Natural variation in Nature

Nature has a whole slew of reviews on the current progress and prospects of mapping the genetic determinants of phenotypic variation:
Association mapping in humans (here)
Mapping behavioral traits in mouse (here)
Genetic variation in malaria (here)
Mapping in plants (here)
and how we should use natural variation to learn about biological systems (here)
quite a fun reading list.

Mapingp cellular susceptibility to HIV

A really neat paper (Loeuillet et al.) in PLoS Biology identifying a candidate SNP for cellular susceptibility to the HIV-1 virus. The paper adding to our growing knowledge of the genetics of HIV susceptibility (see a review of the paper by David Goldstein).

Rather than investigating this in patients with the disease, the paper initially measures how susceptible different cell lines are to HIV. The paper uses the CEPH cell lines (immortalized lymphoblastoid B cells) to do an initial linkage map, and identified a broad candidate region. They followed this up using the CEU HapMap cell lines to confirm and fine map the variant. The authors then confirmed the SNP association was also present using the more biologically relevant CD4+ T-cells. Finally on the association front they showed that the SNP is associated with disease progression in patients.

The use of the HapMap and CEPH cell lines to map variants affecting cellular phenotypes is a really interesting approach. One which I'm sure we will see a lot more of in the future. At least some cellular phenotypes are likely to be easier to map as they likely have a simpler basis than complex diseases. I'm slightly surprised that the authors did not do a genome-wide association study of this cellular trait (after all they are HapMap cell lines) and instead restricted themselves to doing an association study in the region of significant linkage. Obviously a GWAS would have to meet genome-wide significance, but the region of significant linkage could have been up-weighted or considered separately in this analysis.



Hat tip to Tree of Life.

Reference:
Loeuillet C, Deutsch S, Ciuffi A, Robyr D, Taffé P, Muñoz M, Beckmann JS, Antonarakis SE, Telenti A.
In vitro whole-genome analysis identifies a susceptibility locus for HIV-1.PLoS Biol. 2008 Feb;6(2):e32
Goldstein DB.
Genomics and biology come together to fight HIV
PLoS Biol. 2008 Mar 25;6(3):e76

association studies of classic traits

It would be a lot of fun (although also an IRB nightmare) to involve a bunch of schools in an association study. In school we learn about tongue rolling and attached ear-lobes being classic Mendelian traits, but I don't think we (or I anyway) know the genes underlying these traits. It would be great to take classes of kids from around the country and get their teachers to phenotype them (i.e. can you roll your tongue, are your earlobes attached), and then genotype them on SNP arrays. The investigator could then determine the locus underlying these traits presumably fairly easily given how simple the traits are. The whole thing could be a big science project for a load of schools and really get kids and parent excited about science and mapping.

I guess the only problem with this idea (apart from the ethical committees and the like) is that it would give kids and parents the wrong idea about how simple and deterministic genetic variation is.