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Table 2 Disease-associated alleles from different genotyping platforms

From: Disease-associated alleles in genome-wide association studies are enriched for derived low frequency alleles relative to HapMap and neutral expectations

  Mean frequency (disease-associated alleles) Proportion ancestral (disease associated alleles)
Manufacturer   
   Affymetrix (n = 638) 0.387 0.414
   Illumina (n = 852) 0.395 0.444
   Perlegen (n = 90) 0.410 0.434
   Multiple platforms used (n = 430) 0.402 0.419
SNPs genotyped in study   
   < 500,000 (n = 597) 0.399 0.452
   500,00 to 1,000,000 (n = 205) 0.390 0.478
   > 1,000,000 (n = 322) 0.390 0.388
  1. Because many studies used multiple genotyping platforms, the number of disease-associated alleles by platform sums to greater than 1143. In 19 cases, the number of genotyped SNPs was unknown. Importantly, this table only describes the characteristics of disease-associated alleles.