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bioRxiv · 10.1101/457333

Reconstructing and characterizing focal amplifications in cancer using AmpliconArchitect

Deshpande, V.·Luebeck, J.·Bakhtiari, M.·Nguyen, N.-P. D.·Turner, K. M.·Schwab, R.·Carter, H.·Mischel, P. S.·Bafna, V.
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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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Deshpande, V., Luebeck, J., Bakhtiari, M., Nguyen, N.-P. D., Turner, K. M., Schwab, R., Carter, H., Mischel, P. S., Bafna, V.. 2018-10-30. Reconstructing and characterizing focal amplifications in cancer using AmpliconArchitect. https://doi.org/10.1101/457333

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