Precision oncology platforms: practical strategies for genomic database utilization in cancer treatment

Author(s)

Gazola, Antonia A. ; Lautert-Dutra, William ; Archangelo, Leticia Frohlich ; dos Reis, Rodolfo B. ; Squire, Jeremy A.

• Document type: Journal article
• Source: MOLECULAR CYTOGENETICS; v. 17, n. 1, p. 18-pg., 2024-11-14.

Abstract

In recent years, the expansion of molecularly targeted cancer therapies has significantly advanced precision oncology. Parallel developments in next-generation sequencing (NGS) technologies have also improved precision oncology applications, making genomic analysis of tumors more affordable and accessible. Targeted NGS panels now enable the rapid identification of diverse actionable mutations, requiring clinicians to efficiently assess the predictive value of cancer biomarkers for specific treatments. The urgency for timely and accurate decision-making in oncology emphasizes the importance of reliable precision oncology software. Online clinical decision-making tools and associated cancer databases have been designed by consolidating genomic data into standardized, accessible formats. These new platforms are highly integrated and crucial for identifying actionable somatic genomic biomarkers essential for tumor survival, determining corresponding drug targets, and selecting appropriate treatments based on the mutational profile of each patient's tumor. To help oncologists and translational cancer researchers unfamiliar with these tools, we review the utility, accuracy, and comprehensiveness of several commonly used precision medicine software options currently available. Our analysis categorized selected genomic databases based on their primary content, utility, and how well they provide practical guidance for interpreting somatic biomarker data. We identified several comprehensive, mostly open-access platforms that are easy to use for genetic biomarker searches, each with unique features and limitations. Among the precision oncology tools we evaluated, we found MyCancerGenome and OncoKB to be the first choice, offering comprehensive, accurate up-to-date information on the clinical significance of somatic mutations. To illustrate the application of these precision oncology tools in clinical settings, we evaluated three case studies to see how use of the platforms could have influenced treatment planning. Most of the precision oncology software evaluated could be easily streamlined into clinical workflows to provide updated information on approved drugs and clinical trials related the actionable mutations detected. Some platforms were very intuitive and easy to use, while others, often developed in smaller academic settings, were more difficult to navigate and may not be updated consistently. Future enhancements, incorporating artificial intelligence algorithms, are likely to improve integration of the platforms with diverse big data sources, enabling more accurate predictions of potential therapeutic responses. (AU)

• FAPESP's process: 21/15011-4 - Single-cell transcriptomics and in vitro characterization of the molecular causes of immunotherapy failure in advanced prostate cancer
• Grantee: Jeremy Andrew Squire
• Support Opportunities: Research Projects - Thematic Grants
• FAPESP's process: 21/12271-5 - Impact of CDK12 mutation on immune response in prostate cancer
• Grantee: William Lautert Dutra
• Support Opportunities: Scholarships in Brazil - Master