The validation stage of SNP- prediction analysis will be the main focus of this Perspective. Incorrect conclusions at this stage may lead to predictors that will not work as well as inferred or, in the worst case, have no prediction accuracy at all. We organise our Perspective into limitations and common pitfalls of prediction analysis. The limitations are partly inherent given the nature of the trait or the data available. These are factors that users should be aware of but mostly cannot change. The limitations also reflect use of sub-optimal methodology that could be improved upon. The pitfalls are common mistakes in analysis that can lead to over-estimation of the accuracy of a predictor or misinterpretation of results, and we give examples from the literature where these have occurred. We give our opinion on how best to avoid pitfalls in the derivation and application of SNP based predictors for practical applications. There are many aspects of risk prediction that are outside the scope of this article. They include a thorough treatment of the statistical methods that can be used in
