To derive quantitative image features from magnetic resonance (MR) images that characterize the radiographic phenotype of glioblastoma multiforme (GBM) lesions and to create radiogenomic maps associating these features with various molecular data.
MATERIALS AND METHODS:
Clinical, molecular, and MR imaging data for GBMs in 55 patients were obtained from the TCGA-GBM collection after local ethics committee and institutional review board approval. Regions of interest (ROIs) corresponding to enhancing necrotic portions of tumor and peritumoral edema were drawn and saved in AIM format. Quantitative image features were derived from these ROIs. Robust quantitative image features were defined on the basis of an intraclass correlation coefficient of 0.6 for a digital algorithmic modification and a test-retest analysis. The robust features were visualized by using hierarchic clustering and were correlated with survival by using Cox proportional hazards modeling. Next, these robust image features were correlated with manual radiologist annotations from the Visually Accessible Rembrandt Images (VASARI) feature set and GBM molecular subgroups by using nonparametric statistical tests. A bioinformatic algorithm was used to create gene expression modules, defined as a set of coexpressed genes together with a multivariate model of cancer driver genes predictive of the module's expression pattern. Modules were correlated with robust image features by using the Spearman correlation test to create radiogenomic maps and to link robust image features with molecular pathways.
Eighteen image features passed the robustness analysis and were further analyzed for the three types of ROIs, for a total of 54 image features. Three enhancement features were significantly correlated with survival, 77 significant correlations were found between robust quantitative features and the VASARI feature set, and seven image features were correlated with molecular subgroups (P < .05 for all). A radiogenomics map was created to link image features with gene expression modules and allowed linkage of 56% (30 of 54) of the image features with biologic processes.
Radiogenomic approaches in GBM have the potential to predict clinical and molecular characteristics of tumors noninvasively.
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|Segmentation Summary (XLS, 123kB)|
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Image Segmentation summary spreadsheet: tcga-gbm segmentation summary.xls
Citations & Data Usage Policy
Users of this data must abide by the Creative Commons Attribution 3.0 Unported License under which it has been published. Attribution should include references to the following citations:
Gevaert O, Mitchell LA, Achrol AS, Xu J, Echegaray S, Steinberg GK, Cheshier SH, Napel S, Zaharchuk G, Plevritis SK. (2014). Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2014.RJEFTJBU
Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. (2013) The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, Volume 26, Number 6, pp 1045-1057. DOI: https://doi.org/10.1007/s10278-013-9622-7
In addition to the dataset citation above, please be sure to cite the following if you utilize these data in your research:
Gevaert, O., Mitchell, L. A., Achrol, A. S., Xu, J., Echegaray, S., Steinberg, G. K., Cheshier, S.H., Napel, S., Zaharchuk, G., Plevritis, S. K. (2014, October). Glioblastoma Multiforme: Exploratory Radiogenomic Analysis by Using Quantitative Image Features. Radiology. Radiological Society of North America (RSNA). https://doi.org/10.1148/radiol.14131731
Other Publications Using This Data
Version 2: 2020/10/07
Note: as four TCGA-GBM patID were removed from GDC, this downloadable *.tcia manifest was created without those four TCGA-GBM ID.