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Chen et al. 2020, Additional file 10: Performance metrics of 17 algorithms, default categories, benchmark 2 (OncoKB)

13059_2020_1954_MOESM10_ESM.xlsx · Peer-reviewed

DOI: 10.1186/s13059-020-01954-z

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Model or configurationMetricValueDatasetEvaluation
CanDrA (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.49 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)CanDrA on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
CanDrA (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.46 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)CanDrA on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
CanDrA (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.49 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)CanDrA on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
CanDrA (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.80 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)CanDrA on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
CanDrA (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.17 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)CanDrA on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
DEOGEN2 (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.70 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)DEOGEN2 on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
DEOGEN2 (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.79 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)DEOGEN2 on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
DEOGEN2 (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.65 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)DEOGEN2 on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
DEOGEN2 (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.87 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)DEOGEN2 on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
DEOGEN2 (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.51 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)DEOGEN2 on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-disease (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.52 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-disease on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-disease (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.53 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-disease on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-disease (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.51 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-disease on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-disease (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.63 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-disease on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-disease (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.42 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-disease on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-MKL (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.60 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-MKL on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-MKL (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.93 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-MKL on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-MKL (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.56 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-MKL on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-MKL (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.98 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-MKL on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-MKL (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.21 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-MKL on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-XF (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.66 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-XF on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-XF (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.85 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-XF on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-XF (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.60 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-XF on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-XF (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.93 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-XF on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
FATHMM-XF (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.39 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)FATHMM-XF on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
LRT (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.66 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)LRT on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
LRT (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.86 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)LRT on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
LRT (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.60 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)LRT on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
LRT (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.93 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)LRT on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
LRT (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.38 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)LRT on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
M-CAP (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.55 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)M-CAP on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
M-CAP (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.79 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)M-CAP on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
M-CAP (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.53 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)M-CAP on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
M-CAP (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.97 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)M-CAP on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
M-CAP (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.11 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)M-CAP on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaLR (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.57 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaLR on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaLR (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.59 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaLR on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaLR (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.56 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaLR on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaLR (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.67 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaLR on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaLR (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.47 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaLR on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaSVM (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.60 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaSVM on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaSVM (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.62 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaSVM on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaSVM (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.59 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaSVM on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaSVM (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.68 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaSVM on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MetaSVM (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.52 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MetaSVM on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MutationAssessor (Chen et al. 2020)Accuracy (OncoKB benchmark (positive set not stated), default categorical calls)0.58 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MutationAssessor on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MutationAssessor (Chen et al. 2020)Negative predictive value (OncoKB benchmark (positive set not stated), default categorical calls)0.59 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MutationAssessor on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MutationAssessor (Chen et al. 2020)Precision (OncoKB benchmark (positive set not stated), default categorical calls)0.57 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MutationAssessor on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MutationAssessor (Chen et al. 2020)Recall (OncoKB benchmark (positive set not stated), default categorical calls)0.66 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MutationAssessor on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)
MutationAssessor (Chen et al. 2020)Specificity (OncoKB benchmark (positive set not stated), default categorical calls)0.50 fractionOncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral)MutationAssessor on OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020)

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  • Evidence summary: somatic small-variant oncogenicity: Summary Two predictor comparisons join the existing OncoVI evidence; their values cannot be pooled. In Chen et al. 2020 (peer reviewed), 33 predictors scored somatic missense mutations labelled by OncoKB curation or by the authors' own cell viability assays, with likely neutral or assay-neutral somatic negatives. The authors co-developed one scored tool, CanDrA, and developed none of the others. With each tool's own default calls, the highest accuracy was 0.70 on OncoKB labels (DEOGEN2, sensitivity 0.87, specificity 0.51), and several tools called most neutral mutations damaging, for example M-CAP with sensitivity 0.97 and specificity 0.11, and CanDrA with specificity 0.17 and the lowest accuracy, 0.49. On the assay labels the highest default accuracy was 0.65 (PrimateAI). When each tool's median score on the test draw was used as the threshold, which ranks tools but is not an operating point a reviewer could apply, the highest accuracy was 0.69 on OncoKB labels (PROVEAN and VEST4) and 0.70 on assay labels (CTAT-cancer and PrimateAI), and FATHMM-disease scored 0.50 on OncoKB labels. Chen et al. print each value as a mean with a range of two standard deviations over 100 draws, not a confidence interval, and do not say which OncoKB positive set fed these tables. In a single-author bioRxiv preprint that is not peer reviewed (Lee 2026), 49 scores were compared on Cancer Gene Census missense variants whose negatives are germline-benign labels (ClinVar benign or likely benign, and gnomAD common variants), which this use case does not accept as somatic controls. In that table 42 of the 49 scores had a lower AUROC on oncogene variants than on tumour-suppressor variants, for example AlphaMissense 0.885 against 0.900 and CADD 0.821 against 0.894, while popEVE went the other way (0.900 against 0.842). The highest all-gene AUROC was 0.876 (MutScore); these AUROC values are rounded here to three decimals from the table's full precision. None of these comparisons covers small indels, calibrated probabilities, criterion-level evidence strength, drug response or reviewer agreement. (somatic-oncogenicity-20261009-source-chen2020-additional-file-9 and -10: Benchmark 2; somatic-oncogenicity-20261009-source-chen2020-additional-file-21 and -22: Benchmark 5; somatic-oncogenicity-20261009-source-chen2020: Methods and reference 7; somatic-oncogenicity-20261009-source-lee2026-oncocal-tool-performance: tables/tool_performance.tsv; somatic-oncogenicity-20261009-source-lee2026: Methods and Results)
  • Relevance of OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020) to "Assess somatic small-variant oncogenicity": Assessed by OncoKB benchmark (positive set not stated), default categorical calls (Chen et al. 2020 Additional file 10) (somatic-oncogenicity-20261009-source-chen2020-additional-file-10: Additional file 10; somatic-oncogenicity-20261009-source-chen2020: Results 'Benchmark 2'; Methods)

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