by flanking markers, it is possible that the reference panel and the case sample used different genotyping assays that, for technical reasons such as the presence of a polymorphism that overlaps assay primers, give consistently distinct results—again resulting in spurious association. To avoid these sources of spurious association, we recommend that, when analyzing genotype data generated using different platforms, different versions of the same platform, or using the same platform but with experiments carried out at different labs, an initial round of association analysis should be carried out using data from each platform/version/site combination. The results from this initial round of analysis can then be meta-analyzed, minimizing the risk of artifacts. This recommendation does preclude analyses where all cases are genotyped at one site, and all controls are genotyped at a different site.
