Frontiers in Oncology (Mar 2023)

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

  • Richa Malhotra,
  • Vyomesh Javle,
  • Nishtha Tanwar,
  • Pooja Gowda,
  • Linu Varghese,
  • Anju K,
  • Nandhitha Madhusudhan,
  • Nupur Jaiswal,
  • Bhargavi K. S.,
  • Manjima Chatterjee,
  • Kumar Prabhash,
  • Peddagangannagari Sreekanthreddy,
  • Kshitij D. Rishi,
  • Hitesh M. Goswami,
  • Vidya H. Veldore

DOI
https://doi.org/10.3389/fonc.2023.1002792
Journal volume & issue
Vol. 13

Abstract

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IntroductionThe 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.MethodsThe 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.ResultsThe 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.DiscussionThe 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.

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