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Expanding Ploidy and Allele Frequency on Nested Subpopulations ExPANdS

Characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results.

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ExPANdS forum

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ExPANdS classification

ExPANdS specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Java, R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.6
Maintained:
Yes

ExPANdS distribution

versioning

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No versioning.

ExPANdS support

Documentation

Maintainer

  • Noemi Andor <>

Credits

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Publications

Institution(s)

Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA; Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Brain Tumor Research Center, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA; Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universität München, Munich, Germany; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA

Funding source(s)

Voices Against Brain Cancer (VABC) foundation; the NIH Research Project Grant Program (RO1CA164746, RO1NS080619); the NIH T32 Grant Program; Matthew Larson Pediatric Brain Tumor Foundation; the German Academic Exchange Program

Link to literature

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