The genetic architecture toolkit – modeling polygenic disease with rare variants

Architecture. Even though we often write about novel gene findings in the epilepsies, we assume that most epilepsies are complex genetic or polygenic. Polygenic inheritance suggests the genetic architecture is composed of multiple interacting genetic risk factors, each contributing a small proportion to the disease risk. However, when using the phrase genetic architecture, sometimes I am not quite sure what I actually mean by this. For example, how many genes are needed? This is why I wanted to build a model genetic architecture and explore what happens if we build a genetic disease solely from rare risk variants. Follow me to a brief back-of-the-envelope calculation of how this might work.

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Why I am still struggling with SCN9A in Dravet Syndrome

Susceptibility. Two weeks ago, we published a post on rare variants in SCN9A as potential susceptibility genes for Dravet Syndrome with mutations in SCN1A. Ever since reading the article by Mulley and collaborators, I had tried to come up with an idea of what the genetic architecture might look like if both de novo variants and inherited variants contribute. I wanted to follow up on my earlier post with this brief back-of-the-envelope calculation. Continue reading

How to detect de novo mutations in exome data

Taking things apart. Looking for de novo variants using trio exome sequencing is a powerful technique to identify disease-related genes. After having introduced samtools during the last post, this will be post 2/3 in a series on how to perform an analysis of exome data for de novo variants. This time, I would like to take apart the methods that take us from Gigabyte BAM files to small tables with likely variants. So buckle up. Continue reading

Red Johanna Day – The signal and the noise

Predictions. December 17th is the day that I consider my annual anniversary in epilepsy genetics. Exactly eight years ago, I was still a student in my final med school year and went to Australia for a job interview. We took a road trip over the weekend and on the evening of the 17th, I was reading Nigel Tan’s review on epilepsy genes aptly entitled The truth is out there while sitting in a rock pool at Red Johanna Beach, a surfing beach at the Great Ocean Road south of Melbourne. Looking back, I think this was one of the few publications that helped me make sense of all the literature on epilepsy association studies. I thought that I would like to be able to write something like this while shivering in the waters of the Bass Strait that are always a little bit too cool. Today, sitting in the cozy warmth of our apartment in Kiel, I have finished reading Nate Silver’s book The Signal and the Noise, a book about making sense of data and predictions. Eight years later, are we any closer to the truth that is out there? Continue reading