In the current protocol we present two scenarios for SNP selection, involving a candidate-gene and a GWA study, following the example of type 2 diabetes 2. Marker selection for the candidate gene approach will centre around the investigation of the influence of PPARG on type 2 diabetes in a population of European ancestry. Since PPARG (rs1801282) was previously implicated in this disease 21 we ensure that the associated variant is included in the final marker selection. Although the example shown relates to a candidate gene, the same methods are applicable when selecting markers for a larger candidate region.
