How to deal with scientific disappointment

Difficult times. The last two weeks were hard for me scientifically. In addition to having two papers rejected within a week, I learned that a major grant proposal that was rejected. Particularly the latter I didn’t take well, since I was quite convinced that we would make the next round. Also, this was for a project where funding was more than necessary. We all know scientific disappointments in their various forms, and I thought that I would dedicate a post to this topic. Please follow me while I stumble through the internet, looking for the science of disappointment. 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

Of diapers and desktops – a belated Thanksgiving post

The post I didn’t write. Last Thursday was Thanksgiving and my daughter’s second birthday. Therefore, even though I initially had grandiose plans for a Thanksgiving post, I did what a family father would do on days like this – not write blog posts. Therefore, having digested the Thanksgiving dinner and having survived Black Friday, here comes our belated Thanksgiving post. Let’s think for a second how we handle the combination of family and research. Continue reading

The Biobank Dilemma

Killing two birds with one stone. I am currently preparing for a presentation for the Scientific Advisory Board of our local biobank network P2N and I thought that I wanted to share a few thoughts on biobanking and sample collection for epilepsy genetics that have troubled me for a while. Continue reading

The 16p11.2 microdeletion: assessing the phenotypic range

The 16p11.2 story. Among the various microdeletion and microduplication syndromes located on human chromosome 16, the 16p11.2 microdeletion has unique position. Historically, this microdeletion was the first of the “neurodels” to be identified through association studies in autism, where it can be identified in 0.5% of patients. However, there is more to the phenotypes of the 16p11.2 microdeletion, which is now addressed in a recent paper assessing the full phenotypes in 72 microdeletion carriers. 16p11.2 therefore represents one of the best-investigated microdeletions to date. Continue reading

Validation of rare variants – the power of finding anything at all

How much? Last week, we discussed the probability of finding de novo variants in patients with epileptic encephalopathies, but our calculations were only half the story. Genes that are identified through genome-wide sequencing technologies are often validated in additional cohorts. In many cases, we will only be able to establish a given gene as causative if we find another patient with a mutation in this gene. I was therefore asked to write an additional post on power calculations for rare variants in validation cohorts. Let me tell you the story how I stumbled across a little bit of almost forgotten high school math. Continue reading

The Hippocampus Conspiracy

Slightly misleading. The green and blue histological staining that has become the EuroEPINOMICS logo features a human hippocampus, a part of the human brain that is particularly important in human epilepsy. Temporal Lobe Epilepsy (TLE) is the most common epilepsy in adults and involves the hippocampal region. Ironically, TLE is the human epilepsy that has always been at odds with genetic research. Let’s review what we know about the genetics of TLE and “hippocampal genetics”. Continue reading

A new twist on an old gene: EFHC1 in epileptic encephalopathy

A peculiar gene. There is one gene in the small world of epilepsy genetics that has always troubled me. A gene that has an unknown function and is not expressed in the postnatal brain, but is well established as one of the few genes for autosomal dominant Juvenile Myoclonic Epilepsy (JME). This gene is EFHC1. Now, a recent paper in Epilepsia reports EFHC1 as a possible candidate gene in autosomal recessive epileptic encephalopathy with neonatal onset. The mystery surrounding this gene continues. Continue reading

SpotOn 2012 is on air

The biggest European meeting on Science online – policy, outreach, tools – started this Sunday. SpotOn brings  open source coders, librarians, scientists from a variety of fields, and publishers together in London.

You can follow the keynotes and sessions online and evaluation and comments can be followed in real time on Twitter. #solo12 is hashtag of the overall conference, the individual sessions have their own tags. Continue reading

What’s in a phenotype? – the EuroEPINOMICS BENCH database

The backbone. As we have started a new round for BENCH introductory sessions with new collaborators, I thought that it might be timely to talk a little bit about our BENCH phenotype database and the concepts behind it. In addition to the purely technical aspects, there is a more fundamental question behind this: how do we want to document and store epilepsy phenotypes for research purposes, how do we find the balance between precision and efficiency? Continue reading