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- W2912484801 abstract "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." @default.
- W2912484801 created "2019-02-21" @default.
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- W2912484801 date "2019-01-23" @default.
- W2912484801 modified "2023-10-18" @default.
- W2912484801 title "Exploring the landscape of focal amplifications in cancer using AmpliconArchitect" @default.
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- W2912484801 doi "https://doi.org/10.1038/s41467-018-08200-y" @default.
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