On predicting medulloblastoma metastasis by gene expression profiling

Accurately predicting clinical outcome or metastatic status from gene expression profiles remains one of the biggest hurdles facing the adoption of predictive medicine. Recently, MacDonald et al. (Nat. Genet. 2001, 29,143-152) used gene expression profiles, from samples taken at diagnosis, to distinguish between clinically designated metastatic and nonmetastatic primary medulloblastomas, helping to elucidate the genetic mechanisms underlying metastasis and suggesting novel therapeutic targets. The obtained accuracy of predicting metastatic status does not, however, reach statistical significance on Fisher's exact test, although 22 training samples were used to make each prediction via leave-one-out testing. This paper introduces readily implemented nonlinear filters to transform sequences of gene expression levels into output signals that are significantly easier to classify and predict metastasis. It is shown that when only 3 exemplars each from the metastatic and nonmetastatic classes were assumed known, a predictor was constructed whose accuracy is statistically significant over the remaining profiles set aside as a test set. The predictor was as effective in recognizing metastatic as nonmetastatic medulloblastomas, and may be helpful in deciding which patients require more aggressive therapy. The same predictor was similarly effective on an independent set of 5 nonmetastatic tumors and 3 metastatic cell lines also used by MacDonald et al.