The remedy of the pitfall described here is to use conventionally unrelated individuals (in discovery and validation stages). Relatedness can be estimated from SNP data58, 59 and so close relatives can be excluded based upon observed data. More generally, the validation population should be representative of the population in which the predictor will ultimately be applied. In populations with small effective population size, such as some breeds of livestock, all individuals are related. This does not invalidate the prediction but it does mean that the same prediction accuracy cannot be expected when the prediction equation is applied to another population that is less closely related to the discovery population62.
