Background
Methods
Study populations
Polymerase chain reaction (PCR)
Cloning and sequencing
SNP genotyping
Statistical analysis
Results
PNG | Kenya | North America | |||||
---|---|---|---|---|---|---|---|
Gene | Mutant allele | lowlands | lowlands | Highlands | African | Caucasian | Asian |
TLR2 | |||||||
Δ22 | 0.131I | 0.298 | 0.326II | 0.215 | 0.131 | 0.256VI | |
GTS | 0.091 | 0.082 | 0.145 | 0.111 | 0.036 | 0.212 | |
GTM | 0.522I | 0.799 | 0.761 | 0.721 | 0.583 | 0.394VI | |
GTL | 0.387 | 0.120 | 0.094 | 0.168 | 0.381 | 0.394 | |
Arg753Gln | 0.000V | 0.000 | 0.000 | 0.011 | 0.038 | 0.000 | |
TLR4 | |||||||
Asp299Gly | 0.000V | 0.071III | 0.054II | 0.131 | 0.086 | 0.042 | |
Thr399Ile | 0.000V | 0.015 | 0.007 | 0.028 | 0.095 | 0.036 | |
TLR9 | |||||||
-1486T/C | 0.371I | 0.270 | 0.25IV | 0.343 | 0.340 | 0.361 | |
-1237T/C | 0.000 | 0.351 | 0.362 | 0.337 | 0.130 | 0.066 | |
1174G/A | 0.624I | 0.403 | 0.481II | 0.341 | 0.525 | 0.590 | |
MAL | |||||||
Ser180Leu | 0.149 | 0.000 | 0.025 | 0.056 | 0.160 | 0.060VI |
TLR2 polymorphisms
TLR4, TLR9, and MAL SNP allele frequencies
Frequencies of TLR2, TLR 4, TLR9, and MAL genotypes
PNG | Kenya | North America | |||||
---|---|---|---|---|---|---|---|
PolymorphismI | genotype | lowlands | lowlands | highlands | African | Caucasian | Asian |
TLR2 Δ22 | WW | 253(76) | 41(49) | 33(48) | 58(62) | 64(76) | 49(58) |
WDII | 73(22) | 36(43) | 27(39) | 30(32) | 18(21) | 27(32) | |
DD | 7(2) | 7(8) | 9(13) | 5(5) | 2(2) | 8(10) | |
TLR4 Asp299Gly | Asp/Asp | 906(100)IV | 78(86) | 66(89) | 65(74) | 67(83) | 76(92) |
Asp/Gly | 0 | 13(14) | 8(11) | 23(26) | 14(17) | 7(8) | |
TLR4 Thr399Ile | Thr/Thr | 906(100)IV | 64(97) | 69(99) | 84(94) | 64(81) | 77(93) |
Thr/Ile | 0 | 2(3) | 1(1) | 5(6) | 15(19) | 6(7) | |
TLR9 -1486 | TT | 137(41) | 47(54) | 41(54) | 37(42) | 36(44) | 34(41) |
CT | 146(44) | 33(38) | 32(42) | 43(48) | 35(43) | 38(46) | |
CC | 51(15) | 7(8) | 3(4) | 9(10) | 10(12) | 11(13) | |
TLR9 -1237 | TT | 334(100) | 39(45) | 29(38) | 36(40) | 61(75) | 74(89) |
CT | 0 | 35(40) | 39(51) | 46(52) | 19(23) | 7(8)III | |
CC | 0 | 13(15) | 8(11) | 7(8) | 1(1) | 2(2) | |
TLR9 1174 | GG | 53(16) | 29(32) | 17(22) | 35(43) | 22(27) | 14(17) |
GA | 147(44) | 47(53) | 47(60) | 38(46) | 33(41) | 40(48) | |
AA | 136(41) | 12(14) | 14(18) | 9(11) | 26(32) | 29(35) | |
MAL 180 | Ser/Ser | 254(73) | 89(100) | 75(95) | 82(91) | 53(68) | 73(88) |
Ser/Leu | 81(23) | 0 | 4(5) | 6(7)III | 25(32) | 10(12) | |
Leu/Leu | 11(3) | 0 | 0 | 2(2) | 0 | 0 |
Inferred haplotypes and linkage disequilibrium
PNG | Kenya | North America | |||||
---|---|---|---|---|---|---|---|
Gene | Haplotype | lowlands | lowlands | highlands | African | Caucasian | Asian |
TLR2I | |||||||
DL | 0.029 | 0.000 | 0.000 | 0.000 | 0.000 | 0.086 | |
DM | 0.011 | 0.258 | 0.239 | 0.164 | 0.099 | 0.105 | |
DS | 0.093 | 0.041 | 0.092 | 0.051 | 0.033 | 0.063 | |
WL | 0.355 | 0.110 | 0.100 | 0.161 | 0.388 | 0.300 | |
WM | 0.509 | 0.559 | 0.515 | 0.572 | 0.480 | 0.293 | |
WS | 0.003 | 0.033 | 0.054 | 0.052 | 0.000 | 0.154 | |
TLR4II | |||||||
Asp-Thr | 1IV | 0.924 | 0.943 | 0.869 | 0.905 | 0.952 | |
Gly-Ile | 0 | 0.015 | 0.007 | 0.028 | 0.089 | 0.030 | |
Gly-Thr | 0 | 0.061 | 0.050 | 0.102 | 0.000 | 0.012 | |
Asp-Ile | 0 | 0.000 | 0.000 | 0.000 | 0.006 | 0.006 | |
TLR9III | |||||||
C C A | 0.000 | 0.006 | 0.007 | 0.000 | 0.000 | 0.000 | |
C C G | 0.000 | 0.075 | 0.099 | 0.092 | 0.000 | 0.011 | |
C T A | 0.003 | 0.000 | 0.011 | 0.018 | 0.000 | 0.007 | |
C T G | 0.368 | 0.205 | 0.136 | 0.244 | 0.353 | 0.343 | |
T C G | 0.000 | 0.266 | 0.254 | 0.256 | 0.115 | 0.055 | |
T T A | 0.625 | 0.396 | 0.455 | 0.324 | 0.526 | 0.584 | |
T T G | 0.005 | 0.051 | 0.037 | 0.066 | 0.006 | 0.000 |