Tedja et al.
33 reported 161 SNPs associated with refractive error at genome-wide statistical significance (
P < 5 × 10
−8) in a large genome-wide association study (GWAS) meta-analysis of studies by the CREAM consortium and the 23andMe Inc. personal genomics company. We elected to use SNPs from the above GWAS reported by Tedja et al.,
33 rather than those reported more recently in a larger GWAS for refractive error,
38 as the more recent GWAS sample included UK Biobank participants and therefore risked selecting a biased set of instrumental variables due to the winner's curse.
39 Following the criteria adopted by Wood and Guggenheim,
40 we excluded 12 SNPs that did not replicate in an independent sample of 95,505 UK Biobank participants of European ancestry, 18 SNPs in linkage disequilibrium (
r2 > 0.05) with another variant in the set, and two SNPs with Hardy–Weinberg equilibrium test
P < 0.05, leaving 129 SNPs to use in the downstream analyses (
Supplementary Table S1). The functional roles of the 129 SNPs and thus the pathways through which they give rise to an association with refractive error are not known (accordingly, in view of the strong assumption that these SNPs are valid IVs, we describe below sensitivity analyses that are robust to violations of the IV assumptions). We constructed a weighted polygenic score (PGS) for refractive error using these 129 SNPs. A polygenic score is a single value quantifying a person's genetic predisposition to a specific trait or disease.
41 The polygenic score was calculated according to the following equation:
\begin{eqnarray*}{\rm{PGS}} = \;\mathop \sum \limits_{j = 1}^n {X_j} \times {\beta _j}\end{eqnarray*}
where PGS is the polygenic score for an individual,
Xj is the number of effect alleles of SNP
j (0, 1, or 2) carried by the individual, β
j is a weighting factor for SNP
j, and
j = 1,2, …, 129 indexes the SNPs. The weighting factors (SNP weights) quantifying the degree of association between the SNP and refractive error for the polygenic score were calculated as the square of the Z-score from the Stage-3 analysis of Europeans reported by Tedja et al.
33 Note that, conventionally, SNP regression coefficients from a GWAS are used as SNP weights. However, SNP regression coefficients were not reported by Tedja et al. To justify our use of squared Z-scores in place of the conventionally used regression coefficient SNP weights, we examined the relationship between the squared Z-score SNP weights and regression coefficient SNP weights calculated in the UK Biobank analysis sample (
Supplementary Fig. S2). This yielded a linear relationship, justifying our choice of squared Z-scores as SNP weights.