Table 2.
Call rate, HWE and minor allele frequencies in selected SNPs in immune genes
| Gene | SNPs | Genotyping success N (%) |
Overall call ratea | Maj/MinA | MAF | HWE (P value) | Malaria infection | Clinical malaria | ||
|---|---|---|---|---|---|---|---|---|---|---|
| MAF Cases | MAF Controls | MAF Cases | MAF Controls | |||||||
| TLR1 | rs4833095 | 645 (98.3) | 98.8 | C/T | 9.5 | 0.600 | 9.1 | 11.1 | 9.1 | 10.0 |
| TLR4 | rs4986790 | 654 (99.7) | 98.4 | A/G | 9.0 | 0.999 | 9.2 | 8.1 | 9.1 | 8.8 |
| TLR9 | rs5743836 | 653 (99.5) | 98.9 | A/G | 42.3 | 0.600 | 42.4 | 42.2 | 41.3 | 44.1 |
| TLR9 | rs352139 | 654 (99.7) | 99.3 | C/T | 43.0 | 0.018 | 43.6 | 40.6 | 44.1 | 41.2 |
| TLR9 | rs352140 | 645 (98.3) | 98.9 | C/T | 24.2 | < 0.001 | 24.5 | 23.1 | 25.3 | 22.3 |
| IL-4 | rs2243250 | 655 (99.8) | 96.4 | T/C | 22.1 | 0.600 | 21.8 | 23.3 | 22.3 | 21.6 |
| IL-10 | rs1800896 | 619 (94.4) | 98.6 | T/C | 31.1 | 0.024 | 31.4 | 29.9 | 31.5 | 30.4 |
| IL-10 | rs1800890 | 650 (99.1) | 97.8 | A/T | 20.1 | 0.114 | 20.3 | 19.7 | 21.1 | 18.5 |
| IL-17F | rs4715291 | 655 (99.8) | 99.0 | C/T | 15.6 | 0.415 | 16.2 | 13.6 | 16.2 | 14.7 |
| IL-1β | rs1143634 | 654 (99.7) | 99.0 | G/A | 11.7 | 0.960 | 10.5 | 16.7 | 10.1 | 14.3 |
| TNF | rs1800629 | 655 (99.8) | 98.8 | G/A | 14.5 | 0.961 | 14.1 | 16.0 | 14.4 | 14.7 |
| TNF | rs3093664 | 656 (100) | 98.9 | A/G | 5.6 | 0.600 | 5.5 | 6.2 | 5.2 | 6.3 |
| TNF | rs3093662 | 392 (59.7) | 97.4 | A/G | 5.7 | – | – | – | – | – |
| IFNR1 | rs10213701 | 655 (99.8) | 98.6 | T/A | 36.4 | 0.863 | 36.5 | 36.0 | 37.3 | 34.8 |
| IFNR1 | rs10065633 | 656 (100) | 99.0 | T/C | 50.8 | 0.601 | 51.3 | 48.4 | 51.0 | 50.4 |
| NOS2A | rs2297518 | 656 (100) | 99.4 | G/A | 8.2 | 0.180 | 8.5 | 6.6 | 8.4 | 7.8 |
| FcγRIIA/CD32 | rs1801274 | 648 (98.8) | 98.9 | G/A | 32.6 | 0.961 | 30.4 | 41.4 | 29.8 | 37.2 |
SNP single nucleotide polymorphism, MajA major allele, MinA minor allele, MAF minor allele frequency, HWE Hardy–Weinberg equilibrium
aDetermined by the Fluidigm SNP genotyping analysis