The analyses had been run (and re-run), QC was finished, and the only thing left to do was somehow corral all that work into a paper. With that realization, Alice had a vivid flashback to her last collaborative paper:

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Recently I had my DNA genotyped by 23andMe. After working at Sanger for two years, I had been looking forward to finding out what my own genome had to say about myself, particularly regarding my ancestry. I am from Beijing and both of my parents are ethnically Han Chinese – the largest ethnic group which accounts for 92% population in China. Having witnessed my colleagues’ surprise at finding French, Ashkenazi and Scandinavian ancestry in their own DNA data, I could not help but get my hopes up to discover some surprising elements in my own ATGCs.

23andmeHowever, 23andMe left me feeling a little underwhelmed. Its ancestry analysis told me I’m 99.4% East Asian and Native American, a little like finding out that beef is 99.4% cow (something you can not always take from granted in the UK). Compared with the detailed breakdown you receive if you are European, such a vague composition is rather disappointing. Luckily, with a bit of experience in analysing genotype data, I could try other means. I combined my genotype with the east Asian cohort from our Inflammatory Bowel Disease (IBD) studies, and did a standard Principal Component Analysis (PCA) using WDIST, an experimental rewrite of the PLINK command-line tool which benefits from a vastly improved speed-up of the Identity-by-descent (—genome) calculation.

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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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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 »

24. July 2012 · 2 comments · Categories: Editorial · Tags: , ,

About a year ago I tried to regain control of my schedule, my work, my life by fully implementing Getting Things Done. Perhaps unsurprisingly I fell off the bandwagon pretty quickly. I think this is the experience of many people trying to change the way they organize their lives, and I’m planning a reboot soon. Nonetheless, many of the core GTD principles have been incubating in my mind and I’m trying to incorporate them into my day-to-day life even without the overarching organizational system.

One of the most profound of these concepts was the idea of redefining “productivity”. I think too often productivity is conflated with busyness; if we’re busy doing something then we must be being productive. In a great series of podcasts about life as a modern academic, however, MIT Physics Prof. Peter Fisher warns against activities which keep you busy without actually being productive — which raises the question, “What is productivity?”

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