Semantic similarity. The phenotype era in the epilepsies has now officially started. While it is possible for us to generate and analyze genetic data in the epilepsies at scale, phenotyping typically remains a manual, non-scalable task. This contrast has resulted in a significant imbalance where it is often easier to obtain genomic data than clinical data. However, it is often not the lack of clinical data that causes this problem, but our ability to handle it. Clinical data is often unstructured, incomplete and multi-dimensional, resulting in difficulties when trying to meaningfully analyze this information. Today, our publication on analyzing more than 31,000 phenotypic terms in 846 patient-parent trios with developmental and epileptic encephalopathies (DEE) appeared online. We developed a range of new concepts and techniques to analyze phenotypic information at scale, identified previously unknown patterns, and were bold enough to challenge the prevailing paradigms on how statistical evidence for disease causation is generated. Continue reading
Tag Archives: SCN1A
GNAO1 and 13K genomes – rare disease sequencing on a national level
WGS. Whole-genome sequencing is increasingly used to understand the cause of rare diseases in a research and diagnostic context. However, while the usefulness of this technology has been shown in smaller studies, it remains unclear whether strategies to understand the cause of rare disorders through whole genome sequencing can be performed on a national level. A recent study in Nature reported the first results from a national sequencing campaign for rare disorders in the UK, including the analysis of more than 13,000 genomes. In this blog post, I would like to focus on the neurogenetics component of this enormous study, which identified disease-causing variants in GNAO1 as the most common cause within the study’s subgroup of neurological and developmental disorders. Continue reading
Common genetic risk factors for epilepsy in the Japanese population
GWAS. While our blog mainly deals with monogenic epilepsies, assessing common genetic risk factors through genome-wide association studies has been an established way of understanding potential genetic contributors to both common and rare disorders. More recently, polygenic risk scores have entered the stage, composite measures of many common variants which explain a significant proportion of the overall population risk for epilepsy. However, a major limitation of many genome-wide association studies has been the focus on populations of European ancestry. So far, very few studies have examined common genetic risk factors in the epilepsies in non-European populations. In a recent publication examining results from the BioBank Japan Project, 42 disorders were examined in more than 200,000 individuals, including the epilepsies. While no single epilepsy variant stood out, the study provides an interesting confirmation of a previously known common risk factors for the epilepsies. Continue reading
How common is rare? A population-based study into genetic childhood epilepsies
What is the most common monogenic cause of epilepsy? This is a question we often ask students and trainees who rotate with us in our Epilepsy Neurogenetics Clinic. This is not meant to be a trick question, and the answer we previously sought was based largely on published studies, estimates of population frequency of individual genetic epilepsies, and our own clinical experience. And we are sometimes surprised by how skewed such a view can be. Now, a new study by Symonds and colleagues answers the question of population-incidence of common genetic epilepsy syndromes through a prospective population-based cohort study in Scotland. This study provides important data on risk factors that are more likely to predict a genetic diagnosis in infants and young children with seizures and answers the question of which genetic epilepsy is most common. I was initially surprised, but really not surprised at all, by the answer. Continue reading
The second ILAE GWAS or why 30% of genetic generalized epilepsy is explained
Genome-wide association. While most of the neurogenetics community was focused on exome sequencing and the discovery of novel monogenic forms of epilepsy in the last few years, something quite remarkable had happened in the background. Common variants and genome-wide association studies have made a remarkable comeback. The ILAE Consortium for Complex Epilepsy had slowly worked on increasing sample sizes over time, and the second analysis of common variants in common epilepsies was published in late 2018. Sample sizes have almost doubled since the first study in 2014, and as a result, the number of genome-wide significant loci has tripled. However, the most intriguing finding was something that completely caught me by surprise – more than 30% of the heritability of the genetic generalized epilepsies is explained through common variants, approaching the numbers we see in epileptic encephalopathies explained by monogenic causes. This is one more reason to discuss the recent ILAE GWAS in more detail. Continue reading
SCN1A-related epileptic encephalopathy: Beyond Dravet syndrome
SCN1A phenotypes. Readers of Beyond the Ion Channel will know that we often post about SCN1A, one of the first discovered and most common genetic causes of epileptic encephalopathy. We more or less assume that we understand the phenotypes associated with pathogenic variants in SCN1A: most commonly Dravet syndrome, which is associated with de novo variants, and less commonly genetic epilepsy with febrile seizures plus (GEFS+), associated with inherited missense variants. However, a recent publication by Sadleir and colleagues suggests that the phenotypic spectrum of SCN1A-related disorders may be broader than we have previously appreciated. Are there SCN1A-related epileptic encephalopathies in addition to Dravet syndrome? Continue reading
The story of the missed SCN1A mutations
Dravet Syndrome. In 2011, our EuroEPINOMICS-RES program was in full swing. We had recruited a cohort of 31 patients with Dravet Syndrome who had been previously tested negative for mutations in SCN1A with the aim to identify novel genes for this epileptic encephalopathy. Even though this cohort was crucial in our identification of CHD2, HCN1, and KCNA2 as novel genes for genetic epilepsies, the main finding in this cohort was something that we did not expect. Roughly one third of our 31 patients had mutations in SCN1A, even though they had previously been tested negative. In a recent publication in Molecular Genetics and Genomic Medicine, we tried to understand what had happened and joined forces with other groups who had made the same observation. Here is the story of the missed SCN1A mutations. Continue reading
Three novel aspects about epilepsy gene panels
Gene panels. Epilepsy gene panels have emerged as the first line genetic test for most suspected genetic epilepsies. Gene panels for childhood epilepsies are among the most common genetic tests ordered in a pediatric setting. While the role of gene panel testing is well established, the ideal design of gene panels remains an ongoing issue. A recent publication in the Journal of Medical Genetics provides additional evidence for the role of gene panel analysis in patients with genetic epilepsies. There are three aspects of this study that are particularly noteworthy. Continue reading
The three twists in the SCN1A story that you didn’t know about
SCN1A. Finally, after various other epilepsy genes have been added, we are trying to put together a static website on SCN1A rather than updates only. SCN1A is by far the most prominent epilepsy gene and the first genetic etiology that comes to mind for anything relating to fever and seizures. While our Epilepsiome page will give you all the relevant facts regarding this gene, here is my personal view on the SCN1A story. Continue reading
Publications of the week – SCN1A in encephalopathy after febrile seizures, SLC12A5/KCC2 in MMPSI
Issue 14/2015. This week’s publications of the week are about a novel phenotype consisting of persistent encephalopathies with MRI findings associated with SCN1A and SCN2A mutations, a novel gene for Malignant Migrating Partial Seizures of Infancy (MMPSI). Continue reading
