Scalable clinical proteomics from DNA/RNA extraction flowthroughs enables integrated proteogenomic profiling from a single cancer biopsy

Background

Precision oncology has largely relied on genomic and transcriptomic sequencing to guide therapy selection in patients with advanced cancer. However, these molecular layers do not fully capture the functional state of tumors, as proteins largely represent the active effectors of cellular processes and signaling pathways. Integrating proteomic and phosphoproteomic measurements with genomic data has therefore emerged as an important objective in translational oncology. In routine clinical workflows, tumor biopsies are frequently processed using DNA/RNA extraction kits such as the Qiagen AllPrep system, which generates a protein-rich flowthrough that is typically discarded.