Table 1 

Diseaseassociated alleles vs. null expectations 

Mean frequency of a randomly chosen allele 
Proportion ancestral 



Null expectations 

HapMap data (n = 1000, unweighted) 
0.721 
0.623 
HapMap data (n = 1000, weighted) 
0.610 
0.568 
Theoretical (neutral, unweighted) 
0.741 
0.741 
Theoretical (neutral, weighted) 
0.650 
0.650 
Diseaseassociated alleles 

Cancer (n = 112) 
0.362** 
0.446* 
Cardiovascular (n = 145) 
0.364** 
0.379** 
Metabolism (n = 160) 
0.365** 
0.456* 
Miscellaneous disease (n = 290) 
0.413** 
0.434** 
Morphological (n = 276) 
0.409** 
0.467* 
Neurological (n = 135) 
0.429** 
0.430* 
Multiple phenotypic classes (n = 25) 
0.312* 
0.320* 


All GWAS alleles (n = 1143) 
0.394** 
0.437** 
All replicated GWAS alleles (n = 142) 
0.396** 
0.437** 


Unweighted values do not incorporate the probability of detection, and weighted values incoporate the probability of detection in a GWAS. Neutral expectations use a polymorphism threshold (d) of 0.025 and Equations 5 and 10. Relative magnitudes of diseaseassociated and control allele frequencies were compared via MannWhitney U tests, and proportions of ancestral alleles were compared via binomial tests. * indicates significant differences from HapMap and neutral scenarios (pvalue < 0.05), and ** indicates highly significant differences from HapMap and neutral scenarios (pvalue < 0.0001). Totals for GWAS alleles are labeled in boldface type. Replicated alleles are those alleles that have been implicated in multiple studies. 

Lachance BMC Medical Genomics 2010 3:57 doi:10.1186/17558794357 