18. July 2013 · Comments Off on From GWAS to the fishtank · Categories: Science · Tags: , , , , ,

This is a guest post by Mari Niemi, an MSc student visiting the lab this year.

DSC_0283_cleaned_smallIn the last few years, a major focus of the group has been identifying the genomic regions associated with risk of inflammatory bowel disease (IBD). Currently, there are 163 loci associated with the condition; the largest number of associations for a complex disease to date, explaining 13.6% Crohn’s disease and 7.5% ulcerative colitis total disease variance. These lists of associated loci are drawn up with some heavy-duty statistical computing, but still leave key questions about which genes in those regions are actually responsible for susceptibility to IBD – and what their role is in this complex plot? In order to understand more about the disease we need to functionally annotate these IBD candidate genes, and to do so we need to get our hands (quite literally) dirty in a laboratory!

Image credit: Betta Fish Tank Bank
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06. February 2013 · Comments Off on Moving from common to rare · Categories: Conferences, Editorial · Tags: , , ,

One of the main research focuses of the Barrett group is to understand genetic associations with Inflammatory Bowel Disease (IBD), in particular with its two most common subtypes, Crohn’s disease and ulcerative colitis (UC).

Back in November 2012, in preparation for the ASHG meeting, I did a brief literature review on the development of IBD based on a number of selected publications. The motion chart below (created in R as used in the well-known Hans Rosling TED talk) shows an overview of the discovery of IBD disease loci since 2001, when three independent groups identified a CD risk gene on chromosome 16q12, NOD2, using linkage techniques.

MotionChartID17b62b2346c5
Plot: IBD Motion Chart
R version 2.15.2 (2012-10-26) • googleVis-0.2.17Google Terms of UseData Policy

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Out this week in Nature is the first big paper from the inflammatory bowel disease Immunochip project. The international project collected data from over 75 thousand individuals, and brought the total number of known IBD loci to a record-breaking 163. You can read more about the paper on the Sanger Institute website.

One interesting thing about the paper was how difficult it was to visualize the results. With one exception there were no single image that naturally fell out of any of the analyses, and we had to put quite a bit of work into displaying the messages of the paper in the figures. You can judge for yourself how much success we had, but I can say that up until the last few days before submission we still had images that everyone hated but couldn’t think what to replace them with. The last one to be replaced was the evocatively named “Smear-o-venn”, that we were all relieved to see the back of.

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