Papers of the week – DEPDC5, a “female protective model” and rescued KCNT1 mutations

In final week before our EuroEPINOMICS Bild1bioinformatics workshop in Leuven people get a little busy and start reading up on all sorts of things. Accordingly, this week’s papers come from all areas of genetics and life science, including three studies in Annals of Neurology on epilepsy genetics.

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The age of mega-genomics, type 2 diabetes, and protective variants in SLC30A8

Sequence first. There are larger genetic studies but not too many. In a recent study in Nature Genetics, roughly 150,000 individuals were genotyped to assess the importance of rare, disruptive variants in SLC30A8 in type 2 diabetes. This genomic tour de force was made possible by available and curated databases that could be tapped to extract the necessary genetic information. Also, this study highlights some of the surprises that we can expect by mining the human genome for disease-related information. Rare, disruptive variants in SLC30A8 protect against type 2 diabetes. Let’s review why these rare, protective genetic factors might be particularly important for biomedical research and what kind of studies we need to identify them. Continue reading

Five questions you should be asking the ILAE Genetics Commission

Five questions. We are now part of the new Genetics Commission of the International League Against Epilepsy (ILAE), as we already indicated in an earlier post. Here’s what you can expect from the Commission over the course of the next four years. Continue reading

Mining GWAS mountains for missing heritability

What is missing? The catchy term “missing heritability” refers to a long-standing issue in human genetics that is particularly relevant to common diseases that are thought to have complex genetic architecture. Even though we know several thousands of risk factors for common diseases, the sum of all these risk factors only explains a small proportion of the genetic risk for disease. Where is all the remaining genetic disease risk hidden? A recent publication in PLOS Genetics suggests that known association peaks in genome-wide association studies (GWAS) may harbor more than one risk variant, turning GWAS peaks into mountain ranges. Also, this publication provides an interesting state-of-the art review on the role of common and rare variants with respect to missing heritability. Let’s turn back the clock and start with the decade-old debate on common versus rare variant models of human disease. Continue reading

Pharmacogenomics for epilepsy

The treatment options for epilepsy must undoubtedly be improved. More than 20 antiepileptic drugs are licensed but in 30% of patients seizures are not controlled, despite treatment with a number of anti epileptic drugs and the response to medication is difficult to predict. Antiepileptic medications can cause severe adverse reactions and increase the risk of fetal malformations in women taking them during pregnancy. The differences in drug response and the occurrence of rare adverse reactions are believed to be caused by variants in the genetic makeup of individuals. Knowledge of these variants would help us to predict drug response and adverse drug reactions. This personalized treatment would help us to select medications for each individual.

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The genetics of treatment response in newly diagnosed epilepsy

Two questions. There are two main questions that we would like to answer with genetics in the field of epilepsy. First, are there genetic risk factors for epilepsies and if so, what are they? Secondly, are there genetic factors that help us understand how patients react to treatment, i.e. are there genes that predispose to response to antiepileptic drugs or that might be associated with side effects? While we have made much progress in answering the first question by identifying many epilepsy genes, there have been few answers for the second question, the field of pharmacogenomics. Now, a recent study in Human Molecular Genetics looks at potential genetic risk factors for the response to antiepileptic drugs in newly treated epilepsy. This is a study that needed to be performed and that we were waiting for. Continue reading

Guilt by association: SCN1A in Temporal Lobe Epilepsy

GWAS. Genome-wide association studies investigate the association of common genetic variants with disease in large patient samples. While this approach has been very successful in many other diseases, the results in epilepsy research have been less convincing. Given the complexity of epilepsy phenotypes, selection of the right epilepsy phenotype has been an ongoing debate. Now, a recent study in Brain finds an intronic variant of the SCN1A gene that is associated with Temporal Lobe Epilepsy (TLE), the most common epilepsy in man. Interestingly, the association with SCN1A seems to be specific for only a particular subtype of focal epilepsies. Continue reading

Malaria, seizures and genes

Our old genome. When talking about seizures and genes, “malaria” is usually not the first thing that comes to mind. However, malaria-associated seizures are a major cause of neurological disability in Sub-Saharan Africa. Given the frequency of malaria infections on a worldwide scale, Plasmodium falciparum, the parasite causing malaria, is probably one of the most frequent causes of acute seizures. Our genome has adapted to dealing with parasites over evolutionary time and several disease-causing mutations are thought to be relatively frequent, as they also confer resistance to malaria. For malaria-associated seizures, family studies show an increase in epilepsy in relatives, suggesting that these parasite-induced epileptic seizures may also have a genetic predisposition. A recent study in Epilepsia now investigates malaria candidate polymorphisms as genetic risk factors for malaria-associated seizures. Continue reading

5 good reasons for neuroblogging – The EuroEPINOMICS blog celebrates its first birthday

Growing up. Exactly one year ago, we got serious about blogging and started posting regularly on the EuroEPINOMICS blog. Since then, we have published 145 posts on various topics regarding epilepsy, genes and the life of a scientist. In this post, we just wanted to give you five good reasons why we keep on neuroblogging. Continue reading

Spooky, scary, phantom heritability

Twilight zone. Admittedly, Halloween is already a few weeks behind us, but I was reminded of it a week ago when I stumbled across the concept of phantom heritability. And guess what, this concept has already been out there since early 2012 and, scarily enough, we didn’t notice it. So what is this mysterious conspiracy behind phantom heritability? Well, it’s about things out there beyond our understanding and the fact that we might already know more than we think we know. But be warned, if you decide to read this post, your understanding of genetic architecture might be changed forever. And there is no going back. Boo! Continue reading