Genomic sharing. Let’s compare our state of sharing genomic data to the music industry. We are at a point where we share large datasets between genome centers, occasionally shipping hard drives or using fast upload tools. Still, we are copying and transferring terabytes of data from A to B, making copies of datasets locally in order to have them for our local analysis. A BAM file is only useful if it is present on our server. It is like downloading all the Led Zeppelin albums in the early 2000s through sharing platforms. We are currently in the Napster age of genomic data, amazed how quickly these large datasets tend to clog our server space. Let us revisit what happened to Napster and why our current way of thinking will soon be outdated in what will become the genomic sharing economy. Continue reading
Three Things I’ve Learned from Living with the Channelopathist
Today is a big day here at Beyond the Ion Channel – it’s Ingo’s birthday. I clearly remember celebrating Ingo’s birthday a decade ago, while we were living and working together in Melbourne. Back then, life was a little simpler. We were just beginning our careers together at the Epilepsy Research Centre and were a little more fresh faced and greener behind the ears. The GGEs were still the IGEs. Mutation screening was done via dHPLC. Family studies were still the way to go. Genetics was largely confined to the research realm and not a possibility for most patients in clinical practice. A lot has changed in epilepsy genetics in 10 years, and I have been fortunate to have my career run alongside Ingo’s during that time, sometimes running parallel to his and sometimes intertwining. We’ve learned a lot from each other. So what do you give someone like Ingo for his birthday? A blog post, of course. But don’t worry, it won’t be overly sentimental. As Ingo mentioned before, that’s not our style. Here are three things I’ve learned about epilepsy genetics from Ingo over the last ten years. Continue reading
The two dimensions of STXBP1 – a 2016 update
Synaptic. This is STXBP1 week and things are currently happening in rapid succession. We are getting ready for the first STXBP1 Charity Ball and our publication in Neurology reviewing the phenotypic features of 147 patients recently came online. STXBP1 is one of the five most common genes for epileptic encephalopathies and related neurodevelopmental disorders. However, in contrast to SCN1A, SCN2A, CDKL5, or SCN8A, it has received relatively little attention in the past from the epilepsy community. Let’s revisit a common epilepsy gene that holds more secrets than most people would imagine. Continue reading
Introducing EpiGC – a guest post
School days, school days, dear old golden rule days. It has been over two decades since I completed my training as a genetic counselor, but there are several families that I will always remember and find myself frequently talking about when I train students or discuss counseling issues with colleagues. One of them was a young couple, both with mild intellectual disability and epilepsy, expecting their first child.
Familial epilepsies revisited – the big picture
Family genetics. The analysis of epilepsy families helped jumpstart the field of epilepsy genetics by identifying SCN1A and several other epilepsy genes in the late 1990s. However, more recently, gene discovery in familial epilepsies has been overshadowed by the explosion of gene identifications in sporadic epileptic encephalopathies. A recent publication in Neurology now reviews the results of a decade-long endeavor to characterize familial epilepsies in Israel and Palestine. Find out why we are far from understanding the majority of familial epilepsies, why GGE/IGE families are the main problem, and what the “familial four” are.
Five almost forgotten blog posts that are relevant in 2016
Happy 400. Even though I have to admit that my blogging speed has decreased considerably over the last 18 months, we managed to celebrate a small milestone last week. We published blog post #400. As there are highly popular and virtually forgotten blog posts, I wanted to use this opportunity to draw your attention to five blog posts out there that you might want to know about. Continue reading
The 2016 Epilepsiome series
Introduction. The Epilepsiome is our community-driven gene curation project. Ever since we last wrote about this project, many discussions have been going on in our community and we have decided to put together a 10-part post series this year to tell you where the journey is headed. Here is what we would like to put together in the first half of 2016. Continue reading
Research parasites and symbiotes
Parasitic. In the dramatic language that was somewhat reminiscent of the current US primaries, the New England Journal of Medicine warned of an emerging class of researchers referred to as research parasites, researchers who had nothing to do with an initial study, but re-analyze data without being connected to the initial study design, possibly for their own purposes. The NEJM editorial was accompanied by a call for collaborative research on a coordinated basis rather than analyzing data without working with the researchers who were initially involved in the generation of the data. Let’s discuss whether genetics is currently under threat from research parasite infestation and whether this may actually be a good thing. Continue reading
The novel gene dilemma
N-of-1. The use of whole exome sequencing has led to many of the recent genes discovered in the epilepsy field. However, in contrast to established genes or emerging genes that are found in several patients, there is a significant proportion of patients who carry de novo mutations in novel genes. In many cases, these novel genes look very suspicious. One aspect of a recent publication in Genetics in Medicine was to assess how these suspicious candidates convert to established genes over time. Continue reading
My name is Jonas – a blizzard blog post
Do you want to build a snowman? During this weekend, winter storm Jonas descended upon the Eastern United States. Delaware County became covered under about two feet of snow, basically shutting down public life in the Philadelphia and the surrounding suburbs. Being trapped in the house with the kids exhausted from playing outside gave me the opportunity to catch up on my blogging duties and to engage in creative writing. Besides a reference to the 1994 Weezer alternative rock anthem, here is what snow storm Jonas told me about science. Continue reading