Abstracts

Rationale: Advances in sequencing technologies has driven genetic discovery in epilepsy. To date, this has been largely at the germline level. More recently, we have begun to appreciate the contribution of somatic (tissue specific) mutations in epilepsy, in particular in the aetiology of malformations of cortical development (MCD) such as focal cortical dysplasia (FCD II). The aim of this study was to evaluate resected brain tissue in a cohort of patients who underwent epilepsy surgery in a tertiary referral centre in Ireland for somatic mutations.

Methods: Cases, identified via the Beaumont Hospital Electronic Patient Record (EPR) system and Epilepsy Surgery Review Meeting (ESRM), were clinically phenotyped and sub-divided based on the histopathology of the resected brain tissue. Each case, with matched blood-derived and brain-derived DNA samples, was sequenced using high coverage (~500X) targeted panel next generation sequencing (NGS). Variants were identified using GATK4 MuTect-2 and annotated. Candidate variants were confirmed using high-coverage amplicon sequencing.

Results: Forty-one patients were successfully sequenced using the NGS pipeline. Nine patients yielded thirteen candidate somatic variants. Four variants were validated using amplicon sequencing – CBL and ALG13 in the hippocampal sclerosis (HS) group; MTOR and FLNA in the MCD group. The overall diagnostic yield across 41 patients was 10% – 9% in HS and 20% in MCD (FCD).

Table: Breakdown of cases by histopathology, gene identified and confirmation via amplicon sequencing_x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_ _x000D_

Patient	Histopathology	Gene	Somatic VAF Panel	Somatic VAF PCR	Result
Pt 1	hippocampal sclerosis	GRIN2B	0.01	0.00	Not Replicated
Pt 2	hippocampal sclerosis	GABRA1	0.01	0.00	Not Replicated
Pt 2	hippocampal sclerosis	KCNB1	0.01	0.01	Possible
Pt 3	hippocampal sclerosis	SCN2A	0.01	0.00	Unlikely
Pt 3	hippocampal sclerosis	CBL	0.01	0.01	Replicated
Pt 4	hippocampal sclerosis	ALG13	0.01	0.01	Replicated
Pt 5	hippocampal sclerosis	SCN5A	0.07	0.00	Not replicated
Pt 6	FCD 2B	MTOR	0.01	0.01	Replicated
Pt 6	FCD 2B	SLC6A1	0.01	0.00	Unlikely
Pt 7	FCD 2B	KCNQ3	0.01	0.00	Unlikely
Pt 7	FCD 2B	FLNA	0.00	0.00	Replicated
Pt 8	FCD 1B	EEF2	0.00	0.00	Not Replicated
Pt 9	non-lesional focal	ARF1	0.01	0.00	Unlikely

Conclusions: This study has provided novel insights into the aetiology of HS, a condition not previously thought to be associated with somatic genetic mutations. Neither of the two genes in the HS group have previously been reported as somatic variants, nor has FLNA in the MCD (FCD II) group. It has also provided further insights into the importance of MTOR and related genes in FCD.

Funding: This research was supported in part by a research grant from Science Foundation Ireland (SFI) under Grant Number 16/RC/3948 and co-funded under the European Regional Development Fund and by FutureNeuro industry partners. Michael Doyle (presenter) is a scholar on the RCSI StAR MD Programme and receives funding for this programme through Blackrock Clinic, Dublin.