An Open, Harmonized Genomic Meta-Database Enabling AI-Based Personalization of Adjuvant Chemotherapy in Early-Stage Non-Small Cell Lung Cancer

Background: Personalizing adjuvant chemotherapy (ACT) after curative resection in early-stage NSCLC remains unmet because prior ACT-biomarker findings rarely reproduce across studies. Key barriers are platform and preprocessing heterogeneity, dominant batch effects, and incomplete ACT annotations. As a result, many signatures that perform well in a single cohort fail during external validation. We created an open, harmonized meta-database linking gene expression with curated ACT exposure and survival to enable fair benchmarking and modeling. Methods: A PRISMA-guided search of 999 GEO studies (through January 2025) used LLM-assisted triage of titles, clinical tables, and free text to identify datasets with explicit ACT status and patient-level survival. Eight Affymetrix microarray cohorts (GPL570/GPL96) met eligibility. Raw CEL files underwent robust multi-array average; probes were re-annotated to Entrez IDs and collapsed by median. Covariate-preserving ComBat adjusted platform/study while retaining several clinical factors. Batch structure was quantified by principal-component analysis (PCA) variance, silhouette width, and UMAP. Two quality-control (QC) filters, median M-score deviation and PCA leverage, flagged and removed technical outliers. Results: The final meta-database comprises 1340 patients (223 (16.6%) ACT; 1117 (83.4%) observation), 13,039 intersecting genes, and 594 overall-survival events. Batch-associated variance (PC1 + PC2) decreased from 63.1% to 20.1%, and mean silhouette width shifted from 0.82 to −0.19 post-correction. Seven arrays (0.5%) were excluded by QC. Event depth supports high-dimensional survival and heterogeneity-of-treatment modeling, and the multi-cohort design enables internal–external validation. Conclusions: This first open, rigorously harmonized NSCLC transcriptomic database provides the sample size, demographic diversity, and technical consistency required to benchmark ACT-benefit markers. By making these data openly available, it will accelerate equitable precision-oncology research and enable data-driven treatment decisions in early-stage NSCLC.