R code and all research data for: Genetically Elevated Free Thyroxine Increases Luminal A Breast Cancer Risk: A Mendelian Randomization Study

This repository contains reproducible R code and core analytical data for all Mendelian randomization analyses in the manuscript “Genetically Elevated Free Thyroxine Increases Luminal A Breast Cancer Risk: A Mendelian Randomization Study” Included are: Thyroid_BC_analysisCode.zip: Full R code implementing the analyses below. MR_Thyroid_BC_CoreData.xlsx: Curated intermediate datasets generated during the analytical workflow (e.g., harmonized SNP-exposure/outcome associations, MR results, sensitivity metrics, and colocalization outputs), enabling transparency and reuse of core analytical outputs. Analyses performed: Univariable MR: FT4/TSH → Breast cancer subtypes (BCAC) Two-step mediation MR: Sex hormones as mediators Bidirectional MR: Testing reverse causation Multivariable MR: Independent effects of FT4 and TSH Colocalization analysis: coloc.abf and coloc.susie Validation MR: FinnGen R12 replication Data sources: ThyroidOmics Consortium (FT4, TSH) Breast Cancer Association Consortium (BCAC) FinnGen R12 UK Biobank via IEU OpenGWAS