Molecular classification of multiple tumor types

Bioinformatics. 2001:17 Suppl 1:S316-22. doi: 10.1093/bioinformatics/17.suppl_1.s316.

Abstract

Using gene expression data to classify tumor types is a very promising tool in cancer diagnosis. Previous works show several pairs of tumor types can be successfully distinguished by their gene expression patterns (Golub et al. 1999, Ben-Dor et al. 2000, Alizadeh et al. 2000). However, the simultaneous classification across a heterogeneous set of tumor types has not been well studied yet. We obtained 190 samples from 14 tumor classes and generated a combined expression dataset containing 16063 genes for each of those samples. We performed multi-class classification by combining the outputs of binary classifiers. Three binary classifiers (k-nearest neighbors, weighted voting, and support vector machines) were applied in conjunction with three combination scenarios (one-vs-all, all-pairs, hierarchical partitioning). We achieved the best cross validation error rate of 18.75% and the best test error rate of 21.74% by using the one-vs-all support vector machine algorithm. The results demonstrate the feasibility of performing clinically useful classification from samples of multiple tumor types.

Publication types

  • Validation Study

MeSH terms

  • Algorithms
  • Computational Biology*
  • Confidence Intervals
  • Databases, Genetic
  • Gene Expression Profiling / statistics & numerical data
  • Humans
  • Neoplasms / classification*
  • Neoplasms / genetics*