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Reconstructing and characterizing focal amplifications in cancer using AmpliconArchitect

Viraj Deshpande, Jens Luebeck, Mehrdad Bakhtiari, Nam-Phuong D Nguyen, Kristen M Turner, Richard Schwab, Hannah Carter, Paul S Mischel, Vineet Bafna
doi: https://doi.org/10.1101/457333
Viraj Deshpande
aDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093, USA, United States,
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Jens Luebeck
bBioinformatics and Systems Biology Program, University of California at San Diego, La Jolla, California 92093, USA, United States,
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Mehrdad Bakhtiari
aDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093, USA, United States,
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Nam-Phuong D Nguyen
aDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093, USA, United States,
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Kristen M Turner
cLudwig Institute for Cancer Research, University of California at San Diego, La Jolla, California 92093, USA, United States,
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Richard Schwab
dDepartment of Medicine, Division of Hematology-Oncology, School of Medicine, University of California at San Diego, La Jolla, California 92093, USA, United States,
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Hannah Carter
eDepartment of Medicine, Division of Medical Genetics and Moores Cancer Center; University of California at San Diego; La Jolla, CA 92093; USA, United States
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Paul S Mischel
eDepartment of Medicine, Division of Medical Genetics and Moores Cancer Center; University of California at San Diego; La Jolla, CA 92093; USA, United States
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Vineet Bafna
aDepartment of Computer Science and Engineering, University of California at San Diego, La Jolla, California 92093, USA, United States,
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Abstract

Focal oncogene amplification and rearrangements drive tumor growth and evolution in multiple cancer types. We developed a tool, AmpliconArchitect (AA), which can robustly reconstruct the fine structure of focally amplified regions using whole genome sequencing. AA-reconstructed amplicons in pan-cancer data and in virus-driven cervical cancer samples revealed many novel insights about focal amplifications. Specifically, the findings lend support to extrachromosomally mediated mechanisms for copy number expansion, and oncoviral pathogenesis.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 30, 2018.
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Reconstructing and characterizing focal amplifications in cancer using AmpliconArchitect
Viraj Deshpande, Jens Luebeck, Mehrdad Bakhtiari, Nam-Phuong D Nguyen, Kristen M Turner, Richard Schwab, Hannah Carter, Paul S Mischel, Vineet Bafna
bioRxiv 457333; doi: https://doi.org/10.1101/457333
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Reconstructing and characterizing focal amplifications in cancer using AmpliconArchitect
Viraj Deshpande, Jens Luebeck, Mehrdad Bakhtiari, Nam-Phuong D Nguyen, Kristen M Turner, Richard Schwab, Hannah Carter, Paul S Mischel, Vineet Bafna
bioRxiv 457333; doi: https://doi.org/10.1101/457333

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