\usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$[0,2]$$\end{document}[0,2]. Furthermore, standard imputation methods do not take phenotype into account. As a result, effect sizes for imputed SNPs are biased in ways that have not been well characterised. While such biases must be small for well imputed SNPs, and have not created problems for standard GWAS analyses, the effect seems sufficient to bias our index event adjustment unless R2 > 0.98 at least. Noting the compatibility between results for R2 > 0.98 and 0.99, we used pruned SNPs meeting imputation \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$R^2 \, > \, 0.99$$\end{document}R2>0.99 in both incidence and survival GWAS in all further analyses.
