Supplementary Table 1: General characteristics of the two populations recruited for this study.

Bauru / Rio de Janeiro
Patients / Controls / Patients / Controls
Age (mean ± SD) / 39.5 ± 17.61 / 35.93 ± 10.75 / 38.66 ± 16.92 / 33.49 ± 9.6
Sex / Female / 110 (0.29) / 128 (0.34) / 239 (0.36) / 314 (0.45)
Male / 265 (0.71) / 252 (0.66) / 431 (0.64) / 386 (0.55)
Ethnicity / Euro-descendants / 303 (0.81) / 240 (0.65) / 305 (0.55) / 393 (0.57)
Afro-descendants / 71 (0.19) / 132 (0.35) / 255 (0.45) / 300 (0.43)
WHO classification / Paucibacillary / 74 (0.22) / - / 244 (0.36) / -
Multibacillary / 259 (0.78) / - / 426 (0.64) / -

Results are shown as N (%). The number of individuals in each parameter may differ from the total number of genotyped individuals due to missing information.

Supplementary Table 2: Case-control analyses of IFNG SNPs in the Bauru population according to ethnicity.

Euro-descendants / Afro-descendants
SNP / Genotype/
allele / Cases1 / Controls1 / OR (p-value) / OR (p-value)2 / Cases1 / Controls1 / OR (p-value) / OR (p-value)2
IFNG
+874 T>A / AA / 110 (0.38) / 81 (0.35) / reference / reference / 44 (0.67) / 58 (0.45) / reference / reference
AT / 127 (0.43) / 110 (0.47) / 0.85 / 0.85 / 18 (0.27) / 49 (0.38) / 0.48 / 0.46
TT / 55 (0.19) / 42 (0.18) / 0.96 / 0.97 / 4 (0.06) / 21 (0.16) / 0.25 / 0.25
292 / 233 / (p > 0.05) / (p > 0.05) / 66 / 128 / (p = 0.01) / (p = 0.01)
Allele A / 347 (0.59) / 272 (0.58) / reference / reference / 106 (0.80) / 165 (0.64) / reference / reference
Allele T / 237 (0.41) / 194 (0.42) / 0.96 (p = 0.80) / 0.96 (p = 0.83) / 26 (0.20) / 91 (0.36) / 0.45 (p = 0.03) / 0.44 (p = 0.02)
T carriers / 182 (0.62) / 278 (0.65) / 0.88 (p = 0.49) / 0.89 (p = 0.51) / 22 (0.33) / 70 (0.55) / 0.41 (p = 0.005) / 0.40 (p = 0.004)
IFNG
+2109 A>G / AA / 138 (0.61) / 141 (0.59) / reference / reference / 28 (0.53) / 89 (0.70) / - / -
AG / 83 (0.37) / 85 (0.36) / 1.0 / 0.97 / 22 (0.42) / 36 (0.28) / 1.94 / 1.94
GG / 6 (0.03) / 12 (0.05) / 0.51 / 0.50 / 3 (0.06) / 3 (0.02) / 3.18 / 3.12
227 / 238 / (p > 0.05) / (p > 0.05) / 53 / 128 / (p > 0.05) / (p > 0.05)
Allele A / 359 (0.79) / 367 (0.77) / reference / reference / 78 (0.74) / 214 (0.84) / reference / reference
Allele G / 95 (0.21) / 109 (0.23) / 0.89 (p = 0.61) / 0.88 (p = 0.55) / 28 (0.26) / 42 (0.16) / 1.83 (p = 0.12) / 1.82 (p = 0.13)
G carriers / 89 (0.39) / 97 (0.41) / 0.94 (p = 0.73) / 0.92 (p = 0.65) / 25 (0.47) / 39 (0.30) / 2.04 (p = 0.03) / 2.03 (p = 0.03)
IFNG3´UTR
rs2069727 / TT / 89 (0.40) / 83 (0.36) / reference / reference / 38 (0.73) / 64 (0.50) / - / -
TC / 96 (0.43) / 112 (0.48) / 0.80 / 0.80 / 13 (0.25) / 46 (0.36) / 0.48 (p = 0.05) / 0.47 (p = 0.05)
CC / 38 (0.17) / 38 (0.16) / 0.93 / 0.94 / 1 (0.02) / 17 (0.13) / 0.10 / 0.10
223 / 233 / (p > 0.05) / (p > 0.05) / 52 / 127 / (p = 0.04) / (p = 0.04)
Allele T / 274 (0.61) / 278 (0.60) / reference / reference / 89 (0.86) / 174 (0.69) / reference / reference
Allele C / 172 (0.39) / 188 (0.40) / 0.93 (p = 0.70) / 0.93 (p = 0.72) / 15 (0.14) / 80 (0.31) / 0.37 (p = 0.02) / 0.37 (p = 0.02)
C carriers / 134 (0.60) / 150 (0.64) / 0.83 (p = 0.34) / 0.84 (p = 0.36) / 14 (0.27) / 63 (0.50) / 0.37 (p = 0.006) / 0.37 (p = 0.006)
Haplotypes
+874/+2109 / A/A / 0.39 / 0.36 / 1.15 (p = 0.32) / 1.15 (p = 0.32) / 0.54 / 0.48 / reference / reference
A/G / 0.20 / 0.22 / 1.00 (p = 0.99) / 0.99 (= 0.94) / 0.26 / 0.16 / 1.51 (p = 0.19) / 1.46 (p = 0.23)
T/A / 0.41 / 0.41 / reference / reference / 0.20 / 0.35 / 0.47 (p = 0.04) / 0.52 (p = 0.03)

1 Results are shown as N (frequency). 2 OR and p-value adjusted for sex.

Supplementary Table 3: Case-control analyses of the SNP IFNG+874 in the Euro-descendants group from RJ population and both studies combined.

IFNG
+874 T>A / Rio de Janeiro / Bauru + Rio de Janeiro
Cases / Controls / OR (p-value) / OR (p-value)1 / Cases / Controls / OR (p-value) / OR (p-value)2
AA / 77 (0.38) / 118 (0.35) / reference / reference / 187 (0.38) / 199 (0.35) / reference / reference
AT / 90 (0.44) / 152 (0.46) / 0.91 / 0.88 / 217 (0.44) / 262 (0.46) / 0.88 / 0.87
TT / 36 (0.18) / 63 (0.19) / 0.88 / 0.87 / 91 (0.18) / 105 (0.19) / 0.92 / 0.93
203 / 333 / (p > 0.05) / (p > 0.05) / 495 / 566 / (p > 0.05) / (p > 0.05)
Allele A / 244 (0.60) / 388 (0.58) / reference / reference / 591 (0.6) / 660 (0.58) / reference / reference
Allele T / 162 (0.40) / 278 (0.42) / 0.93 (p = 0.67) / 0.92 (p = 0.65) / 399 (0.4) / 472 (0.42) / 0.94 (0.64) / 0.94 (0.65)
T carriers / 126 (0.62) / 215 (0.65) / 0.90 (p = 0.56) / 0.88 (p = 0.50) / 308 (0.62) / 367 (0.65) / 0.89 (0.38) / 0.89 (0.36)

Results are showed as N (frequency). OR and p-values were adjusted for 1sex and 2sex and study.

Supplementary Figure 1: Effect of the SNP IFNG +874T/A in the quantitative Mitsuda response of borderline tuberculoidpatients. Lepromin challenge was performed at diagnosis and evaluated 28 days after inoculation. The lower and upper limits of each box represent the first and the third quartiles, respectively, while the solid line inside the box represents the median. The whiskers indicate the minimum and the maximum values. N = 118 for +874T carriers (AT+TT) and 112 for non-carriers (AA).