Deep learning-based identification of causative genes in lissencephaly using 3D-MRI volumetric datasets

This paper reports a genetic identification task using 3D convolutional neural network (3D-CNN) models applied to a proprietary 3D magnetic resonance imaging (MRI) dataset of patients with lissencephaly. Lissencephaly is a neuronal migration disorder caused by genetic mutations or deletions in which specific causative genes result in distinct morphological alterations in brain structure.

The objective of this study was to identify causative genes through image classification by analysing three-dimensional structural features of brain MRI using deep learning.

In our experiments, we extended representative CNN architectures to handle three-dimensional inputs and performed three-class classification targeting the primary causative genes, LIS1 and DCX, along with a category for other genetic variations.

Our results demonstrated that the 3D-ResNet18 model achieved a mean classification accuracy of over 78%. Furthermore, to enhance the precision for primary genes, we introduced a decision-making process based on prediction probability thresholds.

This approach yielded an average precision improvement of 4.67% for DCX and 4.84% for LIS1 across all the evaluated models.