Deep tissue sequencing improves genetic diagnostic yield in focal cortical dysplasia

Focal cortical dysplasias (FCDs) are malformations of cortical development associated with drug-resistant focal epilepsy. We analysed surgical tissue from 28 consecutive cases recruited from adult and pediatric epilepsy surgery programs. We performed high-depth sequencing of lesional tissue, validated somatic variants using droplet digital PCR, and investigated genotype-phenotype correlations. A pathogenic or likely pathogenic variant was detected in 71% (n=20/28) of cases. Of these, six cases with FCDIIa or FCDIIb had germline variants in NPRL3 (n=4) or DEPDC5 (n=2). Somatic variants were identified in 50% (n=14/28) of cases. The genetic yield for FCDIIb was 85% of cases having a pathogenic mTOR pathway variant detected (n=12/14), and for FCDIIa 66% (n=6/9). This was achieved through high depth sequencing approaches that allowed detection of somatic variants with very low (down to 0.4%) variant allele fractions (VAFs). No pathogenic variants were detected in 3 cases with FCDI. 70% (n=18/26) of the cases with ≥12 months follow up experienced a favourable seizure outcome (Engel 1-2) following surgery. Of note, n=10 patients required repeat surgery to resect residual dysplasia. Determining a genetic diagnosis reveals aetiology and paves the way to precision therapies that may benefit those with FCD who do not respond to current treaments.