Returning genetic results to research participants: challenges and opportunities

A successful partnership. Making progress in understanding the genetics of the epilepsies requires a successful partnership involving many players. Researchers, clinicians, patients, and families must work together in order to advance scientific goals. Since the first genetic etiology was discovered in a large family with Autosomal Dominant Nocturnal Frontal Lobe Epilepsy nearly 20 years ago, we have made many strides scientifically, in terms of technologies, our clinical classifications, and our knowledge of genetics. Our views on how we approach research from an ethical perspective is also continuing to evolve. Genetic research hinges on the participation of patients and families, and returning results to participants is increasingly viewed as imperative. A recent paper has used the Epilepsy Phenome/Genome Project (EPGP) and Epi4K studies as a case example of the challenges and opportunities regarding returning genetic results to research participants. Continue reading

Exploring the dark matter of the human genome – de novo mutations in regulatory elements

Unsolved cases. We are in an era of dramatic progress in understanding the genetic causes of neurologic disorders. In spite of this progress, many cases remain unsolved even after whole exome sequencing. One hypothesis for this missing heritability is that “non-coding” mutations outside the exome may explain at least some of these unsolved cases. A recent study looked at de novonon-coding variants in patients with neurodevelopmental disorders. The study sheds new light on this question and reminds us that, despite all the recent progress, there is much still to learn about vast portions of the genome. Continue reading

Changing the debate on epilepsy genetics – the ILAE Epilepsiome Task Force

Epilepsiome. Within the new structure of the ILAE Genetics Commission, the Epilepsiome has become a Task Force for the current term. Our blog has accompanied the developments in the field of neurogenetics for the last seven years and has seen the rise of next-generation sequencing and formal gene and variant curation frameworks. This has left us with a basic question: what is left to say? Should the future Epilepsiome simply chronicle what is happening in the field or should we try to use our platform to develop novel and potentially provocative thoughts? Within the current Epilepsiome Task Force, we decided to try the latter. There has been much attention paid to, and understandably much excitement about, the prospect of targeted precision treatments based on specific gene mutations. But could this be a Potemkin village based on unrealistic treatment expectations? What else is happening in the field of epilepsy genetics, outside the spotlight? We agreed that the new Epilepsiome Task Force will strive to emphasize a richer, globally oriented, and multifaceted view of the genetic basis of human epilepsies and neurodevelopmental disorders. Here are the three things that our Task Force hopes to accomplish. Continue reading

The 2018 neurological phenotyping course for systems genetics – an invitation to Luxembourg

Computational phenotypes. Clinical epilepsy research requires the capturing of complex information in a way that then can be subjected to statistical analysis. For the analysis on the phenotype level, new standards are emerging that are heavily informed by genetic studies. In fact, in addition to the known domain-specific classifications such as the ILAE classification for epilepsy, interdisciplinary action is often required to improve the classification of neurological syndromes for a larger analysis. During the upcoming EMBO Practical phenotyping course in Luxembourg, we will introduce trainees in the field to concepts like the Human Phenotype Ontology (HPO), a controlled vocabulary to characterize syndromes and one of pillars of research in complex syndromes such as epilepsy and how to address aspects not covered in HPO. The course will be held in Luxembourg from Oct 4 to Oct 10, 2018. There has already been a strong interest in this course, but we have a few spots left if you would like to register!

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Five elements to include in your manuscript to get full ClinGen points

ClinGen Epilepsy Gene Curation Expert Panel. For the past year I have been a member of the ClinGen Epilepsy Gene Curation Expert Panel, which has been a rewarding professional experience. I have gotten to know several colleagues within the epilepsy and ClinGen communities, I’ve become familiar with resources for gene curation including MONDO and HPO, and I’ve dived deeply into the existing literature linking genes with a broad spectrum of epilepsies. But working with ClinGen has had another unexpected benefit – it has influenced my approach to writing scientific manuscripts. I have been able to apply this knowledge recently when writing a manuscript about a new causative gene for developmental and epileptic encephalopathies. In this post I would like to share five insider tips about what to include in your genetics manuscript so that it can receive full consideration from the ClinGen Epilepsy Expert Panel.
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The power of 3 – exome trios in neurodevelopmental disorders with epilepsy

Trio exomes. The concept of neurodevelopmental disorders is an umbrella term including intellectual disability, developmental delay, and autism spectrum disorder. About one quarter of these patients have epilepsy, including epileptic encephalopathy, in which the epileptic activity itself contributes to developmental delay or regression. One major cause of these disorders are de novomutations, which are present in the child but not present in either of the parents. A recent publication in Nature Genetics looked for de novo variants in nearly 6,700 patients with neurodevelopmental disorders, nearly 2,000 of whom had epilepsy. This study is an order of magnitude larger than the largest previous study of this kind and represents an important effort in epilepsy genetics. Here is what we want to review their major findings. Continue reading

Three things the beach told me about science in 2018

Baggersee. With an unprecedented heat wave hitting the northern hemisphere, I eventually found my annual vacation blog post. I wrote blog posts about our beach vacation in Marielyst, Denmark, or Rehoboth Beach, Delaware. However, this year, it took me the better part of two weeks to realize that I had this year’s beach right beneath my feet – the small artificial beach of the Rossenray Lake, a small lake in my home town in Germany where we spent our summer vacation. And here are the three things the beach (and the lake) told me about science in 2018. Continue reading

Somatic mosaicism of SLC35A2 in focal epilepsy: an emerging common genetic mechanism

Somatic mosaicism in focal epilepsy. Recent findings highlighted the role of somatic parental mosaicism in epileptic encephalopathies. However, somatic mosaicism has also emerged over the last few years as a prominent mechanism in the pathogenesis of lesional focal epilepsies, including focal cortical dysplasia (FCD) type 2 and hemimegalencephaly. Previous studies have identified the role of mosaicism of genes such as MTOR, TSC1/TSC2, and genes encoding components of the PI3K/AKT pathway in patients with epilepsy secondary to brain malformations. A recent study in Annals of Neurology has identified a new unrelated genetic cause of refractory non-lesional focal epilepsy, which leads us to wonder what role mosaicism may be playing in focal epilepsies without obvious findings on MRI.
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The genetic architecture of the epilepsies, as told by 8,500 gene panels

Epilepsy gene panel. Testing for genetic causes in human epilepsy is typically performed using gene panels. In contrast to our research-based exome studies in an academic setting, much of the gene panel testing is performed through commercial laboratories and much of the existing data is usually inaccessible to the scientific community. In a recent publication in Epilepsia, a large US-based diagnostic laboratory reports on some of their existing data on epilepsy gene panels by reporting the results of more than 8500 epilepsy gene panels – a cohort size that is more than five times larger than any prior exome or gene panel study in the epilepsy field. I was asked to write an editorial on this publication, and I also wanted summarize on our blog three key messages that you can take away from this study. Continue reading

Paradigm shifts in epilepsy genetics – continuing the ILAE genetic literacy series

Genetic literacy. Sometimes important milestones don’t feel like much when you eventually reach them. Last Thursday, I woke up sleep-deprived after working on a grant all night and found an NCBI update in my mailbox. Primer Part 2 of the genetic literacy series of ILAE Genetics Commission was now published in Epilepsia and available on PubMed. Finally, both the introductory primers of the genetic literacy series are out – Part 1 dealing with the building blocks including general concepts of epilepsy genetics and epidemiology and now Part 2 about the paradigm shifts that were introduced with the advent of massive parallel sequencing. Both publications were revised and re-written over and over again to fit the overall didactic mission of the literacy series, an effort that takes approximately 10x as long as writing a typical review. But finally, as of May 10, 2018, both Primers are now in their final shape, published and open access to the international epilepsy community. And here is just a quick overview of what this paradigm shift is really about. Continue reading