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MR imaging data and molecular information were retrospectively obtained from The Cancer Imaging Archives for 259 patients with either low- or high-grade gliomas. A convolutional neural network was trained to classify IDH1 mutation status, 1p/19q codeletion, and MGMT promotor methylation status. Classification had high accuracy: IDH1 mutation status, 94%; 1p/19q codeletion, 92%; and MGMT promotor methylation status, 83%. The authors conclude that this shows the feasibility of a deep-learning CNN approach for the accurate classification of individual genetic mutations of both low- and high-grade gliomas and that the relevant MR imaging features acquired from an added dimensionality-reduction technique are concordant with existing literature, showing that neural networks are capable of learning key imaging components without prior feature selection or human directed training.

Abstract

Figure 4 from paper
Features most highly correlated with MGMT methylation. Prototypical cases as identified by our convolutional neural network imaging features associated with unmethylated (A and B) and methylated (C and D) MGMT statuses. Features predictive of MGMT unmethylated status include thick enhancement with central necrosis (A) with infiltrative edema patterns (B). In contrast, features predictive of MGMT promoter methylated status include nodular and heterogeneous enhancement (C) with masslike FLAIR edema (D).

BACKGROUND AND PURPOSE

The World Health Organization has recently placed new emphasis on the integration of genetic information for gliomas. While tissue sampling remains the criterion standard, noninvasive imaging techniques may provide complimentary insight into clinically relevant genetic mutations. Our aim was to train a convolutional neural network to independently predict underlying molecular genetic mutation status in gliomas with high accuracy and identify the most predictive imaging features for each mutation.

MATERIALS AND METHODS

MR imaging data and molecular information were retrospectively obtained from The Cancer Imaging Archives for 259 patients with either low- or high-grade gliomas. A convolutional neural network was trained to classify isocitrate dehydrogenase 1 (IDH1) mutation status, 1p/19q codeletion, and O6-methylguanine-DNA methyltransferase (MGMT) promotor methylation status. Principal component analysis of the final convolutional neural network layer was used to extract the key imaging features critical for successful classification.

RESULTS

Classification had high accuracy: IDH1 mutation status, 94%; 1p/19q codeletion, 92%; and MGMT promotor methylation status, 83%. Each genetic category was also associated with distinctive imaging features such as definition of tumor margins, T1 and FLAIR suppression, extent of edema, extent of necrosis, and textural features.

CONCLUSIONS

Our results indicate that for The Cancer Imaging Archives dataset, machine-learning approaches allow classification of individual genetic mutations of both low- and high-grade gliomas. We show that relevant MR imaging features acquired from an added dimensionality-reduction technique demonstrate that neural networks are capable of learning key imaging components without prior feature selection or human-directed training.

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