“Dark social” or “Who is afraid of email?”

Heathrow. Dark social? Threat? I’ll get back to that. I am writing this wrap-up post for the SpotOn 2013 meeting overlooking the British Airways planes on their way to take-off. In the last two days, we caught a glimpse of what online science communication is about. On Saturday, we had our own session #solo13blogs on using blogs for peer-to-peer science communication. As a science communication newbie, I am happy that our session was well received and stimulated quite some discussion. I have taken away three things from this meeting – a new understanding of our readership, an appreciation for Open Access and data sharing, and finally, a fear of the destructive power of dark social that also applies to epilepsy genetics research. But first things first. Continue reading

SpotOn London, Open Access and the Higgs boson

#solo13. Some strange symbols that made it onto our blog originate on Twitter. The “#” (hash) precedes a hashtag, which indicates a Twitter topic. “@” (at) is called a handle, a possibility to contact people. As you might remember from our previous announcements, Roland and me are currently participating in SpotOn 2013, a conference for online science communication. The meeting is held at the British Library in London. This is just a brief update on what #solo13 was about today. Continue reading

Navigating the epilepsiome – live from Tübingen

2D. I am writing this post during our EuroEPINOMICS meeting in Tübingen listening to presentation from CoGIE, the EuroEPINOMICS project working on IGE/GGE and Rolandic Epilepsies and RES, the project on rare epilepsies. At some point during the afternoon, I made my selection for the best graph during the presentations today – an overview of the conservation space of epilepsy genes. Continue reading

Three things you didn’t know about epilepsy and genes

Fall colors. Just a brief summary of how this post originated. Eckernförde is a small city north of Kiel and the weekly Sunday destination of my daughter and me because of the wave pool.  This past Sunday, daylight saving and the fact that she didn’t like her dinner had confused the little girl, and we had been awake since 4AM. As a consequence, she fell asleep on the way, and I kept driving to let her sleep. We made it as far as Haddeby, and I used this time to mentally put a post together that I had been planning for some time. These are the three things that are often misunderstood with regards to epilepsy and genes. Continue reading

The pebbles of Demosthenes, the King’s speech, and the genetics of stuttering

Communication breakdown. The Greek orator Demosthenes was said to treat his speech impediment by talking with pebbles in his mouth and shouting above the roar of the ocean waves. US Vice President Joe Biden, brutally nicknamed Joe Impedimenta in school, worked on his stuttering reading Emerson and Yeats aloud. Hollywood actor Samuel L. Jackson overcame blocks and pauses while talking by interjecting his trade mark profanity. Given the list of famous people who stutter including Isaac Newton, Charles Darwin, and Theodore Roosevelt, I feel in pretty good company. I am a person who stutters myself, even though my speech impediment is currently mild. Stuttering is a neurodevelopmental disorder whose genetic architecture is entirely unexplored on the molecular level but clinically shares resemblance with many other neurodevelopmental disorders that we have written about on this blog. Today is International Stuttering Awareness Day. I have thought back and forth about whether I want to write this post given my personal involvement as a person who stutters and the resulting lack of objectivity. However, I finally decided to do so in order to put stuttering where it belongs – on a research blog about neurogenetics. Continue reading

SpotOn London 2013 – communicating science online

Outreach. SpotOn is a series of community events for the discussion of how science is carried out and communicated online. SpotOn London (November 7-9, 2013) is organized by the Nature Publishing Group and represents the flagship conference of the SpotOn series. SpotOn discussions fall into three broad topic areas – policy, outreach, and tools – and this site collates the conversations and other archive material around all of the events. Within the outreach track, Roland and I will contribute to the session about scientist-to-scientist communication using blogs and other online tools. Here is why this pertains to you: in a semi-strategic last-minute move, we managed to reserve one extra ticket that we would like to give to a young scientist who would like to join us in London. Short notice? Spontaneous ideas are sometimes the best ideas. Also, for everybody else, there is one last chance on Friday at 12:00 London time to get tickets. Continue reading

Beneath the surface – the role of small inherited CNVs in autism

Grey zone. Structural genomic variants or copy number variations (CNV) can be reliably assessed using array comparative genomic hybridization (array CGH) or Single Nucleotide Polymorphism (SNP) arrays.  However, for deletions or duplications smaller than 50-100 kB, these technologies have a poor detection rate with many false positive and false negative findings unless platforms are used that target specific candidate regions. Exome analysis, on the other hand, is capable of assessing genetic variation reliably on the single base-pair level. Between both technologies, there is a grey zone of structural genomic variants that are difficult to detect; CNVs smaller than 50 kB are often difficult to assess, and the extent and pathogenic role of these small CNVs is unclear. Now, a recent paper in the American Journal of Human Genetics manages to detect small CNVs through exome data. Their analysis in patients with autism, parents, and unaffected siblings suggests a contribution of small inherited CNVs to the overall autism risk. Continue reading

Mutation intolerance – why some genes withstand mutations and others don’t

The river of genetic variants. The era of high-throughput sequencing has given us several unexpected insights into the human genome. One of these insights is the observation that mutations or variations can occur in parts of our genome without any major consequences. Every individual is a “knockout” for at least two genes in the human genome. This means that in every individual, both copies of a single gene are disrupted through mutations or small deletions or duplications. In addition, there are dozens, if not hundreds, of genes with disruptive mutations that affect only a single copy of the gene. Similar mutations in specific disease-associated genes, however, will invariably result in an early onset genetic disorder. This comparison already shows that the genes in the human genome differ with respect to the amount of disruptive genetic variation they can tolerate. A recent study in PLOS Genetics now tries to catalogue the genes in the human genome by assessing their mutation intolerance based on the genetic variation seen in large-scale exome datasets. Many genes for neurodevelopmental disorders are highly intolerant to mutations. Furthermore, some genes for monogenic epilepsies show surprising results in this assessment. Continue reading

Are there incidental findings in exomes that require immediate action?

Guidelines. High throughput sequencing generates an unprecedented amount of genetic data. Most exomes are generated in a specific context, i.e. the genetic data is screened for variations in specific candidate genes or screened for de novo mutations. However, these approaches only use a small fraction of the genetic data generated per individual. High-throughput sequencing may also reveal clues towards possibly relevant diseases, and there is an ongoing debate if and how incidental findings should be returned to individuals undergoing high-throughput sequencing. Now, a recent paper in the American Journal of Human Genetics uses a very stringent clinical approach to assess the frequency of medically actionable findings in exome data. The results are not what you would think, and there is an urgent need to fix the existing databases. Continue reading

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