Clonucopya: An end-to-end workflow bridging tumor clonal architecture and drug prioritization
Year: 2026
Type: preprint
Abstract: ABSTRACT Motivation Intra-tumor heterogeneity limits the effectiveness of anticancer treatments, as distinct clonal populations may respond differently to therapy. Although subclonal inference from sequencing data is well established, translating clonal architecture into actionable drug recommendations remains a major bottleneck. Results We present Clonucopya, an end-to-end Snakemake workflow that integrates subclonal inference (PyClone-VI, PhyClone) with drug prioritization (PanDrugs2) to link tumor clonal architecture directly to candidate drugs. From genome sequencing data, Clonucopya reconstructs tumor phylogenies, quantifies clone-level prevalence across samples, and ranks FDA/EMA-approved and experimental therapeutic candidates against the somatic mutations detected in each clone. Outputs include clonality plots, per-clone variant and drug tables, and a summary ranking drugs by clonal coverage to highlight broadly active therapeutic candidates. We assess Clonucopya’s utility through a real-world longitudinal, multi-region use case, revealing clinically actionable clonal dynamics across tumor progression. Availability Clonucopya is available as open-source software with full documentation and tutorials at: https://github.com/cnio-bu/clonucopya Contact [email protected]
Institution: Spanish National Cancer Research Centre
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: green
Awards: G318412399, G4093352487, G4993905653, PDI - Plataforma Digital de IMPaCT para la captura, integración y modelado de datos biomédicos asociados a la Cohorte y proyectos IMPaCT-PMP, G6520718613, G684616945, Genómica funcional: desarrollo e implementación de una plataforma para el estudio de casos de cáncer hereditario sin resolver, G7859506354
OpenAlex ID: W7222695702