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Updated: Oct 18, 2026
Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes
Jens Luebeck1, Ted Liefeld2, Ivy Tsz-Lo Wong3,4
1Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. jluebeck@ucsd.edu.
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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