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Updated: Jan 30, 2026

Focal Laser Ablation of Prostate Cancer: An Office Procedure
Published on: March 30, 2021
Exploring the landscape of focal amplifications in cancer using AmpliconArchitect
Viraj Deshpande1, Jens Luebeck2, Nam-Phuong D Nguyen3
1Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. virajbdeshpande@gmail.com.
Abstract:
Focal oncogene amplification and rearrangements drive tumor growth and evolution in multiple cancer types. We present AmpliconArchitect (AA), a tool to reconstruct the fine structure of focally amplified regions using whole genome sequencing (WGS) and validate it extensively on multiple simulated and real datasets, across a wide range of coverage and copy numbers. Analysis of AA-reconstructed amplicons in a pan-cancer dataset reveals many novel properties of copy number amplifications in cancer. These findings support a model in which focal amplifications arise due to the formation and replication of extrachromosomal DNA. Applying AA to 68 viral-mediated cancer samples, we identify a large fraction of amplicons with specific structural signatures suggestive of hybrid, human-viral extrachromosomal DNA. AA reconstruction, integrated with metaphase fluorescence in situ hybridization (FISH) and PacBio sequencing on the cell-line UPCI:SCC090 confirm the extrachromosomal origin and fine structure of a Forkhead box E1 (FOXE1)-containing hybrid amplicon.
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