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Objective: To determine the genes underlying Dravet syndrome in patients who do not have an SCN1A mutation on routine testing. Methods:We performed whole-exome sequencing in 13 SCN1A-negative patients with Dravet syndrome and targeted resequencing in 67 additional patients to identify new genes for this disorder.Results: We detected disease-causing mutations in 2 novel genes for Dravet syndrome, with mutations in GABRA1 in 4 cases and STXBP1 in 3. Furthermore, we identified 3 patients with previously undetected SCN1A mutations, suggesting that SCN1A mutations occur in even more than the currently accepted ;75% of cases. Conclusions:We show that GABRA1 and STXBP1 make a significant contribution to Dravet syndrome after SCN1A abnormalities have been excluded. Our results have important implications for diagnostic testing, clinical management, and genetic counseling of patients with this devastating disorder and their families. Neurology ® 2014;82:1245-1253 GLOSSARY cDNA 5 complementary DNA; dHPLC 5 denaturing high-performance liquid chromatography; FS 5 febrile seizures; GABA 5 g-aminobutyric acid; GEFS1 5 genetic epilepsy with febrile seizures plus; WES 5 whole-exome sequencing; WT 5 wild-type.

Objective Rare copy number variants (CNVs) – deletions and duplications – have recently been established as important risk factors for both generalized and focal epilepsies. A systematic assessment of the role of CNVs in epileptic encephalopathies, the most devastating and often etiologically obscure, group of epilepsies, has not been performed. Methods We evaluated 315 patients with epileptic encephalopathies characterized by epilepsy and progressive cognitive impairment for rare CNVs using a high-density, exon-focused whole-genome oligonucleotide array. Results We found that 25/315 (7.9%) of our patients carried rare CNVs that may contribute to their phenotype, with at least half being clearly or likely pathogenic. We identified two patients with overlapping deletions at 7q21 and two patients with identical duplications of 16p11.2. In our cohort, large deletions were enriched in affected individuals compared to controls, and four patients harbored two rare CNVs. We screened two novel candidate genes found within the rare CNVs in our cohort but found no mutations in our patients with epileptic encephalopathies. We highlight several additional novel candidate genes located in CNV regions. Interpretation Our data highlight the significance of rare copy number variants in the epileptic encephalopathies, and we suggest that CNV analysis should be considered in the genetic evaluation of these patients. Our findings also highlight novel candidate genes for further study.

Objective: To investigate the role of intragenic deletions of ALDH7A1 in patients with clinical and biochemical evidence of pyridoxine-dependent epilepsy but only a single identifiable mutation in ALDH7A1.Methods: We designed a custom oligonucleotide array with high-density probe coverage across the ALDH7A1 gene. We performed array comparative genomic hybridization in 6 patients with clinical and biochemical evidence of pyridoxine-dependent epilepsy but only a single detectable mutation in ALDH7A1 by sequence analysis. Results:We found partial deletions of ALDH7A1 in 5 of 6 patients. Breakpoint analysis reveals that the deletions are likely a result of Alu-Alu recombination in all cases. The density of Alu elements within introns of ALDH7A1 suggests susceptibility to recurrent rearrangement. Conclusion:Patients with clinical pyridoxine-dependent epilepsy and a single identifiable mutation in ALDH7A1 warrant further investigation for copy number changes involving the ALHD7A1 gene. Neurology ® 2015;85:756-762 GLOSSARY a-AASA 5 a-aminoadipic semialdehyde; CGH 5 comparative genomic hybridization; PDE 5 pyridoxine-dependent epilepsy.First described in 1954, pyridoxine-dependent epilepsy (PDE) is a metabolic epileptic encephalopathy characterized by pharmacoresistant seizures that typically come under control after initial administration followed by supplementation of pyridoxine at pharmacologic doses. The biochemical and genetic bases of this rare familial epilepsy were solved in 2006 when mutations in ALDH7A1 resulting in dysfunction of the protein antiquitin were discovered. 1 Metabolic changes consistent with PDE can be detected by measuring elevated levels of the biomarker a-aminoadipic semialdehyde (a-AASA) in various body fluids.1,2 As elevations of a-AASA are also present in patients with molybdenum cofactor deficiency and isolated sulfite oxidase deficiency, 3 genotyping of ALDH7A1 is required to confirm the diagnosis. In the vast majority of published cases, homozygous or compound heterozygous mutations of both ALDH7A1 alleles have been detected.We investigated 6 patients with a clinical diagnosis of PDE and positive biomarkers in which only a single, heterozygous mutation in ALDH7A1 could be identified by sequence analysis. We designed a custom oligonucleotide array that included high-density probe coverage of the ALDH7A1 gene to look for intragenic deletions or duplications that would have been missed by conventional sequence analysis. Using this strategy, we found partial deletions of ALDH7A1 in 5 of 6 patients, each of which is likely the result of an Alu-Alu recombination event. Our results suggest that in patients with clinical and biochemical evidence of PDE in the setting of a