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Johan den Dunnen

Professor dr. Johan T den Dunnen

"We need to share everything we know long before we start writing a formal publication."

Medical Genomics group / Leiden Genome Technology Centre, Centre for Human and Clinical Genetics, Leiden University Medical Centre
Group size: 45-50

1. What is the leading research theme in your group?
"We focus on hereditary diseases and our work covers the whole track from determining the genetic cause and developing a DNA test for diagnostic purposes to functional analysis of the genes involved and in the case of Duchenne Muscular Dystrophy, even to developing leads for therapy."

2. With what type of groups or organisations do you collaborate most and why?
"Our group is large and the activities are diverse, there are many different types of collaborations. For our work on hereditary muscular dystrophies, we collaborate with several international groups that also work on these diseases. We have collaborations with industry on the application of new genomics techniques that we develop. Not only with pharmaceutical companies interested in drug development, but our techniques are also used by agricultural and animal breeding companies. Then there are collaborations with equipment manufacturers and finally, we participate in a number of international initiatives like the Human Genome Variation Society (HGVS) and the Human Variome Project (HVP), which aim to establish standards for submitting and storing data on human genetic variation and promote to make this data broadly accessible. Our Leiden Open-source Variation Database (LOVD) software is an example of such a standard that is used world-wide."

3. From your research perspective, what are the main challenges in bioinformatics right now?
"It has become very easy, from a technical point of view, to read out the DNA sequence of an individual, but that results in a list of somewhere between 3.5 and 4 million variants. Right now, we have to go through all those variants one by one to determine what they mean. So how does this help us to explain the current health status of an individual or to predict the future status? How can we draw conclusions from this data? That requires two main changes. First, we need to change our attitude from keeping data to ourselves to sharing everything we know long before we start writing a formal publication. Second, we need to make a big leap in improving software-based prediction of the phenotypic outcomes of a variant and especially of combinations of variants."

4. What is the most important task of a group leader?
"Besides ensuring that all the necessary facilities are in place, I think it is important to ask critical questions and act like an ideas-generator. Think along with individual projects and use your experience and broader view to come up with applications, collaborations and theories that can push the research further. In addition, I try to seduce the bioinformaticians in my group to think about the result they expect from an experiment, so that they are forced to consider whether their results make sense. I feel that such a critical perspective is sometimes lacking with bioinformaticians."

5. Where do you see room for improvement within your group?
"Our group is very large and very diverse, so it is important to actively stimulate contact between the group members. The interaction between the bioinformaticians on the one side and the biologists and biomedical researchers on the other side could be improved. It is important to mix people, but I don't have a clear-cut solution on how to achieve that. What I try to do is to make both sides understand each other's problems. What doesn't help is the dynamics of a research group; there is a continuous flow of people. And it is still difficult to keep the good bioinformaticians."