Papers of the week – Copy Number Variations

Dennis' paper of the weekVariations on Copy Numbers. In the third issue of our series on the papers of the week I will focus on the detection and annotation of the most common form of structural variation encountered in genomes. Deletions, duplications and inversions are frequent events, which are surprisingly hard to deal with using sequencing-based tools. Hence, this is an area of active development.

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“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

An inconvenient truth – segregation of monogenic variants in small families

Climate change. In the era of exome and genome sequencing, it might be worthwhile revisiting the merit of family studies in epilepsy research. Seizure disorders are known to have a highly diverse genetic architecture. When singleton studies identify a single, unique gene finding, this discovery usually does not provide much information about the potential causal role of the variant given the high degree of genomic noise. In contrast, family studies are usually considered more robust, as segregation of variants can be traced. Here is the inconvenient truth: unless the family is very large, segregation of possibly monogenic variants adds little information given the vast amount of variants present in our genomes. 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

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

Temperature rising: 17q12 microduplications and GEFS+

GEFS+, meet CNV. Microduplications at 17q12 have been identified in various neurodevelopmental disorders and in some unaffected individuals, a pattern familiar from other structural genomic variants such as microdeletions at 16p13.11 and 15q11.2. In contrast to the corresponding microdeletion, most 17q12 microduplications are inherited. This suggests that the microduplication is a risk factor, but does not fully explain the phenotype. In a recent paper in Neurology, Hardies and collaborators look at the families of 17q12 microduplication carriers with epilepsy. And this is when they noticed something strange. 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

Invitation for the 2013 Young Researchers Meeting

This time, the desert. After the successful meeting for Young Researchers in Epileptology in Kiel last year, we would like to invite young and senior researchers in the field for the 2013 meeting, which will take place on December 14th, 2013 in Sde Boker, Israel. This year’s meeting is embedded in a small international meeting from Dec 12th-14th on epilepsy genetics with the primary aim of bringing together researchers from Israel and Palestine. As last year, we would like to extend the invitation for this year’s Young Researchers Meeting in Epileptology to all young scientists involved in the field. Don’t forget to bring water and sunscreen; we’re going to the Negev Desert. Continue reading

Reinventing a consortium – the RES data sharing policy

Share or be shared. During the last two weeks, the RES consortium has approved a new data sharing policy that will allow us to work with increased transparency and accountability within our upcoming projects. This new data sharing policy is a consequent extension of the previous protocols we had in earlier consortia – with one major difference. This time, it’s in writing. While we are getting ready to tackle the large dataset on epileptic encephalopathies released by the Sanger Institute, we took a moment to talk about how things should be running.

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