Evidence blocks for effective presentation of genomic findings at molecular tumor boards: Single institution experience

Genomic profiling, or molecular profiling of the tumor, is becoming a key component of therapeutic decision making in clinical oncology, and is typically carried out via next generation sequencing. However, the interpretation of the results and evaluation of rationale for targeting the uncovered alterations is challenging and requires a deep understanding of cancer biology, genetics, genomics and oncology. Multidisciplinary molecular tumor boards represent a promising strategy in the facilitation of molecularly-informed therapeutic decisions, and usually consist of specialists with various fields of expertise. To effectively communicate the biological and clinical significance of genomic findings, as well as to make molecular tumor board discussions more productive, we developed and implemented evidence blocks into case discussions in our center. We found that this approach facilitated clinicians' understanding of the results of genomic profiling, and resulted in shorter yet more efficient case discussions within the molecular tumor board. Here, we discuss our experience with evidence blocks and how their implementation influenced the molecular tumor board practice.

Utility of public knowledge bases for the interpretation of comprehensive tumor molecular profiling results

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.

Microsatellite Instability: A Review of Molecular Epidemiology and Implications for Immune Checkpoint Inhibitor Therapy

Microsatellite instability (MSI) is one of the most important molecular characteristics of a tumor, which occurs among various tumor types. In this review article, we examine the molecular characteristics of MSI tumors, both sporadic and Lynch-associated. We also overview the risks of developing hereditary forms of cancer and potential mechanisms of tumor development in patients with Lynch syndrome. Additionally, we summarize the results of major clinical studies on the efficacy of immune checkpoint inhibitors for MSI tumors and discuss the predictive role of MSI in the context of chemotherapy and checkpoint inhibitors. Finally, we briefly discuss some of the underlying mechanisms causing therapy resistance in patients treated with immune checkpoint inhibitors.

Utility of public Knowledge Bases (KB) for comprehensive tumor molecular profiling (CTMP) result interpretation

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Background: With the spread of CTMP in cancer patient management and expansion of molecular-targeted treatment opportunities, resources for quick and efficient molecular profile interpretation are in high demand. Number of public KBs have been introduced. We analysed their utility to compile per patient treatment recommendations. Methods: Analysis was performed across patients, who underwent CTMP. Based on the reported molecular alterations, interpretation and critical evidence evaluation was performed not taking into account the recommendations provided in the original CTMP reports. Therapy recommendations were ranked according to ESCAT. Resistance biomarkers were ranked according to OncoKB V2 level of evidence system. OncoKB, CIViC, CGI, CGA, VICC and MolecularMatch were assessed. KBs were assessed through API or local copy of KB. Results: A total of 222 CTMP reports from 222 patients (35% - NSCLC; 24% - CRC; 8% - pancreas; 7% - breast; 4% - gastric; 22% - other) were analysed. CTMP was performed in Foundation Medicine (82%) or Atlas Oncology Diagnostics (18%). Across 222 patients 932 molecular alterations were identified. A total of 1394 therapy recommendations were compiled associated with 368 molecular alteration across 171 (77%) patients (112 recommendations ESCAT level I; 908 - ESCAT III-IV; 70 - OncoKB R1). Across 181 ESCAT-I/R1 therapy recommendations 172 (95%) were present in at least 1 KB (92% for ESCAT-I recommendations, 100% - R1) with the VICC providing the highest rate of retrieval (80%), followed by OncoKB (78%), MolecularMatch (70%), CIViC - (69%) and CGI (69%). Only 92 (53%) of ESCAT-I/R1 therapy recommendations were present in all KBs. Across 27 patients with ESCAT-I recommendations, at least 1 therapy recommendation was retrieved in any KB for all patients. ESCAT II-IV therapy recommendations were provided for 161 patients and grouped by drug class, resulting in 457 [biomarker]-[drug class] associations. Of them 346 (75%) were present in at least 1 KB with the VICC providing the highest rate of retrieval (69%), followed by CGI (61%), CGA (56%), OncoKB (48%), CIViC (48%) and MolecularMatch (45%). Of 161 patients, for 24 (15%) no recommendations were retrieved in any KB for any biomarker identified. For random 15 (a total of 68 molecular alterations) patients KBs were assessed manually in order to estimate the average time in use. CGI was the most easily accessible (3.2 min per patient in average), following by CGA (5.6 min), OncoKB (7.2 min), CIViC (26.2 min), and VICC (35.9 min). Conclusions: Public KBs provide substantial information on ESCAT-I/R1 biomarkers and decent information on ESCAT II-IV biomarkers, reasoning manual curation. VICC provided the most complete information, though was thorough for manual use. The use of multiple KBs may significantly improve retrieval results, though is time-consuming and results in excess of misleading/outdated recommendations.