In 2007 we performed a GWAS for the Leiden Longevity Study (LLS)11 with an affected sibling pair (ASP) and control design. One sibling from each of 420 long-lived sibling pairs was genotyped with the first generation Affymetrix Gene Chip Human Mapping 500K Array (Affy500, Perlegen Sciences, Mountain View, CA, USA). This Affy500 data set was discarded for the analysis that was eventually published.12 To illustrate the situation in which data obtained by an early platform are combined with data generated on more recent platforms, we have here included the Affy500 data yet again. The remaining siblings were genotyped with Illumina Infinium HD Human660W-Quad BeadChips (Illumina660, San Diego, CA, USA). Using the following per-individual QC6 of GWA data, we excluded individuals with discordant sex information, individuals with sample call rate <0.95, and duplicated individuals. Per-marker QC was carried out for including SNPs with the following criteria: SNP call rate >0.95, MAF >0.01, and HWE P-value >10−4. After QC, 517K SNPs remained on the Illumina and 350K SNPs remained on the Affy500 arrays. Of these, only 60K SNPs of Affy500 overlapped with
