TABLE 4
FROM:
Detect and adjust for population stratification in population-based association study using genomic control markers: an application of Affymetrix Genechip® Human Mapping 10K array
Ke Hao, Cheng Li, Carsten Rosenow and Wing H Wong
BACK TO ARTICLETable 4. Controlling for population stratification with 50 unlinked markers*
| Case/control ratio | 1/0 | 0.75/0.25 | 0.6/0.4 | 0.5/0.5 | 0.4/0.6 | 0.25/0.75 | 0/1 |
|---|---|---|---|---|---|---|---|
| (a) Adjusted rejection rate in association test under the null hypothesis at 0.05 level | |||||||
| Asian vs Caucasian | 4.4% | 4.3% | 4.2% | 3.5% | 4.0% | 4.3% | 4.1% |
| Utah vs Caucasian | 4.4% | 4.1% | 4.0% | 3.8% | 4.0% | 4.0% | 4.4% |
| African-American vs Caucasian | 3.5% | 3.9% | 4.4% | 3.6% | 4.2% | 4.0% | 3.5% |
| Asian vs Utah | 4.6% | 4.6% | 4.2% | 3.6% | 4.0% | 4.5% | 4.7% |
| African-American vs Asian | 3.4% | 4.0% | 3.9% | 3.4% | 3.9% | 3.1% | 3.4% |
| African-American vs Utah | 3.3% | 3.9% | 4.4% | 3.5% | 4.2% | 4.0% | 3.1% |
(b) Mean (variance) of the inflation factor, 
| |||||||
| Asian vs Caucasian | 5.67 (3.63) | 2.20 (0.46) | 1.26 (0.10) | 1.14 (0.05) | 1.24 (0.30) | 2.07(0.40) | 5.84 (3.93) |
| Utah vs Caucasian | 1.22 (0.08) | 1.17 (0.06) | 1.16 (0.06) | 1.18 (0.06) | 1.16 (0.06) | 1.16(0.05) | 1.21 (0.08) |
| African-American vs Caucasian | 8.62 (7.12) | 2.92 (0.82) | 1.38 (0.14) | 1.12 (0.04) | 1.39 (0.17) | 2.91 (0.77) | 8.62 (7.12) |
| Asian vs Utah | 6.49 (4.83) | 2.23 (0.50) | 1.27 (0.10) | 1.12 (0.04) | 1.24 (0.09) | 2.14 (0.41) | 6.52 (4.73) |
| African-American vs Asian | 7.51 (5.39) | 2.42 (0.56) | 1.29 (0.11) | 1.11 (0.04) | 1.34 (0.12) | 2.95 (0.87) | 7.72 (6.83) |
| African-American vs Utah | 10.1 (9.93) | 3.24 (1.10) | 1.36 (0.12) | 1.12 (0.04) | 1.44 (0.18) | 3.25 (1.09) | 10.5 (12.1) |
Estimation was based on 10 000 iterations, the rejection rates were summarized in panel (a). In panel (b), we presented the mean value and variance of the 10 000 s obtained in the 10 000 times simulation. Caucasian, Caucasian samples collected by Coriell Institute. Utah, Caucasian samples collected by CEPH lab.