Table 1

Disease-associated 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

Disease-associated 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 disease-associated and control allele frequencies were compared via Mann-Whitney U tests, and proportions of ancestral alleles were compared via binomial tests. * indicates significant differences from HapMap and neutral scenarios (p-value < 0.05), and ** indicates highly significant differences from HapMap and neutral scenarios (p-value < 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:10.1186/1755-8794-3-57

Open Data