GWA studies in Africa have some methodological challenges that are not usually encountered with studies in Europe or Asia.

An example is the low levels of linkage disequilibrium (LD) in African populations:

“From a statistical genetic perspective, the high levels of haplotype diversity and low levels of LD in African populations have both advantages and disadvantages for genome-wide analysis. High levels of haplotype diversity are potentially a powerful tool for fine mapping the causal variants that underlie disease associations. However, low levels of LD are disadvantageous when screening the genome for disease associations using current SNP-genotyping approaches, which essentially rely on the principle of LD mapping”.

Another is the high levels of population structure in Africa. When trying to replicate a GWA study in a different location, the population structure can have a significant influence on the results.

As well as discussing the methodological challenges, the review looks at new sequencing technologies and the impact that these could have on the way GWA studies are implemented in Africa and the impact they will have on results.

Publication

Teo et al. Methodological challenges of genome-wide association analysis in Africa. Nat Rev Genet. 2010 Feb;11(2):149-60. doi: 10.1038/nrg2731.