• 1 OncoAtlas LLC, Malaya Nikitskaya Str., 31, Moscow, Russia, 121069.
  • 2 OncoAtlas LLC, Malaya Nikitskaya Str., 31, Moscow, Russia, 121069
  • 3 Research Centre for Medical Genetics, Moskvorech'ye Ulitsa, 1, Moscow, Russia, 115478
  • 4 Clinic "Luch'', Savushkina Str., 73, Saint-Petersburg, Russian Federation, 197183
  • 5 Saint-Petersburg Clinical Research Center of Specialized Types of Medical Care (Oncological), Leningradskaya Str., 68A, Saint-Petersburg, Russian Federation, 197758
  • 6 GENETICO LLC, Gubkina Str., 3/1, Moscow, Russian Federation, 119333
  • 7 Higher School of Oncology, Saint Petersburg, Russian Federation
  • 8 Clinical Hospital No. 2, "Medsi" Group of Companies, 5/4 2-Oy Botkinskiy Proezd, Moscow, Russia, 125284
  • 9 Federal State Budgetary Institution, N.N. Blokhin National Medical Research Center of Oncology, Kashira Hwy, 23, Moscow, Russian Federation, 115522
  • 10 MEDSI, Moscow, Russia
Clin Exp Med, 2023 Oct;23(6):2663-2674.
PMID: 36752890 DOI: 10.1007/s10238-023-01011-6


With the growing use of comprehensive tumor molecular profiling (CTMP), the therapeutic landscape of cancer is rapidly evolving. NGS produces large amounts of genomic data requiring complex analysis and subsequent interpretation. We sought to determine the utility of publicly available knowledge bases (KB) for the interpretation of the cancer mutational profile in clinical practice. Analysis was performed across patients who previously underwent CTMP. Independent interpretation of the CTMP was performed manually, and then, the recommendations were compared to ones present in KBs (OncoKB, CIViC, CGI, CGA, VICC, MolecularMatch). A total of 222 CTMP reports from 222 patients with 932 genomic alterations (GA) were identified. For 368 targetable GA identified in 171 (77%) of the patients, 1381 therapy recommendations were compiled. Except for CGA, therapy ESCAT LOE I, II, IIIA and IIIB therapy options were equally represented in the majority of KB. Personalized treatment options with ESCAT LOE I-II were provided for 35 patients (16%); MolecularMatch/CIViC allowed to collect ESCAT I-II treatment options for 34 of them (97%), OncoKB/CGI-for 33 of them (94%). Employing VICC and CGA 6 (17%) and 20 (57%) of patients were left without ESCAT I or II treatment options. For 88 patients with ESCAT level III-B therapy recommendations: only 2 (2%), 3 (3%), 4 (5%) and 6 (7%) of patients were left without options with CIViC, MolecularMatch, CGI and OncoKB, and with VICC-12 (14%). Highest overlap ratio was observed for IIIA (0.81) biomarkers, with the comparable results for LOE I-II. Meanwhile, overlap ratio for ESCAT LOE IV was 0.22. Public KBs provide substantial information on ESCAT-I/R1 biomarkers, but the information on ESCAT II-IV and resistance biomarkers is underrepresented. Manual curation should be considered the gold standard for the CTMP interpretation.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.