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

Focal amplifications in the cancer genome, particularly extrachromosomal DNA (ecDNA) amplifications, are emerging as a pivotal event in cancer progression across diverse cancer contexts, presenting a paradigm shift in our understanding of tumor dynamics. Simultaneously, identification of the various modes of focal amplifications is bioinformatically challenging. We present AmpliconSuite, a collection of tools that enables robust identification of focal amplifications from whole-genome sequencing data. AmpliconSuite includes AmpliconSuite-pipeline; utilizing the AmpliconArchitect (AA) method, and AmpliconRepository.org; a community-editable website for the sharing of focal amplification calls. We also describe improvements made to AA since its initial release that improve its accuracy and speed. As a proof of principle, we utilized publicly available pan-cancer datasets encompassing 2,525 tumor samples hosted on AmpliconRepository.org to illustrate important properties of focal amplifications, showing ecDNA has higher copy number, and stronger oncogene enrichment, compared to other classes of focal amplifications. Finally, we illustrate how AmpliconSuite-pipeline enables delineation of the various mechanisms by which ecDNA forms. ### Competing Interest Statement V.B. is a co-founder, consultant, scientific advisory board (SAB) member and has equity interest in Boundless Bio, Inc. (BBI) and Abterra, and the terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. J.L. has previously received compensation for consulting services rendered to BBI, and the terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. P.S.M. is a co-founder, chairs the scientific advisory board (SAB) of and has equity interest in BBI. V.D. is founder and manager of the Bioinformatics Shop, LLC and has equity interest in BBI. R.G.W.V. is a co-founder of Boundless Bio. H.K. has received research funds from JW Pharmaceutical. M.A. is an employee of MOSEK ApS. The other authors declare no competing interests.