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 (Version 2) was prospectively registered on PROSPERO (CRD420261505625) before any data were downloaded or analysed. Version 2 (17 September 2026): This is an updated version of the original Zenodo record (10.5281/zenodo.22813896). It includes a complete registration statement, clinical translation section for pediatric surgery, the full 18-Step Implementation Guide, detailed data sources table, power calculation examples, and STROBE-MR checklist as Supplementary Materials. This two-sample Mendelian randomization (MR) 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, weighted median, 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) and Supplementary Materials v2 are provided as separate PDF files in this Zenodo record.