Next-generation sequencing allows a diagnostic yield of 23.7% in monogenic epilepsies

Abstract

Objective: Epilepsy is a group of neurological disorders affecting 0.7 to 1% of the population. Etiologies are widely heterogeneous, including monogenic causes. Most of these disorders affect children, which stresses the need for early molecular diagnosis. Methods: We developed an 82-gene panel for the diagnosis of Mendelian epilepsies. Target exon libraries were generated using SeqCapEZ capture technology (Roche®). Sequencing was carried out on a “mid output” flow-cell on a Miseq or a NextSeq500 (Illumina®). Results: A total of 329 DNAs from patients without diagnosis and from 43 controls (with known gene variant or copy-number variants) have been analyzed. Patients had epileptic encephalopathy (301), focal epilepsy (10), benign familial neonatal or infantile epilepsy (5), or other types of epilepsy. Average depth was around 400x and less than 1% of the bases had a read depth below 30x. All mutations and CNVs were found in controls individuals. We identified pathogenic variants in 79 out of 329 patients. These were de novo heterozygous variants in the genes KCNQ2 (6), KCNT1 (5), FOXG1 (2), SLC6A1, SCN8A (4), GNAO1 (3), CHD2 (3), SYNGAP1 (3), DEPDC5 (2), GRIN2A (1), PCDH19 (3), GABRB3 (1), SCN1A, ATP1A3 (3), SCN2A (5), PRRT2 (2), STXBP1, MBD5; homozygous or compound heterozygous in PLCB1, PIGN (2), ST3GAL3, PNPO (2), WWOX (2), POLG, SCARB2, QARS, TBC1D24; and X-linked in PIGA (3), SLC9A6 (3), ALG13 (2), MECP2, CDKL5 (4), SLC35A2 (2), and CASK. Conclusion: This gene panel increased the diagnostic rate of monogenic epilepsies to 23.7%. The identification of the disease-causing mutation(s) will provide accurate genetic counseling and might have therapeutic consequences in a growing number of cases. For example, the identification of a homozygous mutation in PNPO in a patient with neonatal drug-resistant epilepsy led to treatment adaptation (increase and fragmentation of Pyridoxal Phosphate doses), which resulted in satisfactory control of seizures.