Supplementary Material for: Identification of TNF-α as major susceptible risk locus for vitiligo: A systematic review and meta-analysis study in Asian population.

Abstract

Introduction:
Vitiligo is a common depigmentation disorder characterized by defined white patches on the skin and affecting around 0.5 % to 2% of the general population. Genetic association studies have identified several pre-disposing genes and single nucleotide polymorphisms (SNPs) for vitiligo pathogenesis; nonetheless, the reports are often conflicting, and rarely conclusive. This comprehensive meta-analysis study was designed to evaluate the effect of the risk variants on vitiligo aetiology and covariate stratified vitiligo risk in the Asian population considering all the studies published so far.

Methods:
We followed a systematic and comprehensive search to identify the relevant vitiligo related candidate gene association studies in PubMed using specific keywords.
After data extraction, we calculated, for the variants involved, the study-level unadjusted odds ratio (OR), standard errors (SE), and 95% confidence intervals (95% CI) by using logistic regression with additive, dominant effect and recessive models using R software package (R, 3.4.2) ‘metafor'. Subgroup analysis was performed using logistic regression (generalized linear model; ‘glm’) of disease status on subgroup-specific genotype counts. For a better understanding of the likely biological function of vitiligo-associated variant obtained through the meta-analysis, in silico functional analyses, through standard publicly available web tools, were also conducted.

Results:
Thirty-one vitiligo associated case control studies on eleven SNPs were analysed in our study. In the Fixed effect meta-analysis, one variant upstream of TNF-α gene: rs1800629 was found to be associated with vitiligo risk in additive (p=.4.26E-06), dominant (p=1.65E-7) and recessive model (p=.000453). After Benjamini–Hochberg false discovery rate (FDR) correction, rs1800629/TNF α was found to be significant at 5% FDR in the dominant (padj=1.82E-6) and recessive models (padj = .0049). In silico characterization revealed the prioritized variant to be regulatory in nature and thus having potential to contribute towards vitiligo pathogenesis.

Conclusion:
Our study constitutes the first comprehensive meta-analysis of candidate gene-based association studies reported in the whole of Asian population, followed by an in silico analysis of the vitiligo associated variant. According to the findings of our study, TNF-α single nucleotide variant, rs1800629G>A has a risk association, potentially contributing to vitiligo pathogenesis in Asian population.