Table 5. IRGM haplotype associations (8 polymorphisms).
| Haplotype | Cases | Controls | OR | CI | Pnom | |||||||
| Del | −4299 | −566 | −420 | rep | −261 | −71 | 313 | n (%) | n (%) | |||
| M. tuberculosis EUAM | ||||||||||||
| WT | C | G | C | 3 | C | G | T | 28 (1.5) | 65 (1.5) | 1.06 | [0.66–1.70] | 0.8 |
| WT | C | G | C | 4 | T | A | T | 45 (2.3) | 97 (21.9) | 1.16 | [0.80–1.69] | 0.4 |
| WT | T | C | C | 1 | C | A | C | 24 (1.2) | 50 (1.1) | 0.98 | [0.54–1.78] | 0.95 |
| WT | T | C | C | 1 | C | G | C | 452 (23.5) | 1009 (22.8) | 1.05 | [0.92–1.20] | 0.4 |
| WT | T | G | C | 1 | C | A | C | 37 (1.9) | 39 (0.9) | 1.93 | [1.14–3.27] | 0.01 |
| WT | T | G | C | 1 | C | G | C | 340 (17.7) | 784 (17.7) | 1.00 | [0.87–1.16] | 0.96 |
| WT | T | G | C | 3 | C | G | C | 37 (1.9) | 102 (2.3) | 0.84 | [0.57–1.23] | 0.3 |
| WT | T | G | C | 4 | C | G | C | 28 (1.5) | 52 (1.2) | 1.25 | [0.78–2.01] | 0.4 |
| DEL | C | G | C | 3 | C | A | T | 25 (1.3) | 37 (0.8) | 1.38 | [0.75–2.53] | 0.3 |
| DEL | C | G | C | 3 | C | G | T | 264 (13.7) | 553 (12.5) | 1.10 | [0.93–1.29] | 0.3 |
| DEL | C | G | C | 4 | T | A | T | 554 (28.8) | 1459 (32.9) | 0.83 | [0.73–0.93] | 0.001 |
| DEL | C | G | T | 3 | C | G | T | 94 (4.9) | 176 (3.9) | 1.26 | [0.97–1.63] | 0.09 |
EUAM, Euro-American lineages of Mycobacterium tuberculosis; del, deletion; rep, repeat (number of tetranucleotide repeats given in digits; see also Figure 1); OR, odds ratio; CI, 95% confidence interval; Pnom, nominal P value; WT, wild-type; DEL, 20.1 kb deletion. P values refer to comparisons of one haplotype to all other combinations and are adjusted for age, gender and ethnicity. Corrected global P value in cases caused by EUAM infections after 10000 permutations = 0.02. Missing genotypes are compensated for by simulations of all possible completions of the data.