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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Isabelle: About a month ago, I joined the Barrett-group at the Sanger institute. Coming from a molecular biology background and ending up in a team of computational biologists, statistical geneticists and bio-informaticians, it soon became clear that I was going to have to learn a whole new vocabulary: the ‘others’ love terms ending in *ash: bash, hash, slash (forward and backward!), dash…; and their day to day language includes things like grep (‘grepped’), awk, sed, syntax, R, perl, python, unix, linux (what is actually the difference between all these things??), … . Although I thought I was getting along very well before, manipulating datafiles in MS Excel and here and there using some command line programs (already making me feel like a computer wizard), it here turned out quickly that I was far from being a computer genius. I got lucky though, since one of my new colleagues appeared to be a ‘partner in crime’, also having a background in molecular biology, but having been introduced into the wonderful world of scripting and programming already years ago.

Iris: although I made the switch a while ago, until I started at Sanger I have always worked in a clinical setting so the wet lab was always just around the corner. In the Sanger introduction day there is a lot of attention placed on the campus desire to be as green as possible. More »