Development of robust discriminant equations for assessing subtypes of glioblastoma biopsies.

British Journal of Cancer
X CastellsC Arús

Abstract

In the preceding decade, various studies on glioblastoma (Gb) demonstrated that signatures obtained from gene expression microarrays correlate better with survival than with histopathological classification. However, there is not a universal consensus formula to predict patient survival. We developed a gene signature using the expression profile of 47 Gbs through an unsupervised procedure and two groups were obtained. Subsequent to a training procedure through leave-one-out cross-validation, we fitted a discriminant (linear discriminant analysis (LDA)) equation using the four most discriminant probesets. This was repeated for two other published signatures and the performance of LDA equations was evaluated on an independent test set, which contained status of IDH1 mutation, EGFR amplification, MGMT methylation and gene VEGF expression, among other clinical and molecular information. The unsupervised local signature was composed of 69 probesets and clearly defined two Gb groups, which would agree with primary and secondary Gbs. This hypothesis was confirmed by predicting cases from the independent data set using the equations developed by us. The high survival group predicted by equations based on our local and one of the publis...Continue Reading

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Methods Mentioned

BETA
biopsies
biopsy
PCR

Software Mentioned

R package MASS R
LOOCV
R package
ColSBE
R
R R Development Core Team
LeeSBE
eTUMOUR
affy
GeneChip

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