DOI: 10.1101/457333Oct 30, 2018Paper

Reconstructing and characterizing focal amplifications in cancer using AmpliconArchitect

BioRxiv : the Preprint Server for Biology
Viraj DeshpandeVineet Bafna

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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