Real-world genomic profiling of solid tumors: validation and clinical insights from a Brazilian cohort.

BACKGROUND

Precision medicine has transformed cancer management by tailoring treatments to the molecular characteristics of a patient's tumor. Comprehensive Genomic Profiling enables the simultaneous analysis of multiple genomic alterations using next-generation sequencing assays, providing detailed molecular profiles of tumors. This approach allows more accurate cancer classification, guides decisions regarding targeted therapies, enhances the precision of treatment strategies, and improves patient outcomes in oncology.

OBJECTIVE

In this article, we describe the analytical validation of the Illumina TruSight Oncology 500 (TSO500) assay in a (CAP)-certified clinical laboratory in Brazil and present real-world findings from Comprehensive Genomic Profiling performed on 454 patients with cancer, highlighting the genomic landscape, including novel fusion events.

METHODS

Tumor samples collected between January 2020 and September 2023 were subjected to Comprehensive Genomic Profiling using the TSO500 assay. Library preparation and sequencing (Illumina NextSeq) were performed according to the manufacturer's protocol, followed by bioinformatics processing using an in-house pipeline for alignment, variant calling, and annotation. Variants were classified according to the Variant Interpretation for Cancer Consortium guidelines. Analytical performance metrics, including specificity and positive predictive value, were calculated for assay validation.

RESULTS

The test demonstrated a specificity of 93.39% and a positive predictive value of 73.36%. Regarding Comprehensive Genomic Profiling, 57.85% of all detected variants were classified as variants of uncertain significance, and 42.15% were oncogenic. Gene fusions, including both novel and canonical events, were detected in 13% of cases.

CONCLUSION

The TSO500 assay provides crucial insights into patient genomics, aiding diagnosis, prognosis, and treatment decisions. Demonstrating high levels of accuracy, reproducibility, and sensitivity, the TSO500 advances cancer research to the forefront of molecular technology.