Seven of Fifty-One

I am Seven of Fifty-One. I know it doesn't sound quite as good as Seven of Nine, but allow me to explain.

Those of you who have been reading this blog for a while may remember that part of the work I've been doing over the last few years has been related to cancer studies (I've blogged about it here, here, here, and here). Specifically I've been involved with trying to reduce the cost of performing Genome Wide Association Studies, by reducing the number of samples required. We have been doing this by mining the published literature to try and determine the prior probability that a specific single nucleotide polymorphism (SNP) will be related to specific cancers.

Essentially the idea boils down to this (although I have to admit in advance that neither the genetics or the statistics are my strong points). If a SNP occurs near a gene that has been shown to be involved in either the specific cancer under investigation or in the healthy functioning of the organ/tissue that the cancer affects then it is more likely that this SNP might be the cause of the cancer than if it occurs somewhere else in the genome. We calculate the probability that this is the case by mining the published literature and when these priors are combined with results from both healthy controls and diseased patients the statistical power of the tests are improved. As the power of the test is improved we can determine that a SNP is related to a cancer using less samples than previously. While this will save money it is especially important when investigating rare forms of cancer where it might be difficult or impossible to ever assemble the required number of patients for testing using the standard approach.

We'd previously shown that the approach worked, but only by going back and reproducing previous results using less data. Now, however, we've used the same approach to find a new cause for cancer! The results have just been published in the journal PLoS ONE: Using Prior Information from the Medical Literature in GWAS of Oral Cancer Identifies Novel Susceptibility Variant on Chromosome 4 - the AdAPT Method. PLoS ONE is an open access journal so you can all go and read the article if you want to!

By this point you might be wondering what this all has to do with the title and opening paragraph (and I can't say I'd blame you). Well I'm author number seven of fifty-one.

Moving On

The research group I work as part of gets most of it's funding from external sources; government grants or companies wanting R&D. This means that while the style of work stays fairly consistent the actual tasks can vary widely depending on which project I'm currently working on. Since I joined the group at the start of 2009 most of my time has been dedicated to the LarKC project. My recent trip to Vienna, however, marked the end of LarKC and the reviewers from the EU were highly impressed with all the work that has been achieved. The work package I was most involved with helped discover a new genetic mutation which we proved causes oral cancer, and they couldn't help but be impressed by that! Actually I'm pretty impressed by it as well. Finding a new cause for cancer wasn't something I ever imagined being involved with. We are currently in the process of writing up the finding for a journal article so I'm sure I'll tell you more about it when that work is done. LarKC has also allowed me to make good use of my passport with trips to Bled, Milan, Berlin, Lyon, Munich, Sofia, Innsbruck, Beijing, Lund (which I seem not to have blogged about at all), and of course Vienna. Of course, while I do get to briefly see the countries we visit I spend most of my time with the other people who worked on LarKC, and here we all are (well those of us who were at the final meeting in Vienna).

So now that LarKC has finished I'm moving on to work on another large EU funded project called Khresmoi. Khresmoi is about medical information analysis and retrieval and has been running for a year already. From discussions in Sheffield it looks like my work will be similar to stuff I'd been doing for LarKC. I'm sure I'll have a much better understanding in a weeks time as I'm attending a project meeting next week in Prague, so it doesn't look as if my passport will be getting a rest anytime soon!