Genomic and proteomic biomarker landscape in clinical trials

Computational and structural biotechnology journal
Piñero Janet, Rodriguez Fraga Pablo S., Valls-Margarit Jordi, Ronzano Francesco, Accuosto Pablo, Lambea Jane Ricard, Sanz Ferran, Furlong Laura I.
DOI: 10.1016/j.csbj.2023.03.014
PMID: 36968019
Keyword: actionable biomarker · biomarker · clinical trial · genomic biomarker · proteomic biomarker · text mining


The use of molecular biomarkers to support disease diagnosis, monitor its progression, and guide drug treatment has gained traction in the last decades. While only a dozen biomarkers have been approved for their exploitation in the clinic by the FDA, many more are evaluated in the context of translational research and clinical trials. Furthermore, the information on which biomarkers are measured, for which purpose, and in relation to which conditions are not readily accessible: biomarkers used in clinical studies available through resources such as are described as free text, posing significant challenges in finding, analyzing, and processing them by both humans and machines. We present a text mining strategy to identify proteomic and genomic biomarkers used in clinical trials and classify them according to the methodologies by which they are measured. We find more than 3000 biomarkers used in the context of 2600 diseases. By analyzing this dataset, we uncover patterns of use of biomarkers across therapeutic areas over time, including the biomarker type and their specificity. These data are made available at the Clinical Biomarker App at, a new portal that enables the exploration of biomarkers extracted from the clinical studies available at and enriched with information from the scientific literature. The App features several metrics that assess the specificity of the biomarkers, facilitating their selection and prioritization. Overall, the Clinical Biomarker App is a valuable and timely resource about clinical biomarkers, to accelerate biomarker discovery, development, and application.