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Table 2 Call rate, HWE and minor allele frequencies in selected SNPs in immune genes

From: Genetic variation in the immune system and malaria susceptibility in infants: a nested case–control study in Nanoro, Burkina Faso

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
  1. SNP single nucleotide polymorphism, MajA major allele, MinA minor allele, MAF minor allele frequency, HWE Hardy–Weinberg equilibrium
  2. aDetermined by the Fluidigm SNP genotyping analysis