Identifying Somatic Variants using DNA Derived from Stereo-Electroencephalography Electrodes in Patients with Focal Epilepsy
Date
2024-11-04
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Abstract
Brain somatic variants play a crucial role in the etiology of focal epilepsy. Detecting these variants is challenging due to their presence in a subset of cells, resulting in a reduced variant allele frequency (VAF). Traditional methods rely on brain tissue obtained during resective epilepsy surgery, limiting accessibility and applicability, especially in patients with non-lesional epilepsies who are less likely to undergo surgery. In response to these limitations, a novel approach utilizes DNA extracted from depth electrodes employed in stereo-electroencephalography (SEEG) procedures. This method offers several advantages over resected brain tissue, such as the inclusivity of patients not undergoing surgery and access to multiple brain regions through implanted depth electrodes. Recent studies demonstrated the feasibility of detecting somatic variants using SEEG-derived DNA, highlighting its potential in non-lesional epilepsies. However, challenges remain, including potential cell contaminations and lower cell yields, necessitating DNA amplification that introduces associated artifacts. This thesis introduces an improved SEEG harvesting protocol addressing these issues. Our optimized technique purifies neuronal nuclei, mitigating cell contaminations, and incorporates a newer amplification method to minimize artifacts. Additionally, the thesis introduces the implementation of quality control steps for sample selection and a bioinformatic workflow to reduce artifactual and false positive variants, enhancing the reliability of downstream variant identification. With these improvements, this project aims to enhance the reliability and applicability of SEEG-derived DNA in understanding the molecular basis of focal epilepsy, paving the way for diagnosis and improved treatment strategies.
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Keywords
Epilepsy, Focal Epilepsy, Somatic Variants, Somatic Mosaicism
Citation
Mascarenhas, R. (2024). Identifying Somatic Variants using DNA Derived from Stereo-Electroencephalography Electrodes in Patients with Focal Epilepsy (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.