Families. We tend to think that we understand familial epilepsy. The mental image is almost fixed: large pedigrees, clean inheritance, recognizable syndromes, and genes that segregate exactly as expected. But in a recent study from our epilepsy genetics program, we looked at something different. Not discovery cohorts and carefully selected multiplex families, but real-world genetic testing in 484 consecutive families. All families were evaluated in routine clinical care through ENGIN, our Epilepsy Neurogenetics Initiative, which has now evaluated more than 7,000 individuals with epilepsy and related disorders. The result was a picture of familial epilepsy that is both reassuring and unexpectedly complicated. Here is what we found. Continue reading
Tag Archives: SCN2A
Ten Years of Accumulation: Snow-Day Thoughts Between Jonas and Fern
Decade. Over the past week, winter storm Fern has blanketed large parts of the United States with several feet of snow, leading to a virtual standstill in many regions. When I looked back, I realized that the last major snowstorm that paralyzed public life was a decade ago, a storm called Jonas. Snowed in exactly ten years ago, I reflected on the state of epilepsy genetics. Let’s see what has changed in the field since Jonas in 2016.
Five reflections from the FamilieSCN2A Annual Family and Professional Conference
FamilieSCN2A. On July 21-23, the FamilieSCN2A Foundation had their Family & Professional Conference in Boston. Having gone to the conference for the past several years, it is truly remarkable to see the changes over time. Here are five key changes I’ve noticed at this year’s event.
SCN2A – here is what you need to know in 2023
NaV1.2 Today is International SCN2A Day, 2/24/2023. SCN2A is on the long arm (q arm) of chromosome 2 at position 24.3, hence 2/24. In honor of this day, we wanted to refresh the SCN2A gene page, which was long overdue. Much has been learned since our initial post in 2015, so in addition to the gene page, here are three things to know about SCN2A in 2023.
Here are the most frequently read blog posts in epilepsy genetics
2022. In December, our blog passed an important milestone – one million views. Given that Beyond the Ion Channel is a niche blog on epilepsy genetics and pediatric neurogenetics, this is a milestone that we are proud of. In the current post, we would like to examine some of the trends on what people read on our blog. Given that this resource has been around for more than a decade, the topics and genes that people searched for reflect some interesting patterns in the field that may tell us about how information on genetic epilepsy is presented online and what we need to do better. Here are top five most frequently read posts, including some topics that surprised us. Continue reading
ANO3, SCN1A, IL10 – the new genetics of febrile seizures
GWAS. Febrile seizures affect up to 5% of all children between six months and six years and are by far the most common seizure type. While seizures in the setting of fever may be a manifestation of an underlying epilepsy, in the majority of cases, children only have one or two febrile seizures in their lifetimes. We know from twin studies that there is a strong genetic component to febrile seizures, and you might think that we would know more about the most common seizure type. However, this has not been the case until recently. The genetics of febrile seizures have been largely understudied, and we know much more about the genetics of rare epilepsies than about the genetics of febrile seizures. A recent genome-wide association study has been a game changer, highlighting a combination of fever response genes and neuronal genes in the etiology of febrile seizures. Continue reading
This was epilepsy genetics in 2021 – five things to remember
Looking back. Admittedly, I have not written an end-of-the-year review for a quite some time. However, there were a few notable moments in epilepsy genetics in 2021 that I think were worth remembering. The second year of the COVID-19 pandemic started out as a year of recovery and readjustment, only to run into unanticipated supply chain issues and novel COVID variants hanging over our transition into 2022. The scientific community was affected by these developments in different ways that made progress of science somewhat unpredictable and uneven. 2021 was the year when the phrase “unprecedented times” became stale and overused. Here are five things to remember from 2021, which will be remembered as part of a transitional phase in epilepsy genetics. Continue reading
SCN2A – a neurodevelopmental disorder digitized through 10,860 phenotypic annotations
HPO. SCN2A-related disorders represent one of the most common causes of neurodevelopmental disorders and developmental and epileptic encephalopathies (DEE). However, while a genetic diagnosis is easily made through high-throughput genetic testing, SCN2A-related disorders have such a broad phenotypic range that understanding the full scale of the clinical features has been traditionally difficult. In our recent study, we used a harmonized framework for phenotypes based on the Human Phenotype Ontology (HPO) to systematically curate phenotypic annotations in all individuals reported in the literature and followed at our center, a total of 413 unrelated individuals. Mapping phenotypic data onto 10,860 terms with 562 unique concepts and applying some of the computational tools we have developed over the last three years, we were able to delineate the phenotypic range in unprecedented detail. SCN2A is now the first DEE with all available data systematically curated and harmonized in a computable format, allowing for entirely novel insights. Continue reading
Entering the phenotype era – HPO-based similarity, big data, and the genetic epilepsies
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
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