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Article
Predicting Relapse Prior to Transplantation in Chronic Myeloid Leukemia by Integrating Expert Knowledge and Expression Data
Bioinformatics
  • Ka Yee Yeung, University of Washington Tacoma
  • T. A. Gooley
  • A. Zhang
  • A. E. Raftery
  • J. P. Radich
  • V. G. Oehler
Publication Date
3-15-2012
Document Type
Article
Abstract

Motivation: Selecting a small number of signature genes for accurate classification of samples is essential for the development of diagnostic tests. However, many genes are highly correlated in gene expression data, and hence, many possible sets of genes are potential classifiers. Because treatment outcomes are poor in advanced chronic myeloid leukemia (CML), we hypothesized that expression of classifiers of advanced phase CML when detected in early CML [chronic phase (CP) CML], correlates with subsequent poorer therapeutic outcome. Results: We developed a method that integrates gene expression data with expert knowledge and predicted functional relationships using iterative Bayesian model averaging. Applying our integrated method to CML, we identified small sets of signature genes that are highly predictive of disease phases and that are more robust and stable than using expression data alone. The accuracy of our algorithm was evaluated using cross-validation on the gene expression data. We then tested the hypothesis that gene sets associated with advanced phase CML would predict relapse after allogeneic transplantation in 176 independent CP CML cases. Our gene signatures of advanced phase CML are predictive of relapse even after adjustment for known risk factors associated with transplant outcomes.

DOI
10.1093/bioinformatics/bts059
Version
pre print, post print
Citation Information
Ka Yee Yeung, T. A. Gooley, A. Zhang, A. E. Raftery, et al.. "Predicting Relapse Prior to Transplantation in Chronic Myeloid Leukemia by Integrating Expert Knowledge and Expression Data" Bioinformatics Vol. 28 Iss. 6 (2012)
Available at: http://works.bepress.com/ky-yeung/17/