Harmonization and Integration of Pharmacogenomics Screens

MOTIVATION: Large pharmacogenomics screens have generated a wealth of information cataloguing the responses of more than a thousand tumor cell-line models to FDA-approved and exploratory drugs. Although centralized repositories have consolidated data access, the diversity of experimental platforms and response metrics used in these screens have made it challenging to integrate and compare their measured drug responses. Towards better pharmacogenomic data harmonization, we surveyed a range of data analysis protocols based on different curve-fitting functions (sigmoid, piecewise linear), different response metrics (IC50, EC50, integrated AUC), and different drug concentration windows (full range or truncated). RESULTS: We found that an AUC derived from a sigmoidal curve fitted to a truncated dose range yields the strongest agreement between screening platforms, significantly bettering other protocols surveyed. This harmonization procedure also best aligns drug responses across successive iterations of the same platform. These findings broadly inform efforts to integrate drug response data in large-scale analyses. AVAILABILITY: The source code to generate drug response profiles and correlations are available at https://github.com/digitaltumors/Pharmacogenomics_Screens_Harmonization.git. SUPPLEMENTARY INFORMATION: Supplemental figures are available at Bioinformatics online. Supplemental tables are found on Zenodo: https://doi.org/10.5281/zenodo.17196025, https://doi.org/10.5281/zenodo.17981848, and https://zenodo.org/records/20620409.