Comparison of our case-control results to traditional case-control analyses
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A |
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| Length of sequence examineda |
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| Group one freq |
Group two freq |
Single siteb |
5 kb |
10 kb |
20 kb |
50 kb |
Traditional case-control |
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| 0.10 | 0.00 | 0.001 | 0.024 | 0.047 | 0.091 | 0.211 | 0.001 | ||||
| 0.02 | 0.021 | 0.347 | 0.569 | 0.808 | 0.979 | 0.017 | |||||
| 0.03 | 0.057 | 0.678 | 0.889 | 0.985 | 1.0 | 0.045 | |||||
| 0.20 | 0.057 | 0.684 | 0.893 | 0.986 | 1.0 | 0.048 | |||||
| 0.25 | 0.008 | 0.161 | 0.294 | 0.499 | 0.813 | 0.005 | |||||
| 0.38 | 3.0 × 10-6 | 6.2 × 10-5 | 1.2 × 10-4 | 2.5 × 10-4 | 6.2 × 10-4 | 3.6 × 10-6 | |||||
| 0.30 | 0.05 | 2.0 × 10-6 | 4.1 × 10-5 | 8.3 × 10-5 | 1.7 × 10-4 | 4.1 × 10-4 | 3.3 × 10-6 | ||||
| 0.10 | 4.4 × 10-4 | 0.009 | 0.018 | 0.036 | 0.087 | 4.1 × 10-4 | |||||
| 0.18 | 0.056 | 0.671 | 0.885 | 0.984 | 0.999 | 0.047 | |||||
| 0.44 | 0.047 | 0.612 | 0.843 | 0.971 | 0.999 | 0.040 | |||||
| 0.55 | 4.1 × 10-4 | 0.008 | 0.017 | 0.033 | 0.081 | 3.5 × 10-4 | |||||
| 0.62 | 6.2 × 10-6 | 1.3 × 10-4 | 2.6 × 10-4 | 5.2 × 10-4 | 0.001 | 5.6 × 10-6 | |||||
| Number of sites expected
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21
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43
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85
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214
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| B |
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| Sample sizea |
100 |
200 |
500 |
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| Group one freq |
Group two freq |
Case control method |
Our method |
Case control method |
Our method |
Case control method |
Our method |
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| Single site |
5 kb |
Single site |
5 kb |
Single site |
5 kb |
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| 0.10 | 0.05 | 0.058 | 0.069 | 0.799 | 0.007 | 0.008 | 0.200 | 2.2 × 10-5 | 2.2 × 10-5 | 6.9 × 10-4 | |||||||
| 0.06 | 0.140 | 0.164 | 0.975 | 0.037 | 0.042 | 0.674 | 9.8 × 10-4 | 0.001 | 0.032 | ||||||||
| 0.07 | 0.282 | 0.322 | 0.999 | 0.128 | 0.144 | 0.974 | 0.016 | 0.018 | 0.419 | ||||||||
| 0.13 | 0.347 | 0.387 | 1.0 | 0.184 | 0.202 | 0.994 | 0.035 | 0.038 | 0.688 | ||||||||
| 0.15 | 0.131 | 0.149 | 0.966 | 0.033 | 0.036 | 0.621 | 0.001 | 7.9 × 10-4 | 0.024 | ||||||||
| 0.17 | 0.041 | 0.047 | 0.670 | 0.004 | 0.004 | 0.108 | 4.6 × 10-6 | 4.9 × 10-6 | 1.5 × 10-4 | ||||||||
| 0.30 | 0.21 | 0.039 | 0.044 | 0.647 | 0.003 | 0.004 | 0.100 | 3.9 × 10-6 | 4.2 × 10-6 | 1.3 × 10-4 | |||||||
| 0.24 | 0.177 | 0.194 | 0.987 | 0.056 | 0.061 | 0.799 | 0.003 | 0.003 | 0.080 | ||||||||
| 0.26 | 0.373 | 0.403 | 1.0 | 0.208 | 0.222 | 0.996 | 0.046 | 0.049 | 0.773 | ||||||||
| 0.34 | 0.391 | 0.421 | 1.0 | 0.225 | 0.240 | 0.997 | 0.055 | 0.058 | 0.827 | ||||||||
| 0.37 | 0.138 | 0.152 | 0.968 | 0.036 | 0.039 | 0.647 | 0.001 | 9.8 × 10-4 | 0.030 | ||||||||
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0.39
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0.058
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0.065
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0.782
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0.007
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0.008
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0.198
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2.3 × 10-5
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2.5 × 10-5
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7.7 × 10-4
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Note that the length-dependent P-values obtained using our method can be approximated by multiplying the traditional case-control P-value by the number of polymorphic sites expected in the region sequenced. The genome-wide average θ, 8.25 × 10-4, was used.
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A P-values for our method examining 5, 10, 20, and 50 kb and for traditional case-control method at varying case and control allele frequencies using 50 cases and 50 controls.
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B P-values for traditional case-control method and for our method examining 5 kb at varying case and control allele frequencies using 100, 200, and 500 cases and controls. The number of variant sites expected in 5 kb among 100, 200, and 500 cases are 24.2, 27.1, and 30.9, respectively.
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↵a Using our method
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↵b P-value obtained using our method for a single site that is known to be polymorphic
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↵a Sample size refers to the number of individuals in each group, cases, and controls
