Donate your idle CPU time to medicine...

Two worthwhile distributed computing projects that I came across today are Folding@home and Genome@home.

The former seeks to understand the way in which proteins secondary and tertiary structures are formed, whilst the later seeks to use this information to derive novel genes (and hence proteins) for application in theraputic medicines.

If you have a computer on your desk, even if you use it throughout the day there is likely to be time when its full CPU capacity is not being used, and by downloading on of the clients you can help solve some of the computational problems that exist within medical research.

Lost hunting for genes?

The current issue of Nature Genetics has an interesting article entitled "A road map for efficient and reliable human genome epidemiology", which champions the notion that researchers need to co-ordinate their work.

One key point the authors make is that there is still a publication bias which favours positive associations. This clear bias detracts from the scientific quality of the area as a whole, and runs the risk of engendering data dredging.

A number of online databases are also listed (many of these and more can be found here in the Links section of my web-site)...

Human Genetic Epidemiology Network (HuGENet)
(UK HuGENet Coordinating Centre)
Genetic Association Database
PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base
STROBE statement

Common disease variants are invariant

A recent article in The American Journal of Human Genetics by Lohmueller et al shows that SNP variants involved in 'common' diseases tend not to vary considerably between the two populations they compared.

This is good news in the world of gene hunting since it suggests that these variants arose prior to the divergence of human populations, and that they variants are therefore common to most human populations. This is not to say that genetic heterogeneity does not exist, since there are likely to be other mutations that influence disease that are population specific, but it is encouraging since it means that it should be reasonably easy to replicate associations with some of the common variants (indeed that was one of the criteria for selection used in the paper).

Proceedings of Genetic Analysis Workshop 14

The summary papers for the 14th Genetic Analysis Workshop have been published as Supplementary issue to the journal Genetic Epidemiology.

These papers are summaries for each of the working groups that were formed as part of the workshop. Individual work from each members of the group are due to be published as a supplement in BMC Genetics in the not too distant future.

(I attended this meeting and was part of group 7).

Recommended Reading

I've just finished reading James Watson's "DNA: The Secret of Life" and can highly recommend it to anyone interested in the area, even if they are already familiar with the field.

Personally I found it very interesting from a historical point of view since it discussed a lot of the origins of the field, and it should be on the recommended reading list of any undergraduate human genetics course.

Interesting Blogs

Nothing much to add today, but here are a few links to other blogs readers may find interesting.

Free Association is the Nature Genetics blog.

And after reading the above blog Paul Myer's blog Pharyngula would be of general interest as well.

When I've got more time I shall add a blog links section to the right.

R for Statistical Genetics

R is becoming increasingly popular as a tool for statistical genetics. There are already a number of packages available, and these are detailed at the CRAN Task View: Statistical Genetics.

R has also been extended considerably as part of the Bioconductor project which develops tools for bioinformatics and micro-array analyses.

Pan autoimmune genes...

Okay so I guess I should start adding stuff to this blog.

Theres an interesting article on the role of PTPN22, which shows numerous associations with autoimmune diseases. The article is in Nature Genetics and can be read
here.

Welcome

Welcome to my blog!

I work in the fast-moving (exciting?) world of human genetics and am a genetic statistician.

I intend to use this page to detail useful information about statistical genetics, so if you work in the field as well you may find it interesting, if you don't then I hope you enjoy reading it anyway.