Exploring the landscape of focal amplifications in cancer using AmpliconArchitect

Viraj Deshpande; Jens Luebeck; Nam-Phuong D. Nguyen; Mehrdad Bakhtiari; Kristen M. Turner; Richard Schwab; Hannah Carter; Paul S. Mischel; Vineet Bafna

doi:10.1038/s41467-018-08200-y

Nature Communications (Jan 2019)

Exploring the landscape of focal amplifications in cancer using AmpliconArchitect

Viraj Deshpande,
Jens Luebeck,
Nam-Phuong D. Nguyen,
Mehrdad Bakhtiari,
Kristen M. Turner,
Richard Schwab,
Hannah Carter,
Paul S. Mischel,
Vineet Bafna

Affiliations

Viraj Deshpande: Department of Computer Science and Engineering, University of California at San Diego
Jens Luebeck: Bioinformatics and Systems Biology Program, University of California at San Diego
Nam-Phuong D. Nguyen: Department of Computer Science and Engineering, University of California at San Diego
Mehrdad Bakhtiari: Department of Computer Science and Engineering, University of California at San Diego
Kristen M. Turner: Ludwig Institute for Cancer Research, University of California at San Diego
Richard Schwab: Department of Medicine, Division of Hematology-Oncology, School of Medicine, University of California at San Diego
Hannah Carter: Department of Medicine, Division of Medical Genetics, University of California at San Diego
Paul S. Mischel: Ludwig Institute for Cancer Research, University of California at San Diego
Vineet Bafna: Department of Computer Science and Engineering, University of California at San Diego

DOI: https://doi.org/10.1038/s41467-018-08200-y
Journal volume & issue: Vol. 10, no. 1
pp. 1 – 14

Abstract

Read online

Focal amplifications are prevalent in many cancer genomes. Here, the authors present AmpliconArchitect (AA), a computational tool for reconstructing their architecture, and reveal an extrachromosomal origin for focal amplifications, including hybrid human-virus elements in HPV-mediated cancers.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

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