Table 4.
Results of robust stepwise conditional logistic regression analysis to look for independent associations between SNPs on chromosome 5q23.3-q31.1 and two leishmaniasis-related phenotypes (DTH+ and DTH−).
| NULL MODEL | ALTERNATIVE MODEL | Na | Wald χ2 | df | P-valueb |
|---|---|---|---|---|---|
| DTH+ phenotype – within LD blocks | |||||
| LD Block 1 SNPs | Adding Block 1 SNP to Block 1 | ||||
| (L) rs248158 | (L+M) | 182 | 0.00 | 1 | 0.985 |
| (L) rs248158 | (L+N) | 212 | 0.03 | 1 | 0.863 |
| (M) rs2526146 | (M+L) | 182 | 2.36 | 1 | 0.125 |
| (M) rs2526146 | (M+N) | 220 | 3.13 | 1 | 0.077 |
| (N) rs2526152 | (N+L) | 212 | 2.80 | 1 | 0.094 |
| (N) rs2526152 | (N+M) | 220 | 0.06 | 1 | 0.811 |
| LD Block 2 | Adding Block 2 SNP to Block 2 | ||||
| (R) rs4976360 | (R+T) | 154 | 2.07 | 1 | 0.150 |
| (R) rs4976360 | (R+U) | 192 | 1.99 | 1 | 0.160 |
| (T) rs1054124 | (T+R) | 154 | 2.63 | 1 | 0.105 |
| (T) rs1054124 | (T+U) | 180 | 0.35 | 1 | 0.554 |
| (U) rs4669 | (U+R) | 192 | 4.60 | 1 | 0.032 |
| (U) rs4669 | (U+T) | 180 | 1.60 | 1 | 0.206 |
| DTH+ phenotype – between LD blocks | |||||
| LD Block 1 SNPs | Adding Block 2 SNP to Block 1 | ||||
| (L) rs248158 | (L+R) | 176 | 9.93 | 1 | 0.002 |
| (L) rs248158 | (L+T) | 152 | 5.12 | 1 | 0.024 |
| (L) rs248158 | (L+U) | 180 | 10.02 | 1 | 0.002 |
| (M) rs2526146 | (M+R) | 180 | 9.24 | 1 | 0.002 |
| (M) rs2526146 | (M+T) | 158 | 7.11 | 1 | 0.008 |
| (M) rs2526146 | (M+U) | 202 | 4.54 | 1 | 0.033 |
| (N) rs2526152 | (N+R) | 188 | 4.39 | 1 | 0.036 |
| (N) rs2526152 | (N+T) | 178 | 7.78 | 1 | 0.005 |
| (N) rs2526152 | (N+U) | 214 | 4.71 | 1 | 0.030 |
| LD Block 2 SNPs | Adding Block 1 SNP to Block 2 | ||||
| (R) rs4976360 | (R+L) | 176 | 6.23 | 1 | 0.013 |
| (R) rs4976360 | (R+M) | 180 | 9.20 | 1 | 0.002 |
| (R) rs4976360 | (R+N) | 188 | 1.21 | 1 | 0.272 |
| (T) rs1054124 | (T+L) | 152 | 8.33 | 1 | 0.004 |
| (T) rs1054124 | (T+M) | 158 | 12.06 | 1 | 0.001 |
| (T) rs1054124 | (T+N) | 178 | 4.28 | 1 | 0.039 |
| (U) rs4669 | (U+L) | 180 | 11.51 | 1 | 0.001 |
| (U) rs4669 | (U+M) | 202 | 7.95 | 1 | 0.005 |
| (U) rs4669 | (U+N) | 214 | 6.60 | 1 | 0.010 |
| DTH− phenotype | |||||
| (D) rs2070874 | (D+O) | 116 | 2.80 | 1 | 0.095 |
| (O) rs30740 | (O+D) | 116 | 3.61 | 1 | 0.057 |
a
N = number of observations in the conditional logistic regression stepwise comparison based on the number of cases and ‘pseudo-sib’ controls from trios fully genotyped for both markers being compared.
b
Bold indicates significant independent effects for the SNP when added to the alternative model.