz-Lo Wong, Edwin Huang, Forrest Kim, Bhargavi Dameracharla, Michael Chan, Rohil Ahuja, Kyra Fetter, Dhruv Khatri, Kaiyuan Zhu, Thorin T. Tabor, Daniel Schreyer, Gino Prasad, Aditi Gnanasekar, Siavash R. Dehkordi, Simone Spandau, Michał Adamaszek, Rishaan Kenkre, Tushar Agashe, Devika Torvi, Mădălina Giurgiu, Soyeon Kim, Hoon Kim, Peter Bailey, Roel G.W. Verhaak, Viraj Deshpande, Michael M. Reich, Paul S. Mischel, Jill P. Mesirov, Vineet Bafna
Institutions: Shanghai Jiao Tong University, University of California San Diego, Charité - Universitätsmedizin Berlin, University of Glasgow, Yale University, Stanford University, Stanford Medicine, Sungkyunkwan University, Moores Cancer Center, Stanford Health Care, Champalimaud Foundation, Mabvax Therapeutics (United States)