Code for exploratory single-SNP Mendelian randomization of six candidate proteins and hand osteoarthritis (version 1.1.0)

Abstract

Code for calculating first-order delta-method single-SNP Wald estimates from user-supplied, already harmonized summary data. The archive contains software and a synthetic self-test only; it does not redistribute source summary statistics or real participant-level data. Users must obtain source data from the providers and follow their terms. The analysis assumes zero exposure-outcome covariance and is intended for exploratory candidate analyses.Version 1.1.0 adds extension analyses under extensions_v1.1.0/: (i) single-causal-variant colocalization of erosive hand osteoarthritis with cis-pQTL instruments for SPP1, MGP and IBSP, with a prior-sensitivity grid, an LD peak-independence audit against 1000 Genomes high-coverage EUR genotypes, and replication of the MGP signal across three independent exposure resources; (ii) cross-joint single-SNP Wald transportability of the six pooled protein instruments to finger and thumb osteoarthritis outcomes with heterogeneity assessment; and (iii) an external check of the MGP variant in FinnGen R10 knee and hip osteoarthritis endpoints. All analyses are code-only; source summary statistics must be obtained from the original providers under their access terms.