Tissue-aware genetic prioritization across autoimmune and proliferative thyroid diseases: analysis code and derived data

Abstract

Journal-independent reproducibility archive for tissue-aware genetic prioritization across autoimmune and proliferative thyroid diseases. Version 1.1.1 aligns Tier 2 with the implemented external replication or consistency criterion, separately records exact phenotype-matched MVP evidence, and corrects the MVP flags for TRMO, HLA-A and ATP6V1G2. All numerical results, original correction families, 14-gene membership and tier assignments (4/4/1/5) are unchanged. This release contains current analysis and audit code, 51 derived TSV files, two XLSX workbooks, and four main plus three supplementary scientific figures in 600-dpi TIFF and editable PDF/SVG. Supplementary figures follow first-citation order: S1, complete MVP results; S2, pQTL window comparisons; S3, evidence matrix. Superseded legacy ranking and rendering scripts are excluded; earlier public versions remain available. All missing estimates, unresolved and non-converged comparisons, claim-limiting sensitivity results, four primary Treg studies and all specified spatial pairs remain traceable to source tables. The final tier builder reproduces its four derived outputs byte for byte. The seven TIFF figures are reproducible with the recorded plotting environment. Full upstream analyses require separately obtained provider files, access permissions, LD/genotype references and configured local paths; a fresh full upstream rerun is not claimed. Source-level GWAS, eQTL, pQTL, genotype, LD, single-cell and spatial inputs are not redistributed. Genetic prioritization and shared-signal evidence do not establish clinical efficacy or therapeutic safety. Associated manuscript: Tissue-aware genetic prioritization identifies shared-signal anchors across autoimmune and proliferative thyroid diseases.