For validation, the 89 top-ranking SNPs (MACH r2>0.3) resulting from the association analysis using the first design were retyped with the Sequenom MassArray platform. We checked the quality of genotyping (of the different platforms) as well as that of imputation. Figure 4 illustrates the comparison of minor allele frequencies (MAFs) in the long-lived siblings. In the left panel, the deviation of the points from first diagonal (dashed line) indicates the poor match of the Affy500 data and retyped sample. Meanwhile, the retyping of the Illumina660 data shows better agreement (bottom panel). Visual inspection of cluster plots of the sole exception (the red filled circle) confirmed the results of the Sequenom array.
