Table 1.
IgG3 rs4042056 variation in pemphigus vulgaris by KASP assay.
| KASPa | Cases | Controls | Recessivec | Dominantc | Co-dominantc | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs4042056 | AA | AG | GG | MAF (%)b | AA | AG | GG | MAF (%)b | OR (95% CI) | p | OR (95% CI) | p | OR (95% CI) | p | ||
| Germany | 4 | 0 | 83 | 4.6* | 0 | 1 | 180 | 0.28 | 19 (1–350) | 0.0074 | 5.2 (1–27) | 0.037 | 3.2 (1.1–9.5) | 0.014 | ||
| 4.6% | 0% | 95% | 0% | 0.55% | 99% | |||||||||||
| Iran | 5 | 1 | 72 | 7.1* | 3 | 0 | 87 | 3.3* | 1.9 (0.5–7.4) | 0.37 | 2.1 (0.6–7.5) | 0.24 | 1.4 (0.7–2.8) | 0.28 | ||
| 6.4% | 1.3% | 92% | 3.3% | 0% | 97% | |||||||||||
| Turkey | 9 | 1 | 63 | 13* | 0 | 0 | 19 | 0 | 5.8 (0.33–100) | 0.12 | 3.4 (0.4–28) | 0.19 | 2.2 (0.6–7.6) | 0.15 | ||
| 12% | 1.4% | 86% | 0% | 0% | 100% | |||||||||||
| Egypt | 2 | 0 | 99 | 2* | 0 | 0 | 126 | 0 | 6.4 (0.3–130) | 0.16 | 6.4 (0.3–130) | 0.16 | 2.5 (0.6–12) | 0.16 | ||
| 2% | 0% | 98% | 0% | 0% | 100% | |||||||||||
| Totalg | 20 | 2 | 317 | 6.2 | 3 | 1 | 412 | 0.84 | 4.28 (1.6–11.9) | 0.0051 | 3.7 (1.5–9) | 0.0038 | 2.78 (1.0–7.6) | 0.047 | ||
| 5.9% | 0.6% | 94% | 0.7% | 0.2% | 99% | |||||||||||
| ELISAd | Cases | Controls | Dominantc | ELISA/KASP combined dominanth | ||||||||||||
| G3m15 | Positive | Negative | MAF (%)e | Positive | Negative | MAF (%)e | OR (95% CI) | p | OR (95% CI) | p | ||||||
| Germany | 1 | 49 | 1.0 | 1 | 77 | 0.6 | 1.6 (0.2–15) | 0.7 | 4.9 (0.9–25.4) | 0.061 | ||||||
| 2.0% | 98.0% | 1.3% | 98.7% | |||||||||||||
| Iran | n.a.f | n.a.f | n.a.f | n.a.f | n.a.f | n.a.f | n.a. | n.a. | n.a. | n.a. | ||||||
| Turkey | 4 | 71 | 2.7 | n.a.f | n.a.f | n.a.f | n.a. | n.a. | n.a. | n.a. | ||||||
| 5.3% | 94.7% | |||||||||||||||
| Egypt | 2 | 50 | 1.9 | 2 | 59 | 1.7 | 1.6 (0.33–8) | 0.54 | 2.5 (0.4–13.7) | 0.298 | ||||||
| 3.8% | 96.2% | 3.3% | 96.7% | |||||||||||||
| Totalg | 7 | 170 | 2 | 3 | 136 | 1.1 | 1.75 (0.4–7.6) | 0.83 | 3.6 (1.5–8.8) | 0.0041 | ||||||
| 4% | 96% | 2.2% | 97.8% | |||||||||||||
aThe KASP assay directly determined the genotype of rs4042056 SNP that corresponds to the amino acid at residue 435. The minor A allele (g.1053927G>A) allele corresponds to p.Arg435His.
bMAF, minor allele frequency, i.e., frequency of the A allele. An asterisk (*) indicates that the respective genotype distribution is not in Hardy–Weinberg equilibrium.
cLogistic regression (recessive, dominant, and co-dominant models) stratified by ethnic cohort. The 95% confidence interval is given for the odds ratio (OR); the p value (p) is given for the likelihood ratio test (LR test) on the genotype. For origin-wise models, the raw ORs are shown. In the combined analysis, a generalized linear mixed effects (with implicit adjustment) model with logit link function was applied. In case of 0 values in corresponding data, Lidstone additive smoothing was used to allow calculation of ORs and ensure convergence of the fitting routine.
dThe ELISA detects the G3m15 allotype of IgG3 that is linked to the p.Arg435His variation.
eMAF, minor allele frequency, i.e., frequency of the allele encoding the G3m15 allotype, inferred assuming Hardy–Weinberg equilibrium.
fn.a., no serum samples available.
gRegression calculated with a generalized linear mixed effects model (uncorrelated intercept and genotype effect as random effects).
hLogistic regression of combined ELISA and KASP results. The genotyping method was used for stratification in a random effects model (compare table footnote c). For the calculation across all ethnicities, ethnic origin was used together the genotyping method for stratification.