Abstracts

Rationale: Epilepsy is a heterogeneous disorder with a multitude of known causes. In over half the cases, however, the cause remains unknown. Identification of single gene mutations in families with inherited epilepsy has greatly contributed to our understanding of the underlying mechanisms of seizures, but despite significant advances many causative genes remain to be identified. Exome sequencing employs targeted capture of the 1% of the genome that encodes for proteins and given that an estimated 80% of variants causing Mendelian disease are located in the exome, there is great anticipation that applying this technique to families with inherited epilepsy will lead to the identification of novel epilepsy-causing genes. Methods: We have ascertained over 70 consanguineous families with recessive epilepsy to be used in exome sequencing studies and have sequenced the exomes of 35 probands thus far. Genetic variants were delineated using the Genome Analysis Tool Kit and variants were subsequently filtered for those that were in coding/splice regions, non-synonymous, not found in Hardy-Weinberg equilibrium with the disease frequency in control populations, homozygous, and found in linkage intervals. The remaining variants were ranked by type of mutation, amino acid conservation across species, protein damage prediction and relevance to disease. Results: Exome sequencing produced an average coverage of 96% of the exome at >10X depth and a total of 26,393 +/- 4,971 variants were identified per proband. In 5 of the 35 families sequenced, we have identified a single potentially deleterious sequencing variant not previously implicated in epilepsy. In the remaining families, we have generated a final variant list with a mean of 8 (range 3-18) novel, coding, homozygous variants in linkage intervals which may be causal of the disease. Compared to previous studies of similar families, this approach is extremely efficient for identifying strong candidate genes. Conclusions: Exome sequencing is an attractive method for interrogating the coding portion of the genome and identifying rare variants of high effect. This method is extremely efficient in identifying strong candidate genes for families with Mendelian forms of epilepsy and the scientific and clinical utility of exome sequencing is only just being realized.