Whole blood transcriptomics atlas across human diseases

We present a WBT Atlas, comprising 4444 WBT samples across 98 distinct health conditions, enabling systematic exploration of disease-associated transcriptomic signatures. Health condition–specific profiles are characterized across immune, metabolic, and cell-type specific features at the gene, gene module, and pathway levels. By integrating matched plasma proteomics data from 1280 participants across 28 health conditions, we further assess blood RNA–protein relationships and demonstrate their complementary biological roles. By integrating RNA and protein signatures, we develop multi-class classification models that accurately distinguish among a wide range of health conditions, with integrated models consistently outperforming those based on single-omics data alone. The identified RNA and protein signatures are validated across ten independent WBT cohorts and the UK Biobank. Together, the WBT Atlas provides a genome-wide resource that enables translational discovery in precision medicine.