Table 2.
Selection of SNPs in the FAP-IFIH1-GCA-KCNH7 LD region that are significantly associated with susceptibility to candidemia
| SNP | Immunochip | Closest gene(s) | Alleles (dbSNP) | Functional class (AA change) | BH-corrected genotypic P value | |
|---|---|---|---|---|---|---|
| rs984971 | imm_2_162932767 | GCA | KCNH7 | A/G | intergenic | 6.9 × 10−4 | |
| Genotypes | GG | GA | AA | |||
| Controls | 25 (14.2%) | 103 (58.5%) | 48 (27.3%) | P = 2.2 × 10−5 | ||
| Cases | 25 (11.0%) | 89 (39.2%) | 113 (49.8%) | |||
| Alleles | G | A* | ||||
| Controls | 153 (43.5%) | 199 (56.5%) | P = 2.2 × 10−4 | |||
| Cases | 139 (30.6%) | 315 (69.4%) | OR, G vs. A = 0.57 (0.43 – 0.77) | |||
| rs1990760 | imm_2_162832297 | IFIH1 | C/T | missense (Ala946Thr) | 3.0 × 10−3 | |
| Genotypes | CC | CT | TT | |||
| Controls | 31 (17.6%) | 99 (56.3%) | 46 (26.1%) | P = 1.9 × 10−4 | ||
| Cases | 37 (16.3%) | 87 (38.3%) | 103 (45.4%) | |||
| Alleles | C | T* | ||||
| Controls | 161 (45.7%) | 191 (54.3%) | P = 3.7 × 10−3 | |||
| Cases | 161 (35.5%) | 293 (64.5%) | OR, C vs. T = 0.65 (0.49 – 0.87) | |||
| rs3747517 | imm_2_162837070 | IFIH1 | T/C (A/G) | missense (His843Arg) | 8.7 × 10−3 | |
| Genotypes | TT | TC | CC | |||
| Controls | 12 (6.8%) | 88 (50.0%) | 76 (43.2%) | P = 1.4 × 10−3 | ||
| Cases | 20 (8.8%) | 73 (32.2%) | 134 (59.0%) | |||
| Alleles | T | C* | ||||
| Controls | 112 (31.8%) | 240 (68.2%) | P = 3.3 × 10−2 | |||
| Cases | 113 (24.9%) | 341 (75.1%) | OR, T vs. C = 0.71 (0.52 – 0.97) | |||
Genotypic and allelic associations were assessed using the Fisher's exact test. P values are shown next to the corresponding contingency tables. Odds ratios (OR, with 95% confidence intervals) are reported for the allelic association tests and represent the odds of disease for individuals carrying the non-risk allele versus the risk allele. Risk alleles are denoted by an asterisk. BH-corrected genotypic P value: Benjamini-Hochberg correction of the genotypic association test P values for testing multiple SNPs (64 in total). Immunochip: the identifier of the SNP on the Immunochip SNP array. Alleles: the alleles measured with the Immunochip, and the complementary alleles reported by dbSNP (build 138), if they are different. The table shows the top SNP in the LD region, along with the only two significant missense SNPs. All SNPs tested are in Hardy–Weinberg equilibrium in the controls (P > 1 × 10−3). See Table S1 for the full list of significant SNPs.