Causal effects of maternal smoking, BMI and GDM on esophageal atresia and Hirschsprung disease risk in offspring: two-sample MR with paternal negative control

This protocol was prospectively registered on PROSPERO (CRD420261505625) before any data were downloaded or analysed. This two-sample Mendelian randomization study examines the causal effects of maternal smoking, BMI, and gestational diabetes mellitus (GDM) on esophageal atresia with or without tracheoesophageal fistula (EA/TEF, primary outcome) and Hirschsprung disease (HSCR, secondary outcome) in offspring. The key methodological innovation is the paternal negative control design using a Z-test to compare maternal versus paternal genetic effects. Stronger maternal associations would support intrauterine causation. Analyses will use the latest GWAS summary statistics (Brosens et al. 2022 for EA/TEF; 2025 HSCR meta-GWAS + FinnGen R14), include comprehensive sensitivity analyses (IVW, MR-Egger, MR-PRESSO, CAUSE, colocalization, MVMR), a priori power calculations, and grade evidence as robust, suggestive, or null. All procedures follow STROBE-MR 2021 and 2026 Nature Genetics MR guidelines. The full detailed protocol (Version 2.1), data sources table, 18-step implementation guide, STROBE-MR checklist, and analysis code are provided as separate PDF files in this Zenodo record.