Table 7.
Association of CTLA4 polymorphisms with hypoadrenocorticism in cocker spaniels. Markers are as Table 1, 5′ to 3′ SNPs then indels top to bottom. MAF: minor allele frequency; NaN: not a number; N/A: not calculable; OR: odds ratio; 95% CI: 95% confidence intervals of the OR. Max (T) p value calculated by permutation analysis; FDR: false discovery rate
| Marker | Minor allele | MAF in cases | MAF in controls | Max (T) p value |
FDR | OR (95% CI) |
|---|---|---|---|---|---|---|
| SNP1 | A | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP2 | A | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP3 | A | 0 | 0.0098 | 1 | 1 | 0 (0 - NaN) |
| SNP4 | A | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP5 | A | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP6 | A | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP7 | G | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP8 | N/A | 0 | 0 | 1 | 1 | N/A |
| SNP9 | A | 0 | 0.01961 | 1 | 1 | 0 (0 - NaN) |
| SNP10 | G | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP11 | N/A | 0 | 0 | 1 | 1 | N/A |
| SNP12 | T | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP13 | T | 0.105 | 0.0098 | 0.016 | 0.09887 | 11.88 (1.2–110) |
| SNP14 | C | 0.184 | 0.059 | 0.031 | 0.09887 | 3.61 (1.1–11.5) |
| SNP15 | C | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP16 | G | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP17 | N/A | 0 | 0 | 1 | 1 | N/A |
| SNP18 | N/A | 0 | 0 | 1 | 1 | N/A |
| SNP19 | A | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| SNP20 | N/A | 0 | 0 | 1 | 1 | N/A |
| indel1 | N/A | 0 | 0 | 1 | 1 | N/A |
| indel2 | – | 0.158 | 0.059 | 0.082 | 0.09887 | 3 (0.9–9.9) |
| indel3 | + | 0.263 | 0.067 | 0.0097 | 0.05783 | 4.85 (1.6–13.9) |