This repository contains the core R analysis code for the manuscript "A Cost-Optimized 5-Protein Panel Revolutionizes Systemic Lupus Erythematosus Diagnosis".Study summary:Using plasma protein data from 544 SLE cases and 48,036 controls in the UK Biobank, we applied a balanced case-control sampling (BCCS) approach with LASSO regression to identify 35 high-confidence SLE-associated proteins. A protein risk score (ProtRS) derived from these proteins achieved excellent diagnostic performance (AUC = 0.91), outperforming polygenic risk scores and clinical factors alone. A cost-optimized 5-protein panel (TRIM21, SOD2, KLK3, IL15, ADIPOQ) retained high accuracy (AUC = 0.82) while reducing testing costs by ~87%. Population attributable fraction (PAF) analysis further underscored the dominant contribution of ProtRS to SLE burden.Code contents:The scripts (numbered 1–10) cover the core analysis pipeline:• Data preparation, scaling, and mean imputation.• 10,000 LASSO iterations with BCCS to select stable protein biomarkers.• Computation of ProtRS and evaluation of the 35-protein model (1,000 BCCS).• Comparison with polygenic risk score (PRS) and clinical risk factors.• Integration of risk factors and categorical variable creation.• Cost‑optimization by incremental protein addition.• Population attributable fraction (PAF) calculations (single‑ and multi‑variable).• Reproducibility check between 10,000 and 1,000 LASSO runs.• Sensitivity analysis comparing MICE, median, and kNN imputation methods.All scripts are fully reproducible and require the R packages listed in the README.The UK Biobank data are not included due to access restrictions; please refer to the manuscript for data application procedures.