Table 3.
Estimated Genetic Variance on the Observed and Liability Scale Explained by All SNPs for Crohn Disease in WTCCC Data
| Thresholda | No. SNPb | Estimatec(SE) | LR | Adjustedd(SE) | Transformede(SE) |
|---|---|---|---|---|---|
| MAF > 0.01 | |||||
| 200 | 322,142 | 0.56 (0.07) | 63.16 | 0.64 (0.08) | 0.24 (0.03) |
| 20 | 294,850 | 0.53 (0.07) | 57.48 | 0.61 (0.08) | 0.22 (0.03) |
| 7 | 248,791 | 0.52 (0.07) | 57.30 | 0.61 (0.08) | 0.22 (0.03) |
| 4 | 195,977 | 0.50 (0.07) | 54.94 | 0.60 (0.08) | 0.22 (0.03) |
| MAF > 0.05 | |||||
| 200 | 293,269 | 0.56 (0.07) | 69.00 | 0.63 (0.08) | 0.23 (0.03) |
| 20 | 266,843 | 0.53 (0.07) | 63.27 | 0.60 (0.08) | 0.22 (0.03) |
| 7 | 225,043 | 0.52 (0.07) | 63.94 | 0.60 (0.08) | 0.22 (0.03) |
| 4 | 177,615 | 0.50 (0.07) | 62.14 | 0.60 (0.08) | 0.22 (0.03) |
a
Excluding SNPs with more than the listed number of missing genotypes.
b
After filtering on the basis of SNP missing rate.
c
Estimate of genetic variance proportional to the total phenotypic variance on the observed scale.
d
Estimate adjusted for reduced number of SNPs.
e
Transformed genetic variance proportional to the total phenotypic variance on the liability scale under the assumption that the population prevalence is 0.1%, the heritability on the liability scale explained by the SNPs.