Table 1. Candidate gene association study of CD1A and tuberculosis in Vietnam.
Association between SNPs in CD1A and pulmonary (PTB), meningeal (TBM), or pulmonary + meningeal (TB) tuberculosis in Vietnam. SNP genotypes are shown as n(frequency) of total for common homozygous (AA), heterozygous (Aa), and minor homozygous (aa) genotypes. The p-value for deviation from Hardy-Weinberg equilibrium among cord blood controls was calculated using a χ2 goodness-of-fit test and is indicated under “HWE.” Genotypic analysis compares frequencies in a 2×3 contingency table. For the recessive model analysis, AA + Aa was compared to aa in a 2×2 contingency table. Two-sided hypothesis testing was used for all comparisons. Unadjusted p-values of significance are noted in bold italic.
| Discovery Cohort | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Group | HWE | Genotypic Analysis | Recessive Analysis | |||||||||
| AA | Aa | aa | χ2 | p-value | AA+Aa | aa | χ2 | p-value | OR | 95% CI | |||
| rs366316 | CTRL | 0.20 | 192 (0.5) | 164 (0.43) | 25 (0.07) | 356 (0.93) | 25 (0.07) | ||||||
| T → C | ALL | 161 (0.58) | 86 (0.31) | 30 (0.11) | 11.36 | 0.003 | 247 (0.89) | 30 (0.11) | 3.82 | 0.051 | 1.73 | (0.96-3.15) | |
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| rs411089 | CTRL | 0.18 | 192 (0.5) | 165 (0.43) | 25 (0.07) | 357 (0.93) | 25 (0.07) | ||||||
| T → C | ALL | 171 (0.49) | 138 (0.39) | 42 (0.12) | 6.64 | 0.036 | 309 (0.88) | 42 (0.12) | 6.47 | 0.011 | 1.94 | (1.13-3.4) | |
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| rs2269714 | CTRL | 0.56 | 120 (0.32) | 192 (0.51) | 68 (0.18) | 312 (0.82) | 68 (0.18) | ||||||
| C → T | ALL | 116 (0.33) | 168 (0.48) | 68 (0.19) | 0.60 | 0.742 | 284 (0.81) | 68 (0.19) | 0.24 | 0.621 | 1.10 | (0.74-1.62) | |
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| rs389293 | CTRL | 0.80 | 159 (0.42) | 176 (0.46) | 46 (0.12) | 335 (0.88) | 46 (0.12) | ||||||
| G → A | ALL | 161 (0.47) | 143 (0.42) | 38 (0.11) | 2.09 | 0.352 | 304 (0.89) | 38 (0.11) | 0.16 | 0.687 | 0.91 | (0.56-1.47) | |
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|
Validation Cohort
| |||||||||||||
| rs366316 | CTRL | 0.91 | 214 (0.58) | 133 (0.36) | 20 (0.05) | 347 (0.95) | 20 (0.05) | ||||||
| T → C |
ALL | 156 (0.59) | 93 (0.35) | 17 (0.06) | 0.31 | 0.858 | 249 (0.94) | 17 (0.06) | 0.25 | 0.618 | 1.18 | (0.57-2.43) | |
| rs411089 | CTRL | 0.56 | 171 (0.47) | 159 (0.44) | 32 (0.09) | 330 (0.91) | 32 (0.09) | ||||||
| T → C | ALL | 161 (0.51) | 110 (0.35) | 46 (0.15) | 8.80 | 0.012 | 271 (0.85) | 46 (0.15) | 5.35 | 0.021 | 1.75 | (1.06-2.92) | |
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Combined Cohort
| |||||||||||||
| rs366316 | CTRL | 0.33 | 406 (0.54) | 297 (0.4) | 45 (0.06) | 703 (0.94) | 45 (0.06) | ||||||
| T → C | ALL | 317 (0.58) | 179 (0.33) | 47 (0.09) | 7.90 | 0.019 | 496 (0.91) | 47 (0.09) | 3.31 | 0.069 | 1.48 | (0.95-2.32) | |
| PTB | 217 (0.57) | 126 (0.33) | 35 (0.09) | 6.88 | 0.032 | 343 (0.91) | 35 (0.09) | 4.00 | 0.045 | 1.59 | (0.97-2.59) | ||
| TBM | 100 (0.61) | 53 (0.32) | 12 (0.07) | 3.35 | 0.188 | 153 (0.93) | 12 (0.07) | 0.36 | 0.546 | 1.23 | (0.58-2.42) | ||
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| rs411089 | CTRL | 0.27 | 367 (0.49) | 325 (0.43) | 59 (0.08) | 692 (0.92) | 59 (0.08) | ||||||
| T → C | ALL | 327 (0.5) | 245 (0.37) | 87 (0.13) | 12.96 | 0.002 | 572 (0.87) | 87 (0.13) | 10.81 | 0.001 | 1.78 | (1.24-2.57) | |
| PTB | 182 (0.49) | 137 (0.37) | 52 (0.14) | 11.96 | 0.003 | 319 (0.86) | 52 (0.14) | 10.57 | 0.001 | 1.91 | (1.26-2.89) | ||
| TBM | 145 (0.5) | 108 (0.38) | 35 (0.12) | 6.01 | 0.050 | 253 (0.88) | 35 (0.12) | 4.67 | 0.031 | 1.62 | (1.01-2.57) | ||