Klein, Karl MartinTarailo-Graovac, MajaMascarenhas, Rumika2024-11-042024-11-042024-11-04Mascarenhas, 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.https://hdl.handle.net/1880/120042Brain 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.enUniversity of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.EpilepsyFocal EpilepsySomatic VariantsSomatic MosaicismNeuroscienceGeneticsBioinformaticsmaster thesis