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

Table 2 Disease-associated alleles from different genotyping platforms

	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

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.

ISSN: 1755-8794