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

Area of Science:

• Neuroscience
• Genetics
• Molecular Biology

Background:

• Somatic variants causing epilepsy are difficult to detect due to mosaicism and low variant allele frequencies.
• Current detection methods are limited to surgically resected brain tissue, restricting patient cohort size.
• Stereoelectroencephalography (SEEG) offers a potential source of brain tissue for broader patient access.

Purpose of the Study:

• To develop an improved protocol for detecting somatic variants in epilepsy using DNA from SEEG depth electrodes.
• To mitigate challenges of low DNA yield and contamination in SEEG samples.
• To enable broader access to diverse brain regions for somatic variant analysis in epilepsy.

Main Methods:

• Collection of SEEG depth electrodes from affected and unaffected brain regions in epilepsy patients.
• Isolation of neuronal nuclei using fluorescence-activated nuclei sorting (FANS) to purify samples.
• Whole exome sequencing (WES) coupled with a specialized bioinformatic workflow for somatic variant detection.

Main Results:

• Successfully generated high-quality neuronal DNA from 14 SEEG samples across seven patients.
• Identified four candidate pathogenic somatic variants in genes (MTOR, CSDE1, KLLN, NLE1) in four patients.
• Validated candidate variants using digital droplet polymerase chain reaction (ddPCR).

Conclusions:

• The developed SEEG-derived DNA protocol enhances reliability and applicability for epilepsy research.
• This approach provides insights into the molecular basis of epilepsy and aids in epileptogenic zone identification.
• Advances precision medicine by enabling more comprehensive somatic variant analysis in epilepsy.