Abstracts

Rationale: Background: Epileptic Encephalopathies (EE) are a group of severe epilepsy syndromes associated with intractable epilepsy and cognitive impairment. Massively parallel sequencing (MPS) technologies have contributed to the discovery that many EE are monogenic and caused by de novo mutations. At our institution MPS had hitherto not been available as a diagnostic test. Aim: To report our institutional experience of MPS testing in children with epileptic encephalopathy. Methods: Methods: Using the Illumina TruSight One panel, a diagnostic panel of 47 EE genes with clear evidence for pathogenicity was designed as part of Western Sydney Genomic project at the Children's Hospital at Westmead, that was later upgraded to include 74 EE genes. Patients were selected for MPS if they had intractable epilepsy of unknown cause or if specific monogenic epilepsy was suspected and were phenotyped at a monthly neurology clinical review meeting (neurology referrals). The pathogenicity of variants was classified according to the Association for Clinical Genetic Science (ACGS) guidelines. All detected pathogenic/likely pathogenic mutations were confirmed by Sanger sequencing. The MPS panel results were analysed between June 2014 to June 2016 and results of 66 of 110 enrolled patients were available at the time of this study. We also compared yield of MPS testing in non-neurology referrals (n=62), who did not undergo clinical review meeting with those who had undergone clinical review by neurologists. Results: Results: Amongst neurology referrals 31.8% (n=21/66) patients obtained a genetic diagnosis using the EE MPS panel, the yield was highest in early onset EE (50%, n=9/18) and lowest in genetic generalized epilepsy (8%, n=1/12). Thirty three percent (n=22/66) of patients had variants of unknown significance and no pathogenic variants were found in 34.8 %( n=23/66) of patients. Pathogenic/likely pathogenic mutations were found in the following genes: SCN1A (5), CDKL5 (3), SCN2A (2), SCN8A (2), KCNQ2 (2), GRIN2A (1), FOXG1 (2), SYNGAP1 (1), WWOX (1), CACNA1A (1) and ALDH7A1 (1). The pathogenic mutations included missense (n=9), frame shift (n=4), and nonsense (n=7) mutations, five of which were previously reported. The yield of pathogenic mutations was lower in non-neurology referrals (8%, n=5/62). The MPS panel results had a number of benefits in terms of cost-effectiveness, the provision of a diagnosis, prenatal counselling and strongly guided clinical decision-making. Conclusions: MPS enables the identification of mutations in epileptic encephalopathy patients, especially early onset epileptic encephalopathies highlighting its usefulness for rapid, comprehensive and cost effective genetic testing. Careful clinical phenotyping and prioritizing cases maximizes yield of MPS panel testing, reduces incidental findings and allows patients without a pathogenic variant to progress to further investigations such as full exome or whole genome sequencing. Funding: Authors report no funding disclosures