An absolute approach to using whole exome DNA and RNA workflow for cancer biomarker testing

• Published in: Frontiers in oncology 2023-03, Vol.13, p.1002792-1002792
• Main Authors: Malhotra, Richa, Javle, Vyomesh, Tanwar, Nishtha, Gowda, Pooja, Varghese, Linu, K, Anju, Madhusudhan, Nandhitha, Jaiswal, Nupur, K S, Bhargavi, Chatterjee, Manjima, Prabhash, Kumar, Sreekanthreddy, Peddagangannagari, Rishi, Kshitij D, Goswami, Hitesh M, Veldore, Vidya H
• Format: Article
• Language: English
• Subjects: comprehensive genomic profiling (CGP); microsatellite instability (MSI); Oncology; RNA exome; tumor mutational burden (TMB); whole exome sequencing (WES)
• ISSN: 2234-943X; 2234-943X
• DOI: 10.3389/fonc.2023.1002792

The concept of personalized medicine in cancer has emerged rapidly with the advancement of genome sequencing and the identification of clinically relevant variants that contribute to disease prognosis and facilitates targeted therapy options. In this study, we propose to validate a whole exome-based tumor molecular profiling for DNA and RNA from formalin-fixed paraffin-embedded (FFPE) tumor tissue. The study included 166 patients across 17 different cancer types. The scope of this study includes the identification of single-nucleotide variants (SNVs), insertions/deletions (INDELS), copy number alterations (CNAs), gene fusions, tumor mutational burden (TMB), and microsatellite instability (MSI). The assay yielded a mean read depth of 200×, with >80% of on-target reads and a mean uniformity of >90%. Clinical maturation of whole exome sequencing (WES) (DNA and RNA)- based assay was achieved by analytical and clinical validations for all the types of genomic alterations in multiple cancers. We here demonstrate a limit of detection (LOD) of 5% for SNVs and 10% for INDELS with 97.5% specificity, 100% sensitivity, and 100% reproducibility. The results were >98% concordant with other orthogonal techniques and appeared to be more robust and comprehensive in detecting all the clinically relevant alterations. Our study demonstrates the clinical utility of the exome-based approach of comprehensive genomic profiling (CGP) for cancer patients at diagnosis and disease progression. The assay provides a consolidated picture of tumor heterogeneity and prognostic and predictive biomarkers, thus helping in precision oncology practice. The primary intended use of WES (DNA+RNA) assay would be for patients with rare cancers as well as for patients with unknown primary tumors, and this category constitutes nearly 20-30% of all cancers. The WES approach may also help us understand the clonal evolution during disease progression to precisely plan the treatment in advanced stage disease.