Capturing data. While genetic analysis can be performed and investigated on an industrial scale in thousands of individuals in parallel, the analysis of clinical data is frequently still the domain of manual data curation. Clinical data is typically collected in a non-standardized way, which makes it difficult for information generated in a clinical context to be used in a systematic data analysis as can be performed with genomic data. However, the tide is turning, and we are slowly coming around to the idea that clinical data also requires the same degree of standardization in order to be used at scale. For none of the epilepsies is such standardization more important than for the rare epilepsies, which include many of the genetic epilepsies. Our lab has been working on frameworks and methods to allow for this kind of analysis in genetic epilepsies. Here is a brief summary of what it actually means to “make data speak”, which has become the mission statement of our lab. Continue reading
Tag Archives: exome
Cost-effectiveness of genetic testing in patients with epilepsy: which test is the right test?
Which test is the right test? In clinical practice, determining an appropriate genetic testing strategy in the evaluation of a patient with unexplained epilepsy is often inconsistent and left to the treating provider, given the lack of evidence-based guidelines. Oftentimes external factors, such as insurance hurdles, dictate the genetic testing that can be ordered. A recent meta-analysis in Neurology attempts to answer the question about which genetic test is most cost-effective in patients with epilepsy, which may aid in the decision making when considering a genetic evaluation of a person with epilepsy. Continue reading
Publications of the week: SCN8A, SYN1, ZDHHC9, and SCNM1
Power outage. This week’s publications of the week were conceptualized in complete darkness. A thunderstorm had hit the Philadelphia area on Tuesday, leading to widespread power outages in the region. I found myself in the strange position of being without power for a night, but with full strength cell phone reception and a completely charged laptop battery. Here is our post on the most relevant publications of the last few weeks, written in the calm of a dark night where the only sound around was the howling of our neighbor’s backup generator. Continue reading
TADA – a joint analysis of de novo and inherited risk factors in autism
Beyond de novo. One of the most robust ways to interpret exome data is the analysis of de novo mutations. However, in addition to the 1-2 de novo events that we can identify in every individual, there is a plethora of inherited variants that often look suspicious. Unfortunately, other than looking at monogenic recessive disorders, we are often incapable of understanding the importance of these inherited variants and tend to ignore them. A recent publication in Nature now overcomes this difficulty by applying a joint analysis of inherited and de novo variants in autism. Continue reading
Red Johanna Day, Ninja Turtles and my decade in epilepsy genetics
Where do you see yourself in ten years? You probably might not imagine yourself wearing Ninja Turtle pajama pants, getting up at 4:00 in the morning for a teleconference. For some reason, I kept track of my very early beginnings in epilepsy genetics when I was still a medical student. According to my calendar, today is precisely my tenth anniversary in epilepsy genetics, a day that I refer to as Red Johanna Day. Let’s revisit what happened over the last decade and what I learned from my mentors and friends in the field. And let’s find out about the Ninja Turtles. Continue reading
Three reasons why exomes are like MRIs – and three reasons why they are not
Exome rounds. How will next-generation sequencing technologies impact on patient care in the future? What role will genetic analyses play in routine health care? Sometimes, the possible role of genetic information is compared to the role of MRI imaging, including the general expertise that is required of clinicians who apply these technologies but are not necessarily dedicated experts in the field. Here are three interesting parallels between exomes and MRI – and three examples how the impact of these technologies differs drastically. Continue reading
Program or be programmed – the EuroEPINOMICS bioinformatics workshop 2014
Join the genome hacking league. We are preparing a EuroEPINOMICS bioinformatics workshop in Leuven and I really, really encourage you to join us, as there are handful of place left. This will be the workshop that I always wanted to attend, but never got a chance to take part in. And yes, there is a final exam, but there is a chance that you might pass it. If you’re worried, skip ahead two paragraphs.
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
Invitation for the EuroEPINOMICS General Assembly in Tübingen
We need to talk. Much has happened in EuroEPINOMICS land ever since the launch of this Eurocores activity in 2011. Back then, exomes were still a realistic, but somewhat remote possibility and the complexity and ambiguity of the human genome was only beginning to be revealed. Now, roughly two years later, we have witnessed major breakthroughs in understanding epilepsy through genetic findings and we have generated large datasets on common and rare epilepsy syndromes that require an unanticipated effort for data mining and sharing. The EuroEPINOMICS Consortium will hold its 2013 General Assembly in Tübingen, Germany, from 30.10-01.11.2013. This meeting will connect all four Collaborative Research Projects and will be the central meeting of this year to jointly discuss our current activities and plans for the future. Continue reading
Three things the beach taught me about science
Endless summer. I am quoting from a representative email that I received this summer from a fellow scientist in the EuroEPINOMICS consortium: “XYZ will reply to you once he is back from his holiday – IF he comes back”. A metereological anomaly had given us one of the longest and most intense summers that I can remember. No rain for roughly four weeks, a new temperature record and a heat that was so intense that the tarmac on the highways started to melt. Accordingly, the motivation in EuroEPINOMICS land to leave the beach behind and return to the office was at an all time low. We spent our summer holiday in Marielyst, Denmark and I just wanted to share some thoughts on how the world of science looks when you’re at the beach. Yes, this post is not too serious. Continue reading