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Family Sequencing Ties De Novo Sodium Channel Gene Mutation to Epilepsy

NEW YORK (GenomeWeb News) – By sequencing the genomes of four individuals from a single family, researchers from the University of Arizona and elsewhere have identified another sodium channel gene with ties to epilepsy — the fifth so far.

As they reported online yesterday in the American Journal of Human Genetics, researchers linked a missense mutation in the SCN8A gene to infantile epileptic encephalopathy condition by sequencing the genome of an affected girl, both her parents, and her unaffected brother.

"This work identifies SCN8A as the fifth sodium channel gene to be mutated in epilepsy and demonstrates the value of [whole-genome sequencing] for the identification of pathogenic mutations causing severe, sporadic neurological disorders," senior author Michael Hammer, with the University of Arizona's Arizona Research Laboratories, and colleagues wrote.

The affected individual, who began having seizures when she was just six months old, died unexpectedly at the age of 15 from what was classified as a "sudden unexplained death in epilepsy." Her condition prior to that had been characterized by seizures, autistic symptoms, intellectual disability, and other neurological, language, and movement-related problems.

Because the condition was severe and turned up in an individual with no obvious family history that might offer clues to the cause, Hammer and colleagues suspected that the girl's disease might be due to a dominant de novo mutation.

When they failed to detect any suspicious, rare copy number changes by array comparative genomic hybridization, the team decided to turn to whole-genome sequencing to search for de novo alterations that might explain the girl's disease.

All four family member's genomes were sequenced to a mean depth of 57 times to 77 times over 96 to 97 percent of the genome at Complete Genomics.

Of the nearly 32,000 variants detected in protein-coding sequences in the genomes, 13,395 of the autosomal variants were predicted to have functional effects.

The researchers further refined their variant set by looking for blocks of inherited sequence in each of the children's genomes before focusing in on variants that did not fit with predicted inheritance patterns.

"For the 11,292 variants fully called within the quartet," the study authors explained, "34 violated the Mendelian inheritance rules and would be consistent with a de novo mutation within the proband (i.e., the mutation is present in the proband but not in either parent or the sibling.)"

From there, the researchers weeded out variants that did not seem to be disease-related, first tossing out variants found in 1000 Genomes Project data or in other genomes sequenced at Complete Genomics, and then sorting variants based on whether they occurred in error-prone or repeat rich parts of the genome.

The two-dozen variants that remained were tested by Sanger sequencing, which verified just one de novo variant in the affected child: a missense mutation in SCN8A, the latest in a string of sodium channel genes that have been linked to epileptic conditions.

In this case, the patient's missense mutation is predicted to swap out an asparagine for an aspartate in a highly conserved region of a sodium channel sub-unit called Nav1.6 that's found throughout the brain and central nervous system.

Indeed, the team's follow-up experiments in cell lines indicate that neurons containing this dominant mutation are prone to spontaneous and excessive firing — features consistent with the patient's seizure symptoms.

Meanwhile, when they analyzed the data assuming homozygous recessive inheritance, researchers found alterations in two genes — NRP2 and UNC13C — that were previously implicated in autism, epilepsy, and neuronal-related functions.

The team speculated that these recessive changes may have influenced the way the affected child's condition manifested itself — and the severity of her symptoms. Nevertheless, they cautioned that additional research is needed to test that notion.

"It has often been suggested that the inheritance of modifier loci contributes to the wide phenotypic variability of individuals with SCN1A mutations," researchers noted. "With [whole-genome sequence] data, it is now possible to predict the identity of specific candidate modifier variants in individuals."

Analysis of non-coding regions in the family's genomes led to 23 potential regulatory mutations, the researchers reported, though none of those alterations could be confirmed by Sanger sequencing.

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