Detecting somatic variants in purified brain DNA obtained from surgically implanted depth electrodes in epilepsy

Abstract

AbstractSomatic variants causing epilepsy are challenging to detect as they are only present in a subset of brain cells (e.g., mosaic) resulting in low variant allele frequencies. Traditional methods that rely on surgically resected brain tissue are limited to patients undergoing brain surgery. We developed an improved protocol to detect somatic variants using DNA from stereo- electroencephalography (SEEG) depth electrodes, enabling access to a larger patient cohort and diverse brain regions. This protocol mitigates issues of cell contamination and low yields by purifying neuronal nuclei using fluorescence-activated nuclei sorting. Furthermore, we employed advanced amplification techniques, stringent quality control and an optimized bioinformatic workflow to decrease false positives. Using digital droplet polymerase chain reaction, we confirmed all four selected candidate somatic variants. Our approach enhances the reliability and applicability of SEEG-derived DNA for epilepsy, offering insights into its molecular basis, facilitating identification of the epileptogenic zone and other advancements in precision medicine.