Neuromag July 2018 - Page 20

Why do you study genome variation? Neurodegenerative diseases are very common diseases of the elderly popu- lation and there is currently no effec- tive therapy or cure available. Genetic mutations play an important role in the risk for developing neurodegener- ative diseases such as Alzheimer’s and Parkinson’s disease. Mutations that are biologically damaging can have such a strong effect that they cause a disease without other influencers. Although they are usually rare in the general population you find them in a few families where the disease fol- lows a Mendelian inheritance pattern. Other mutations have a much small- er effect and by themselves are not strong enough to cause a disease and they can be quite frequent in the pop- ulation because there is no evolution- ary selection against them. However, if an individual carries several of these risk factors and is exposed to environ- mental risk factors as well, the combi- nation could also lead to disease. We try to identify genetic risk factors because they give us a unique handle to study the mechanisms that result in a disease. The mutations are the di- rect cause of the disease and we carry genetic mutations with us our whole life from the moment of conception, therefore they function at the very beginning of the disease process. The mutations are therefore an ideal start- ing point for research that aims to un- derstand the mechanisms that lead to a disease and to start to work towards developing a therapy to fix or prevent the problem. How exactly do you study genetic risk factors? In genetics we look for genome vari- ants that are shared between pa- tients, but not shared with healthy individuals. There are many ways to look at DNA and to study variations in our genome but nowadays the most widely used techniques are DNA se- quencing and genotyping. The field of genetics has benefitted greatly from the technological devel- opments that are the direct result of the Human Genome project. The goal of the Human Genome project was to sequence a complete human genome but the technology to do this efficiently 20 | NEUROMAG | July 2018 did not exist at the start of the project in 1990. It took 10 years to complete the first draft of the human genome. Now, we can sequence a full genome in a matter of days. This allows us to compare the complete genomes of patients and healthy individuals and identify the differences. The costs for whole genome sequencing are still very high but there are good alterna- tives that work well for a fraction of the costs. Based on the variation that has been found in all the sequencing efforts on the human population we have collected 100 thousands vari- ants that have been spotted on glass arrays that we can use to find regions of the genome shared much more fre- quently by patients than by healthy individuals. With these arrays we can now test thousands of individuals to search for genetic risk variants using what we call Genome Wide Associa- tion Studies (GWAS). How is it possible to link genome mutations with a disease? For Mendelian diseases, where a sin- gle mutation is enough to cause dis- ease, we search for variants that are present in patients but not in healthy individuals. Often we have families available with multiple affected indi- viduals and the variants should co- segregate with the disease. Once we have a list of these variants we use bioinformatics approaches to deter- mine which of these variants are likely to have a damaging effect. Finally, we will test the identified variants in a cel- lular model system to confirm their damaging effect and study the mech- anism by which they could cause the disease. For weaker risk factors the situation is more complicated because a single risk factor is not sufficient to cause the disease and therefore also many healthy people in the population can carry some of the risk variants. We therefore have to use statistical meth- ods and large numbers of patients and healthy individuals to find variants that are significantly more present in disease cases versus healthy con- trols. A second complication is that since whole genome sequencing on thousands of samples is still very, very expensive and we have to use geno- typing arrays. With these arrays we can find a region where the risk vari- ant is located using GWAS but we can’t detect the variant itself. In fact these regions often contain multiple genes and it remains difficult to prove which gene and risk variant is responsible for the increased risk. Our lab uses a series of approaches to resolve this problem. We can sequence the region identified by GWAS in our study samples and then use bioinfor- matics to identify those variants that are most likely to have a functional effect. Unfortunately, the knowledge of all the functions encoded in the hu- man genome is still limited, especially for the noncoding part of the genome which is more the 98% of our genome. We work tirelessly to improve this by participating in international consortia such as the FANTOM consortium that has helped to find many new noncod- ing RNA genes, microRNAs and regu- latory elements, such as enhancers, and we use this information to help find the most likely gene or variant that increases the risk for a given dis- ease.