Table 1.
Summary of the four GWAS analyzed in this study
| Number of SNPs (post QC) | CHIP platform | Excluded SNPs (%) | Number of SNPs with LD (r2 = 1) | Number of LD Clusters (r2 = 1) | Number of Independent Tests | |
|---|---|---|---|---|---|---|
| Li et al. (2008) | 469,438 | Affymetrix 500K | 5% | 128,139 | 42,634 | 383,933 |
| Reiman et al. (2007) | 312,316 | Affymetrix 500K | 38% | 83,739 | 29,678 | 258,255 |
| Beecham et al. (2008) | 532,000 | Illumina 550 | 4% | - | - | - |
| Carrasquillo et al. (2009) | 313,330 | Illumina 300 | 1% | 26,284 | 11,539 | 298,585 |
The number of SNPs following QC, the platform utilisied and the percentage of SNPs excluded in each study is listed. Also shown are the number of perfect proxies (r2 = 1) in the QC'd data together with the number of clusters into which these SNPs fall. The number of independent tests for multiple test correction of combined p-values (listed in the supplementary tables) is shown in the last column and was calculated as described in the methods section.