Genetic diagnosis of drug-resistant epilepsy by whole exome sequencing and chromosomal array in Hong Kong

Abstract

Background and Aims: Drug-resistant epilepsy is a neurological disorder which two antiepileptic drugs fails to sustain the seizure free status of the patient. Heterogeneous clinical presentations makes the diagnosis challenging. Recent research has identified various disease causing aberrations in more than 500 genes, including single nucleotide variation, small in-dels, and copy number variations. We aim to identify the genetic cause of our patient cohort by the approach of whole exome sequencing (WES) and chromosomal microarray testing. Method: This is an ongoing project. Up till now, WES was performed on 31 patients (Male n=18, Female n=13, age of onset: Day 1 to 5 years old). Analysis was based on a 546-gene panel established by integrating ten commercially available epilepsy panels, an OMIM search with the term 'epilepsy', and the NIH epilepsy genetics initiative database. Coding variants were identified and filtered based on a population frequency of less than 0.01 listed in 1000 genomes, ESP6500 and ExAC. Rare variants were interrogated for pathogenicity. All detected mutations were validated by Sanger sequencing and segregation analysis performed if parental samples available. If no disease-causing variants can be found, aCGH and trio-based exome wide analysis will be performed. Results: Four de novo mutations (MECP2 n=2, SCN1A n=1, 2q24.3q31.1 del involving SCN1A, SCN2A and SCN9A n=1) and a mosaic splice site mutation (CDKL5) were detected in 5 patients. The patient's phenotype correlated well with the reported clinical features of those carrying the mutations. These mutations were classified as pathogenic/likely pathogenic according to ACMG guideline, giving a diagnostic yield of 16% (5/31) in this cohort. Interestingly, an incidental finding of pathogenic SCN5A mutation (Brugada syndrome) was noted in a patient and this has led to increased ECG surveillance of the patient and family cascade testing. Conclusion: The study suggests that WES and aCGH are effective diagnostic tools of drug resistant epilepsy. Importantly WES can generate both primary and secondary/incidental findings that may have impact on clinical management and will challenge traditional medical concepts like the 'one man, one disease' hypothesis. Acknowledgements: We would like to thank The Society for the Relief of Disabled Children and The Edward and Yolanda Wong Fund for the support.