Precise detection of low-level somatic mutation in resected epilepsy brain tissue

Area of Science:

• Neuroscience
• Genetics
• Molecular Biology

Background:

• Low-level somatic mutations are the primary genetic cause of intractable epilepsy.
• Systematic exploration in large cohorts and precise detection tools for formalin-fixed paraffin-embedded (FFPE) samples are lacking.

Purpose of the Study:

• To systematically analyze low-level somatic mutations in a large cohort of intractable epilepsy brain tissues.
• To develop and validate precise analysis tools for detecting these mutations in FFPE samples.

Main Methods:

• Deep sequencing of 28 known epilepsy-related genes in 446 tissue samples from 232 patients.
• Confirmatory site-specific amplicon sequencing.
• Deep sequencing replicates in eight major focal epilepsy genes for validation.

Main Results:

• Pathogenic mutations found in 31.9% of epilepsy tissues, recurrent in eight major genes (AKT3, DEPDC5, MTOR, PIK3CA, TSC1, TSC2, SCL35A2, BRAF).
• Somatic mutations (22.0%), two-hit (0.9%), and germline (9.1%) mutations identified.
• Majority of somatic mutations (62.3%) had low variant allelic frequency (<5%).
• Deep sequencing replicates achieved high positive predictive values (50-100%) and sensitivities (71-100%).
• In FCDII FFPE samples, deep sequencing replicates detected somatic mutations in 33.3% without false positives.

Conclusions:

• Deep sequencing replicates of major focal epilepsy genes accurately and efficiently detect low-level somatic mutations in FFPE brain tissues.
• This method improves genetic counseling and informs treatment decisions for intractable epilepsy patients.