Objectives: In 2017, AMP, ASCO and CAP jointly published the first formalized classification system for the interpretation and reporting of sequence variants in cancer. The challenges of incorporating new variant interpretation guidelines into existing, validated workflows have likely hampered adoption and implementation in labs with classification methods in place. Ambiguity in assigning clinical significance across guidelines is grounded in differential weighting of evidence used in variant assessment. Therefore, we undertook an internal process-improvement exercise to correlate the two classification schemes using historical laboratory data.
Design and methods: Existing clinical variant assignments from 40 consecutive oncology cases comprising 150 somatic variants were re-assessed according to the 2017 AMP/ASCO/CAP scheme. Approximately 50% of these were cancers of the gynecologic tract.
Results: Our laboratory-developed (GPS) classifications for 'actionable' variants and variants of uncertain clinical significance mapped consistently with the AMP/ASCO/CAP Tiers I-III. The majority of Level 1 variants were reclassified to Tier I (21/25; 84%) while all Level 2 and Level 4 variants were assigned to Tier II (9/9; 100%) and Tier III (17/17; 100%), respectively. The greatest variability was seen for GPS Level 3 variants, which was strongly influenced by TP53 interpretations. Ultimately, we found that most GPS Level 3 variants were classified as Tier III (77/99; 77.8%).
Conclusions: Our internally developed 5-level classifications mapped consistently with the proposed AMP/ASCO/CAP 4-Tiered system. As a result of this analysis, we can provide a framework for other labs considering a similar transition to the 2017 AMP/ASCO/CAP guidelines and a rationale for explaining specific discrepancies.
Keywords: Clinical sequencing; Somatic variant classification; Variant guidelines.
© 2020 The Authors.