Liam F Spurr1,2, Mehdi Touat2,3,4, Alison M Taylor1,2,5, Adrian M Dubuc6, Juliann Shih2, David M Meredith3,6, William V Pisano3, Matthew L Meyerson1,2, Keith L Ligon2,3,6,7,8, Andrew D Cherniack1,2, Yvonne Y Li1,2, Rameen Beroukhim1,2,9,10. 1. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA. 2. Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA. 3. Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA. 4. Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière-Charles Foix, Service de Neurologie, Paris, France. 5. Department of Pathology and Cell Biology and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, 10032 NY, USA. 6. Department of Pathology, Brigham and Women's Hospital, Boston, 02215 MA, USA. 7. Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, 02215 MA, USA. 8. Department of Pathology, Boston Children's Hospital, Boston, 02215 MA, USA. 9. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA. 10. Department of Medicine, Brigham and Women's Hospital, Boston, 02215 MA, USA.
Abstract
SUMMARY: The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data. AVAILABILITY AND IMPLEMENTATION: ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data. AVAILABILITY AND IMPLEMENTATION: ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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