Abstracts

Rationale:
Genetic variants arising post-zygotically over the course of brain development are increasingly being recognized as important genetic contributors in intractable neocortical epilepsy, and particularly pediatric focal malformations of cortical development (MCDs). Somatic variants in PI3K-AKT-mTOR signaling pathway in hemimegalencephaly and type 2 focal cortical dysplasia (FCD) were first identified more than five years ago. More recently, somatic variants in SLC35A2, an essential galactose transporter at the Golgi membrane, were found in type 1a FCD and radiographically nonlesional intractable focal epilepsy. In this study we sought to further study the role of somatic variants in 120 children with focal MCDs.
Method:
We enrolled 120 patients with focal MCDs, including FCD and focal polymicrogyria, who underwent surgical resection of an epilepsy focus in one of five collection sites.  All cases were non-syndromic in order to enrich for cases with a genetic variant localized to the brain. We performed high-depth exome sequencing in 90 brain-blood DNA pairs and an additional 30 cases where only brain tissue-derived DNA was available. Somatic variants were called with Mutect2 and MADSEQ to identify mosaic single nucleotide, indel, and large copy number variants.
Results:
Exomes were sequenced to an average of 250-fold. We identified on average 55 high quality somatic variants enriched in brain tissue in the protein-coding regions of the genome per brain-blood pair. Likely pathogenic germline variants were identified in three cases, including one DEPDC5 diagnosis. Among those with hemimegalencephaly or type 2 focal cortical dysplasia, eighteen individuals (15%) had a likely genetic diagnosis in or including a PI3K-AKT-mTOR signaling pathway gene previously implicated in MCD, including three mosaic duplications of chromosome 1q. Ten cases (8%) had a likely pathogenic somatic variant in multiple known epilepsy genes associated with severe early onset epilepsy that have been associated in other cases with germline variants, including SLC35A2, GNB1, and CASK. The likely pathogenic somatic variants were rarely found in paired leukocyte DNA suggesting that these variants are typically localized to the brain and possibly only in the cortical tissue studied. Comparisons of the landscape of somatic variants in our MCD cohort to controls to ensure the genetic variant profiles are distinctive are on-going.
Conclusion:
These findings suggest that at least some fraction of the genetic risk of focal brain malformations can be attributed to somatic variants in known epilepsy genes. Tissue and cellular localization of variant in the brain may contribute to the phenotypic spectrum associated with epilepsy genes.  
Funding:
:R01NS094596