This repository contains the code book used in our comment on "Lowering of Circulating Sclerostin May Increase Risk of Atherosclerosis and its Risk Factors: Evidence From a Genome-Wide Association Meta-Analysis Followed by Mendelian Randomization" by Zheng et al. These analyses use genetic variants in cis of the SOST gene (the gene that encodes sclerostin) that are associated with circulating sclerostin protein levels, known as protein quantitative trait loci (pQTL). We visualize the SOST gene region for each phenotype and perform Mendelian randomization (MR) and colocalization analyses for the cardiovascular events and risk factors tested using results from the same (or equivalent) genome-wide association studies (GWAS) as used by Zheng et al. Sensitivity Mendelian randomization analyses using European only samples where possible and cis sclerostin pQTLs from UK Biobank were also performed.
All of the code was written in R (version 4.3.1). The code book was written using Quarto (version 1.3.433).
The code book is available here: https://jrs95.github.io/sclerostin_pqtl_mr
Staley JR et al. Genetic data do not provide evidence that lower sclerostin is associated with increased risk of atherosclerosis: comment on the article by Zheng et al. Arthritis Rheumatol 2023; DOI: 10.1002/art.42751
The code is available under the GPL-3 license and the analysis results are available under the CC-BY-4.0 license.
