Quantification of aneuploidy in targeted sequencing data using ASCETS

Liam F Spurr; Mehdi Touat; Alison M Taylor; Adrian M Dubuc; Juliann Shih; David M Meredith; William V Pisano; Matthew L Meyerson; Keith L Ligon; Andrew D Cherniack; Yvonne Y Li; Rameen Beroukhim

doi:10.1093/bioinformatics/btaa980

Quantification of aneuploidy in targeted sequencing data using ASCETS

Bioinformatics. 2021 Aug 25;37(16):2461-2463. doi: 10.1093/bioinformatics/btaa980.

Authors

Liam F Spurr^{1

2}, Mehdi Touat^{2

3

4}, Alison M Taylor^{1

2

5}, Adrian M Dubuc⁶, Juliann Shih², David M Meredith^{3

6}, William V Pisano³, Matthew L Meyerson^{1

2}, Keith L Ligon^{2

3

6

7

8}, Andrew D Cherniack^{1

2}, Yvonne Y Li^{1

2}, Rameen Beroukhim^{1

2

9

10}

Affiliations

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Aneuploidy*
Documentation
Genome
Genomics
Humans
Software*

Abstract

Publication types

MeSH terms

Grants and funding