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Table 2 The percentage of influential genes among the top 100 most significant SNPs, as ranked by LogiCALL, a likelihood ratio test, and a standard test.

From: Genotyping and inflated type I error rate in genome-wide association case/control studies

   RR = 1.5 RR = 2.0 RR = 2.5
Shift Difference LogiCALL LR Standard LogiCALL LR Standard LogiCALL LR Standard
0.5 0 4.4 4.6 4.5 41.8 41.8 41.3 78.8 79.2 79.3
  0.2 4.4 4.6 4.5 42.0 41.8 41.3 78.8 79.3 79.4
0.3 0 4.4 4.6 4.6 42.0 41.9 41.2 78.8 79.2 79.4
  0.2 4.4 1.9 0.2 41.6 29.5 14.4 78.8 67.3 42.7
0.2 0 4.4 4.4 2.1 42.0 41.4 25.9 78.8 78.9 47.1
  0.2 3.7 0.1 0.0 38.9 3.4 0.0 75.3 21.3 0.0
  1. Simulated data sets are full described in the Methods Section. The shift is the distance between the and μ AA and ( μ A B A + μ A B U ) / 2 MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeiikaGIaeqiVd02aa0baaSqaaiabdgeabjabdkeacbqaaiabdgeabbaakiabgUcaRiabeY7aTnaaDaaaleaacqWGbbqqcqWGcbGqaeaacqWGvbqvaaGccqGGPaqkcqGGVaWlcqaIYaGmaaa@3A89@ . The Difference is the distance between μ A B A MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeqiVd02aa0baaSqaaiabdgeabjabdkeacbqaaiabdgeabbaaaaa@30DB@ and μ A B U MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeqiVd02aa0baaSqaaiabdgeabjabdkeacbqaaiabdwfavbaaaaa@3103@ . RR is the genotype relative risk for subjects homogeneous for the minor allele.