Table 2.
Performance of no adjustment, PCA, EMMAX and PCAPS evaluated using the significantly associated SNPs from each method under moderate population stratification in GWAS simulation
| Method | Number of SNPs* | False Positive | False Negative | Positive Predict | Accuracy | |||
|---|---|---|---|---|---|---|---|---|
| TP | FP | FN | TN | Rate (95%CI) | Rate (95% CI) | Value (95%CI) | Rate (95%CI) | |
| FP / (FP+TN) | FN / (TP+FN) | TP / (TP+FP) | (TP+TN) / (TP+FP+FN+TN) | |||||
| No Adjustment | 9 | 1628 | 0 | 6 | 99.6% (99.2 – 99.9%) | 0% (0 – 34%) | 0.5% (0.3 – 1%) | 0.9% (0.5 – 1.5%) |
| PCA-10 | 8 | 6 | 1 | 6 | 50% (21 – 79%) | 11% (0.3 – 48%) | 57% (29 – 82%) | 67% (43 – 85%) |
| PCA-TW | 8 | 4 | 1 | 6 | 40% (12 – 74%) | 11% (0.3 – 48%) | 67% (35 – 90%) | 74% (49 – 91%) |
| EMMAX | 9 | 7 | 0 | 6 | 54% (25 – 81%) | 0% (0 – 34%) | 56% (30 – 80%) | 68% (45 – 86%) |
| PCAPS-10 | 8 | 6 | 1 | 6 | 50% (21 – 79%) | 11% (0.3 – 48%) | 57% (29 – 82%) | 67% (43 – 85%) |
| PCAPS-TW | 8 | 0 | 1 | 6 | 0% (0 – 46%) | 11% (0.3 – 48%) | 100% (63 – 100%) | 93% (68 – 99.8%) |
PCA-10, principal components analysis correcting for the first 10 principal components; PCA-TW, principal components analysis correcting for Tracy-Wisdom significant principal components; EMMAX, efficient mixed-model association expedited; PCAPS-10, principal components and propensity score correcting for the first 10 principal components; PCAPS-TW, principal components and propensity score correcting for Tracy-Wisdom significant principal components; SNP, single nucleotide polymorphism; CI, confidence interval. The 95% confidence intervals were calculated using the Binomial distribution.
Positive disease SNP is the pre-defined SNP with odds ratio 1.5 or 2, or linkage disequilibrium (r2 ≥ 0.3) with pre-defined disease SNP. If p-value is less than 7.5X10−6 for a SNP using a given method, then the SNP is identified as disease SNP by that method. Otherwise, the SNP is identified as non-disease SNP. Negative disease SNP is defined as pre-defined SNP with odds ratio 1 or linkage disequilibrium (r2 ≥ 0.3) with pre-defined non-disease SNP. TP – true positive, i.e. identified disease SNP is disease SNP; FP – false positive, i.e. identified disease SNP is non-disease SNP; FN – false negative, i.e. identified non-disease SNP is disease SNP; TN – true negative, i.e. identified non-disease SNP is non-disease SNP.