Converging thoughts. During late 2013, I had several unrelated discussions about the possible role of genetic modifiers of SCN1A in Dravet Syndrome. To some extent, SCN1A is a paradox. One the one hand, the connection between Dravet Syndrome and SCN1A is one of the clearest connections between gene and disease that we see in genetic epilepsies. On the other hand, we see a remarkable phenotypic heterogeneity in families, and some presumably pathogenic SCN1A variants can also be identified in unaffected control individuals. This leaves us with the question whether there are genetic modifiers in Dravet Syndrome that might help provide some insight into additional mechanisms of disease. This post is a collection of 10 individual thoughts that emerged during the discussions last year. Continue reading
My untested assumption. Recently, I have boasted quite a bit about the power of the trio design, i.e. the inclusion of patients and parents in the analysis of rare genetic variants. Rare variants, in contrast to monogenic variants that arise de novo, are usually transmitted from unaffected parents and are the big unknown of modern day genetic studies. Much of the missing heritability may be accounted for by rare variants, but identifying these variants from genomic noise is difficult. Power calculations for association studies usually suggest that thousands, if not tens of thousands, of patients are necessary to identify these variants with sufficient statistical certainty, a sample size that the field of epilepsy research may never arrive at. So what about switching to parent-offspring trios? Would this help us? Follow me on a brief statistical journey through the land of rare variants. Continue reading
The power, over and over again. I must admit that I am thoroughly confused by power calculations for rare genetic variants, particularly for de novo variants that are identified through trio exome sequencing. Carolien has recently written a post about the results we can expect from exome sequencing studies. For a current grant proposal, I have now tried to estimate the rate of de novos using a small simulation experiment. And I have realized that we need to re-think the concept of power. Continue reading
Now the experiments to find de novo variants for epileptic encephalopathies within the Euroepinomics RES-project are well underway and first data are coming out, it is a good moment to pause and think about what results we can expect, and how these should be interpreted. For this it is very nice that recent large experiments in autism have provided so much useful data. In this post, I will explore what we can expect in experiments in which we perform whole exome sequencing in a group of patients and their parents to identify de novo variants that could be the cause of the disorder.