AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes
Year: 2026
Type: article
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.
Source: Nature Methods
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 Tabor, Daniel Schreyer, Gino Prasad, Aditi Gnanasekar, Siavash Raeisi Dehkordi, Simone Spandau, Michał Adamaszek, Rishaan Kenkre, Tushar Agashe, Devika Torvi, Mădălina Giurgiu-Kraljič, Soyeon Kim, Hoon Kim, Peter Bailey, Roel G. W. Verhaak, Viraj Deshpande, Michael Reich, Paul S. Mischel, Jill P. Mesirov, Vineet Bafna
Institutions: University of California San Diego, Stanford Health Care, Stanford Medicine, Stanford University, Shanghai Jiao Tong University, University of Glasgow, Charité - Universitätsmedizin Berlin, Sungkyunkwan University, Champalimaud Foundation, Yale University, Mabvax Therapeutics (United States), Moores Cancer Center
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $12,690
OpenAlex ID: W7222401541