Mailund on the Internet

Today, Aarhus University holds its traditional boat race at our university park.

This is a rowing competition where student groups from all over the university competes.  It isn’t quite like the traditional Oxford/Cambridge boat race.  For one thing, the race is across a lake that is only a few meters wide (but you have to cross it more than once). Another difference is that only inflatable boats are allowed in the race.

Well, with one exception.  The group that I belong to (although no longer a student I am still a proud member), TAAGEKAMMERET, can compete in any home made boat we want as long as we promise not to win.  So far we have kept that promise and I am sure we will keep up this proud tradition.

Another thing that differs a bit is that it is not just a rowing competition, but also a drinking competition.

Each time you reach the other shore, you have to drink a beer before you can get back in the boat for the next lap.

Beer sale starts at noon, the race is two to five, and after that it breaks into different parties at the various departments around the university.

Tomorrow is a holiday here, which is probably good since those parties tend to last all night.

There’s a paper that came out yesterday in PLoS ONE on visualising LD structure:

The Textile Plot: A New Linkage Disequilibrium Display of Multiple-Single Nucleotide Polymorphism Genotype Data

Kumasaka, Nakamure and Kamatani

Linkage disequilibrium (LD) is a major concern in many genetic studies because of the markedly increased density of SNP (Single Nucleotide Polymorphism) genotype markers. This dramatic increase in the number of SNPs may cause problems in statistical analyses, such as by introducing multiple comparisons in hypothesis testing and colinearity in logistic regression models, because of the presence of complex LD structures. Inferences must be made about the underlying genetic variation through the LD structure before applying statistical models to the data. Therefore, we introduced the textile plot to provide a visualization of LD to improve the analysis of the genetic variation present in multiple-SNP genotype data. The plot can accentuate LD by displaying specific geometrical shapes, and allowing for the underlying haplotype structure to be inferred without any haplotype-phasing algorithms. Application of this technique to simulated and real data sets illustrated the potential usefulness of the textile plot as an aid to the interpretation of LD in multiple-SNP genotype data. The initial results of LD mapping and haplotype analyses of disease genes are encouraging, indicating that the textile plot may be useful in disease association studies.

An example of this new kind of plots looks like this:

At a quick glance it looks like it is displaying haplotype blocks, like you can get in HaploView (although in a nicer graphics).

It isn’t quite that, though.

The textile plot is showing LD between genotypes and not haplotype blocks, so you always have three “blocks” per column, and so you don’t know the phase of the genotypes you are looking at.

The plot simply visualises the genotype LD structure, and I am sure that with a bit of practice they can be used to explore that.

I don’t have that practice, though, so I find them a bit hard to interpret.  They are beautiful, though.