Wednesday, December 9, 2015

Whole exome sequencing and epilepsy

Research suggests that whole exome sequencing can identify the genetic cause of seizures in children under the age of 5 with onset of epilepsy, with more than 15% of the diagnoses having immediate treatment implications.

The findings were presented at the 2015 American Epilepsy Society Annual Meeting in
Philadelphia.  Michelle K. Demos, MD, study investigator from the University of British Columbia in Vancouver, Canada, told Neurology Advisor that the potential of whole exome sequencing (WES) to influence treatment and outcome supports its early use in the diagnostic process; however, access to WES or gene panels remains variable.

“Despite reductions in cost and turn-around times, in British Columbia, Canada, [WES] testing requires approval by our provincial funding agency, which often delays testing even when it's approved,” Dr. Demos said. “Given this, in this ongoing study we aim to demonstrate that compared to our current clinical approach, performing targeted analysis of WES in early onset epilepsy will increase our diagnostic yield of single gene disorders (>20%), shorten time to diagnose and implement specific treatments, and reduce additional investigations and cost.”

For the study, Dr. Demos and colleagues enrolled 50 patients with a history of early onset epilepsy (≤5 years) of unknown cause who attended the BC Children's Hospital. All patients were classified as either retrospective (epilepsy >6 months) or prospective (epilepsy <6 months), and received WES between December 2014 and June 2015.

Overall, researchers made definitive diagnoses in 13 (26%) patients, of whom 5 were in the prospective group and 8 were in the retrospective group. According to Dr. Demos, WES identified a definite/likely diagnosis in 32% of patients and a possible diagnosis in 22% of patients, for an overall yield of 54%, which she said supports the clinical utility of using WES in this cohort.
In addition, 16% of patients (2 prospective, 6 retrospective) had a diagnosis with possible treatment implications.

The mean time from enrollment with genetic counseling to diagnosis confirmation was 50 days.

“Comparing time from epilepsy diagnosis to genetic diagnosis in [the] prospective or new onset epilepsy group and retrospective group (previously no diagnosis by current standards of testing) revealed that a diagnosis could have been made 95 months sooner if performed at onset of epilepsy in the retrospective group,” Dr. Demos said.

Although the study is ongoing, Dr. Demos noted that the data so far have exceeded expectations.
“Our results support WES as an effective method of identifying the genetic cause of seizures in patients with early onset epilepsy,” she said. “Given the potential for specific treatment implications, its use should be considered early in the diagnostic workup of early onset epilepsy."

“Besides the possible impact on treatment, identifying a specific genetic cause can also benefit families by allowing for more accurate counseling regarding prognosis and recurrence risks for future pregnancies,” Dr. Demos continued. “A genetic diagnosis also puts an end to the diagnostic odyssey and prevents further unnecessary medical investigations.”

Currently, an economic analysis is underway that will assess the cost savings associated with this study, Dr. Demos said.

(Abst. 1.311), 2015Targeted Analysis of Whole Exome Sequencing in Early Onset EpilepsyAuthors: Michelle Demos, Sarah E. Buerki, Ilaria Guella, Eric Toyota, Daniel Evans, Marna Mckenzie, Cyrus Boelman, Linda Huh, Anita Datta, Aspasia Michoulas, K Selby, Bruce Bjornson, Graham Sinclair, Gabriella Horvath, Erin Slade, Clara DM van Karnebeek, Patrice Eydoux, Shelin Adam, Margot Van Allen, Tanya Nelson, Mary Connolly, Matt Farrer


Rationale: Advances in genomic technologies, including targeted next generation sequencing and whole exome sequencing (WES), enables identification of pathogenic variants in 10 – 78 % of select patients with unexplained epilepsy. The clinical impact is significant and includes earlier diagnosis of disorders with specific treatment implications. In an ongoing study, we report the results of WES on 50 patients with early onset epilepsy of unknown cause.

Methods: Between December 2014 - June 2015 WES was performed on 50 patients attending BC Children’s hospital with a history of early onset epilepsy (≤ 5 years) of unknown cause. Patients were classified as retrospective (epilepsy > 6 months) or prospective (epilepsy < 6 months). Detailed clinical data was abstracted in a REDCap database. WES was performed using the Ion AmpliSeq™ Exome Kit and Ion Proton™ System within 2 weeks of receiving samples. Reporting was restricted to the sequences of 557 genes previously implicated in epilepsy, with exon sequence average read depths >80X. Putative causative mutations were validated by Sanger sequencing and by parental testing (when possible). Diagnostic yield and time to diagnosis was obtained.

Results: A definite diagnosis was made in 13 out of 50 patients (26%: 5/7 prospective; 8/43 retrospective). This included known pathogenic and novel variants in SCN1A, ATP1A2, ALG13, STXBP1, POLG, SCN1B, KCNQ2 x 3, PAFAH1B1, TUBB2B, GABRA1 and CACNA1H. A possible diagnosis was identified in 5 additional retrospective patients for which supporting evidence is pending (GABRB3, ARHGEF9, CHD2, KCNQ2, SCN3A). An additional retrospective patient was identified to have a diagnosis which did not fully explain her phenotype (2 variants in BTD recognized to cause partial biotinidase deficiency, with biochemical support of low biotinidase). Eight patients (16%: 2 prospective, 6 retrospective) had a diagnosis with possible treatment implications (ATP1A2, SCN1A, SCN1B, BTD, KCNQ2 x 3, POLG). The patient with compound heterozygous mutations in POLG was on valproic acid which was stopped due to study results. Her liver enzymes were increasing at time of diagnosis and normalized with valproic acid removal. The patient with SCN1A mutation (Dravet syndrome) was also heterozygous for a maternally inherited SCN5A variant of uncertain clinical significance. SCN5A is associated with epilepsy, cardiac arrhythmias and sudden death. Time from enrollment with genetic counselling to diagnosis with Sanger confirmation was 21 – 105 days (mean 48 days).

Conclusions: The clinical utility of using WES in this cohort is supported by potential diagnoses in 19/50 patients (38%: 5/7 prospective; 14/43 retrospective) within a mean time of 48 days. Diagnoses in 8 (16%) patients had immediate treatment implications. WES also facilitated multi-locus variant identification that may further impact the phenotype (SCN5A). Genome-wide WES from patients/families with no genetic diagnosis will also be analyzed to implicate novel genes in epilepsy and likely increase the diagnostic yield.

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