Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets

Songjian Lu, Kevin Lu, Shi Yuan Cheng, Bo Hu, Xiaojun Ma, Nicholas Nystrom, Xinghua Lu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

An important goal of cancer genomic research is to identify the driving pathways underlying disease mechanisms. It is well known that somatic genome alterations (SGAs) affecting the genes that encode the proteins within a common signaling pathway exhibit mutual exclusivity, in which these SGAs usually do not co-occur in a tumor. With some success, this property has been utilized as an objective function to guide the search for driver mutations. However, the mutual exclusivity alone is not sufficient to indicate that genes affected by such SGAs are in common pathways. Here, we propose a novel, signal-oriented framework for identifying driver SGAs, such that our new method constrains the mutual exclusivity only on tumors that have SGAs to perturb a common signal (not on all tumors as previous methods used). We apply this framework to the OV and GBM data FROM TCGA, and perform systematic evaluations. Our results indicate that the signal-oriented approach enhances the ability to find informative sets of driver SGAs that likely constitute signaling pathways.

Original languageEnglish (US)
Title of host publicationProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Editorslng. Matthieu Schapranow, Jiayu Zhou, Xiaohua Tony Hu, Bin Ma, Sanguthevar Rajasekaran, Satoru Miyano, Illhoi Yoo, Brian Pierce, Amarda Shehu, Vijay K. Gombar, Brian Chen, Vinay Pai, Jun Huan
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1728-1730
Number of pages3
ISBN (Electronic)9781467367981
DOIs
StatePublished - Dec 16 2015
EventIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 - Washington, United States
Duration: Nov 9 2015Nov 12 2015

Publication series

NameProceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Other

OtherIEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
CountryUnited States
CityWashington
Period11/9/1511/12/15

Keywords

  • formatting
  • insert
  • style
  • styling

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence
  • Health Informatics
  • Biomedical Engineering

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  • Cite this

    Lu, S., Lu, K., Cheng, S. Y., Hu, B., Ma, X., Nystrom, N., & Lu, X. (2015). Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets. In L. M. Schapranow, J. Zhou, X. T. Hu, B. Ma, S. Rajasekaran, S. Miyano, I. Yoo, B. Pierce, A. Shehu, V. K. Gombar, B. Chen, V. Pai, & J. Huan (Eds.), Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 (pp. 1728-1730). [7359942] (Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2015.7359942