A targeted resequencing gene panel for focal epilepsy

Michael Hildebrand

Candace Myers

Gemma Carvill

Brigid Regan

Elena Gazina+6 authors

Objectives:

We report development of a targeted resequencing gene panel for focal epilepsy, the most prevalent phenotypic group of the epilepsies.

Methods:

The targeted resequencing gene panel was designed using molecular inversion probe (MIP) capture technology and sequenced using massively parallel Illumina sequencing.

Results:

We demonstrated proof of principle that mutations can be detected in 4 previously genotyped focal epilepsy cases. We searched for both germline and somatic mutations in 251 patients with unsolved sporadic or familial focal epilepsy and identified 11 novel or very rare missense variants in 5 different genes: CHRNA4, GRIN2B, KCNT1, PCDH19, and SCN1A. Of these, 2 were predicted to be pathogenic or likely pathogenic, explaining ∼0.8% of the cohort, and 8 were of uncertain significance based on available data.

Conclusions:

We have developed and validated a targeted resequencing panel for focal epilepsies, the most important clinical class of epilepsies, accounting for about 60% of all cases. Our application of MIP technology is an innovative approach that will be advantageous in the clinical setting because it is highly sensitive, efficient, and cost-effective for screening large patient cohorts. Our findings indicate that mutations in known genes likely explain only a small proportion of focal epilepsy cases. This is not surprising given the established clinical and genetic heterogeneity of these disorders and underscores the importance of further gene discovery studies in this complex syndrome.

Supplementary Material

Data Supplement:

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From the Epilepsy Research Centre (M.S.H., B.M.R., J.A.D., S.A.M., M.R.N., I.E.S., S.F.B.), Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia; Division of Genetic Medicine (C.T.M., G.L.C., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Florey Institute for Neuroscience and Mental Health (U.N., E.V.G., C.J.M., C.A.R., S.P., I.E.S.), University of Melbourne, Melbourne, Victoria, Australia; Department of Neurology (I.E.S.), Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia; and Department of Pediatrics (I.E.S.), University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.

^{Corresponding author.}

Correspondence to Dr. Mefford: ude.wu@droffemh or Dr. Berkovic: ua.ude.bleminu@civokreb.s

^{These authors contributed equally to the manuscript.}

Go to Neurology.org for full disclosures. Funding information and disclosures deemed relevant by the authors, if any, are provided at the end of the article.

Correspondence to Dr. Mefford: ude.wu@droffemh or Dr. Berkovic: ua.ude.bleminu@civokreb.sGo to Neurology.org for full disclosures. Funding information and disclosures deemed relevant by the authors, if any, are provided at the end of the article.

Received 2015 Jul 28; Accepted 2016 Jan 19.

Abstract

Objectives:

We report development of a targeted resequencing gene panel for focal epilepsy, the most prevalent phenotypic group of the epilepsies.

Methods:

The targeted resequencing gene panel was designed using molecular inversion probe (MIP) capture technology and sequenced using massively parallel Illumina sequencing.

Results:

Conclusions:

Abstract

Investigation of genetic epilepsies has proven highly successful in recent years in a subset of cases. A variety of genes that cause human epilepsies have been discovered, revealing novel and unexpected biological pathways and providing important diagnostic and counseling information for patients and their families.¹ Focal epilepsies account for about 60% of all epilepsies.²,³ Despite being the most common form of epilepsy, focal epilepsies had been definitively associated with only 11 genes at the time of platform design, mostly as a result of genetic analysis of large multiplex families. De novo mutations (likely occurring in parental gametes) of a number of genes have been discovered,⁴^–⁷ indicating genetic causation in patients with focal epilepsy even without a family history. In this study we sought to determine the contribution of known genes to the causation of a broad spectrum of focal epilepsies.

To unravel this contribution, we studied a large resource of patients with focal epilepsy (n = 251). The phenotypic and genetic heterogeneity of focal epilepsies warranted a comprehensive targeted resequencing approach. We applied single molecule molecular inversion probes (smMIPs⁸) to focal epilepsies, arguably the most clinically important group of epilepsies, to develop a focal epilepsy targeted resequencing gene panel.

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ACKNOWLEDGMENT

The authors thank the family for their participation in this study. Elena Aleksoska (Epilepsy Research Centre) is acknowledged for performing genomic DNA extractions.

ACKNOWLEDGMENT

GLOSSARY

ExAC	Exome Aggregation Consortium
MIP	molecular inversion probe
NFLE	nocturnal frontal lobe epilepsy
smMIP	single molecule molecular inversion probe
TLE	temporal lobe epilepsy

GLOSSARY

Footnotes

Supplemental data at Neurology.org

Footnotes

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