2.2 Genetic instrumental variables selection
To obtain robust instrumental variables that are sufficiently correlated
with the exposure of interest, SNPs related to IMIDs were chosen with a
genome-wide significance threshold of p < 5e-08. Only
two potential instrumental variables associated with AA were identified
at the threshold of p < 5e-08. Therefore, we modified a
more lenient threshold of p < 5e-06 for genome-wide
significance to search for additional SNPs. Then, we set parameters
related to linkage disequilibrium (r2 = 0.001, distance = 10000 kb) to
clump these genetic loci, in which all loci exhibit complete
independence in order to avoid double-count the contribution of any
particular variants(29). Next, with the help of the online tool
PhenoScanner v2 (http://www.phenoscanner.medschl.cam.ac.uk/ ), we
checked genotype-phenotype associations between potential IVs and
outcome(30), and removed SNPs associated with confounders. Then, SNP
harmonization was conducted to correct the orientation of the
alleles(31). Finally, we assessed IVs strength by calculating the
genetic instruments (R2) and F-statistic for each
instrumental variable. R2 and F-statistic was
calculated as following formula:
R2=[2β2 × MAF × (1-MAF)] /
[2β2 × MAF × (1-MAF)+2β2 × MAF ×
(1-MAF) × N × SE], and F=[R2 × (N-k-1)
/k(1-R2)] (where β = effect estimate of the SNP in
the exposure, MAF = minor allele frequency, N = sample size of the GWAS
dataset, k = number of IVs, SE=the standard error of genetic effect)
(32). Theoretically, all selected genetic IVs should have F-statistics
greater than 10.