Abstracts

Rationale: We set out to determine the frequency and size of microchromosomal copy number variants (CNVs) affecting the alpha1-subunit gene (SCN1A) in Dravet Syndrome(DS), other severe epileptic encephalopathies with infantile onset and generalized epilepsy with febrile seizures plus (GEFS+). Methods: Multiplex ligation-dependent probe amplification (MLPA) was applied to detect SCN1A CNV among 288 cases. CNVs extending beyond SCN1A were further characterized for size and gene content, by comparative genome hybridiation (CGH). Results: Novel SCN1A CNVs were found 12.5% of DS patients where sequence based mutations had been previously excluded. There were partial and whole SCN1A deletions and a partial SCN1A amplification of 5-6 copies. One DS case with a partial SCN1A deletion had an affected sibling with the same deletion, implying gonadal mosaicism in a parent. In the non-DS cases, a partial SCN1A duplication was detected in a patient with early-onset severe symptomatic generalized epilepsy. Array CGH showed intragenic deletions of 90kb and larger, with one as big as 9.3Mb and extending well beyond SCN1A. Conclusions: MLPA is now an established second line testing strategy to reliably detect all CNV of SCN1A from the megabase range down to one exon. MLPA detected CNV in 12.5% of DS patients where the initial sequencing test had failed to detect a mutation. Sequencing of SCN1A remains the primary test as it detects mutations in 70-80% of DS cases, followed by MLPA which shows that SCN1A CNV account for a further 2-3% of DS cases. Large CNVs extending beyond SCN1A and involving contiguous genes can be precisely characterized by array CGH.