Quantification of aneuploidy in targeted sequencing data using ASCETS.

Autor:	Spurr LF; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA., Touat M; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA.; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; 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., Taylor AM; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA.; Department of Pathology and Cell Biology and Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, 10032 NY, USA., Dubuc AM; Department of Pathology, Brigham and Women's Hospital, Boston, 02215 MA, USA., Shih J; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA., Meredith DM; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Department of Pathology, Brigham and Women's Hospital, Boston, 02215 MA, USA., Pisano WV; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA., Meyerson ML; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA., Ligon KL; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA.; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Department of Pathology, Brigham and Women's Hospital, Boston, 02215 MA, USA.; Center for Patient Derived Models, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Department of Pathology, Boston Children's Hospital, Boston, 02215 MA, USA., Cherniack AD; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA., Li YY; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA., Beroukhim R; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, 02215 MA, USA.; Department of Medicine, Brigham and Women's Hospital, Boston, 02215 MA, USA.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2021 Aug 25; Vol. 37 (16), pp. 2461-2463.
DOI:	10.1093/bioinformatics/btaa980
Abstrakt:	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. (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Databáze:	MEDLINE
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