Ion Channel Project

Parallel Sequence Profiling of Ion Channels in Epilepsy

The BCM Ion Channel Project is a collaboration of BCM-HGSC with a clinical research team in the BCM Department of Neurology, led by Jeff Noebels, M.D., Ph.D., to investigate genetic factors in ion channelopathy and specific epilepsy phenotypes.

The project employs BCM-HGSC's large scale gene sequencing capacity and mutation analysis resources to test the general hypothesis that profiling the coding sequences of large numbers of channel genes in individual epilepsy patients can reveal novel mutations and patterns of common allelic variants that determine epilepsy susceptibility and pharmacoresistance.

Ion channel genes constitute about 1.2% of known protein coding genes, and inherited mutations of these genes elicit a diverse array of clinical disorders of brain, nerve, muscle and heart. In brain, single gene channelopathies are the predominant cause (13/14) of rare Mendelian idiopathic epilepsy syndromes, but their contribution to common sporadic epilepsy is unknown.

High rates of de novo mutation and complex polygenic inheritance (the "common disease-common variant" model) are two attractive explanations for the role of ion channel variation in sporadic cases. Together with their important pathogenic role, ion channels are also the primary molecular targets of most antiepileptic drugs, and genetic variation in channel subunits may independently contribute to pharmacoresistance.

BCM-HGSC is undertaking rapid and scalable parallel exon sequencing of 250 candidate ion channel genes in 500 patients with specific clinical epilepsy phenotypes and in 500 ethnically-matched controls.

These data will be used in two ways:

  • First, the biophysical and pharmacological properties of a subset of channel gene polymorphisms with predicted protein coding variation will be analyzed in mammalian expression systems in order to define a validated subset of functional gene variants of human ion channels relevant to epilepsy. This list is essential to examine models relating specific pathophysiological properties of ion channels to the patterns associated with epilepsy.

  • Second, the sequence of the channel genes will be assembled into a profile of each individual (their "channotype") and used to test the statistical association of different channotypes with epilepsy phenotypes.

Preliminary analyses have detected many novel and previously reported SNPs (coding and non-coding) and microdeletions.

The associations identified in this study will address a major hypothesis underlying the complex genetics of epilepsy, accelerate development of individualized clinical risk assessments for epilepsy, and examine a novel mechanism of resistance to antiepileptic drugs in children and adults with common idiopathic forms of the disorder.

Related Publications

Kanost MR, Arrese EL, Cao X, Chen Y-R, Chellapilla S, Goldsmith MR, et al. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Biochem Mol Biol. 2016 ;76:118-47.

Stray-Pedersen A, Cobben J-M, Prescott TE, Lee S, Cang C, Aranda K, et al. Biallelic Mutations in UNC80 Cause Persistent Hypotonia, Encephalopathy, Growth Retardation, and Severe Intellectual Disability. Am J Hum Genet. 2016 ;98(1):202-9.

Klassen T, Davis C, Goldman A, Burgess D, Chen T, Wheeler DA, et al. Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy. Cell. 2011 ;145(7):1036-48.