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Genome Biol. 2016 Oct 3;17(1):204.

Importance of rare gene copy number alterations for personalized tumor characterization and survival analysis.

Author information

1
Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, Institute for Medical Informatics and Biometry, Fetscherstr. 74, Dresden, 01307, Germany. michael.seifert@tu-dresden.de.
2
National Center for Tumor Diseases (NCT), Dresden, Germany. michael.seifert@tu-dresden.de.
3
Cellular Networks and Systems Biology, CECAD, University of Cologne, Joseph-Stelzmann-Str. 26, Cologne, 50931, Germany. michael.seifert@tu-dresden.de.
4
Institute of Molecular Systems Biology, Auguste-Piccard-Hof 1, Zurich, 8093, Switzerland.
5
Cellular Networks and Systems Biology, CECAD, University of Cologne, Joseph-Stelzmann-Str. 26, Cologne, 50931, Germany.

Abstract

It has proven exceedingly difficult to ascertain rare copy number alterations (CNAs) that may have strong effects in individual tumors. We show that a regulatory network inferred from gene expression and gene copy number data of 768 human cancer cell lines can be used to quantify the impact of patient-specific CNAs on survival signature genes. A focused analysis of tumors from six tissues reveals that rare patient-specific gene CNAs often have stronger effects on signature genes than frequent gene CNAs. Further comparison to a related network-based approach shows that the integration of indirectly acting gene CNAs significantly improves the survival analysis.

KEYWORDS:

Bioinformatics; Cancer genomics; Computational systems biology; Gene copy number mutations; Network biology; Network inference; Network propagation

PMID:
27716417
PMCID:
PMC5046221
DOI:
10.1186/s13059-016-1058-1
[Indexed for MEDLINE]
Free PMC Article

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