Protocol

SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3)

SNV F1 per purity-coverage pair for nine callers and eight NeuSomatic models.

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

17 recorded evaluations, 816 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

17 evaluations · 816 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	62.6% F1 (SNVs, average over the 47 purity-coverage pairs as printed) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'Average', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	53.8% F1 (SNVs, tumour SPP_100x_10%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_100x_10%T vs SPP_100x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	95.6% F1 (SNVs, tumour SPP_100x_100%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_100x_100%T vs SPP_100x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	77.8% F1 (SNVs, tumour SPP_100x_20%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_100x_20%T vs SPP_100x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	24.5% F1 (SNVs, tumour SPP_100x_5%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_100x_5%T vs SPP_100x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	92.4% F1 (SNVs, tumour SPP_100x_50%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_100x_50%T vs SPP_100x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	94.3% F1 (SNVs, tumour SPP_100x_75%T with normal SPP_100x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_100x_75%T vs SPP_100x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	1% F1 (SNVs, tumour SPP_10x_10%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_10x_10%T vs SPP_10x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	46.1% F1 (SNVs, tumour SPP_10x_100%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_10x_100%T vs SPP_10x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	5% F1 (SNVs, tumour SPP_10x_20%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_10x_20%T vs SPP_10x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	0.2% F1 (SNVs, tumour SPP_10x_5%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_10x_5%T vs SPP_10x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	22.7% F1 (SNVs, tumour SPP_10x_50%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_10x_50%T vs SPP_10x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	35.9% F1 (SNVs, tumour SPP_10x_75%T with normal SPP_10x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_10x_75%T vs SPP_10x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	74.6% F1 (SNVs, tumour SPP_200x_10%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_200x_10%T vs SPP_200x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	97.2% F1 (SNVs, tumour SPP_200x_100%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_200x_100%T vs SPP_200x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	87.9% F1 (SNVs, tumour SPP_200x_20%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_200x_20%T vs SPP_200x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	46.4% F1 (SNVs, tumour SPP_200x_5%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_200x_5%T vs SPP_200x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	95% F1 (SNVs, tumour SPP_200x_50%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_200x_50%T vs SPP_200x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	96.5% F1 (SNVs, tumour SPP_200x_75%T with normal SPP_200x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_200x_75%T vs SPP_200x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	77.6% F1 (SNVs, tumour SPP_300x_10%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_300x_10%T vs SPP_300x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	97.3% F1 (SNVs, tumour SPP_300x_100%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_300x_100%T vs SPP_300x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	88.9% F1 (SNVs, tumour SPP_300x_20%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_300x_20%T vs SPP_300x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	52.6% F1 (SNVs, tumour SPP_300x_5%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_300x_5%T vs SPP_300x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	95.9% F1 (SNVs, tumour SPP_300x_50%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_300x_50%T vs SPP_300x_100%N', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, SNV F1 (Sahraeian et al. 2022 Table S3) Dataset: SEQC2 tumour-normal titration: HCC1395 gDNA mixed with HCC1395BL gDNA at 5-100% tumour purity, 10x-300x WGS	95.8% F1 (SNVs, tumour SPP_300x_75%T with normal SPP_300x_100%N) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source DRAGEN on SEQC2 tumour-normal titration, SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv Aggregation: Not reported Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample; Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Additional file 2 Table S3, SNVs section, row 'SPP_300x_75%T vs SPP_300x_100%N', column 'DRAGEN'

Source checking is not independent reproduction. Release 2026-10-10-457d7eaef7d6.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

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Sources and history

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2 source records and release history

Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample · Original source · Genome Biology 23:12, published 2022-01-07; PMC8740374 full-text XML
Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Original source · 13059_2021_2592_MOESM2_ESM.pdf

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Technical metadata and extraction receipts

Stable ID: somatic-neusomatic-20261010-protocol-sahraeian2022-titration-snv

areas: dna-genomes
contexts: clinical_research
protocol: Paired tumour-normal calling of each purity-coverage pair; PASS calls scored by exact match. All callers and models were scored on the 50% of the SEQC2 high-confidence genome held out from SEQC-WGS-GT-50 training (about 1.4 Gb; about 21K truth SNVs and 1.3K truth indels), against SEQC2 HighConf and MedConf calls (v1.0), LowConf calls blacklisted and ambiguous private calls excluded.
version: Additional file 2 Table S3
metric: f1-score
limitations: Developer paper: the authors developed NeuSomatic (two hold a patent application on it; Competing interests) and trained and selected every NeuSomatic model; NeuSomatic rows are author_reported.; One cell-line pair (HCC1395/HCC1395BL). The SEQC2 truth set (v1.0, 39,536 SNVs and 2,020 indels) was built by the SEQC2 somatic working group, whose reference papers have co-authors W. Xiao and L. T. Fang as first authors, with the SomaticSeq classifier, which co-authors L. T. Fang and M. Mohiyuddin helped develop (references 2, 3 and 20). It has a 5% VAF and 50x depth detection limit, LowConf calls are blacklisted, and ambiguous private calls are excluded from scoring (Methods 'Evaluation process').; Scored on the 50% of the high-confidence genome held out from SEQC-WGS-GT-50 training (about 21K truth SNVs and 1.3K truth indels). The NeuSomatic and NeuSomatic-S SEQC-WGS-Spike, SEQC-WGS-GT-50 and SEQC-WGS-GT50-SpikeWGS10 models were trained on this cell line and are excluded from this judgement, as is Octopus-RF, whose forest is not identified. The DREAM3 models, trained on DREAM Challenge Stage 3 data, are kept.; The NeuSomatic ensemble mode takes calls from MuTect2, SomaticSniper, Strelka2, MuSE and VarDict as input channels.; Only F1 is printed; no precision, recall or uncertainty in these tables.; Caller versions as in Methods (for example MuTect2 4.beta.6, Strelka2 2.8.4, Lancet 1.0.7, NeuSomatic 0.1.4).; Tumour purity is a gDNA mixture of the same cell lines, not a different tumour; the 95% normal rows mix 5% tumour into the normal.
source locator: Additional file 2 Table S3 (SNVs section); Methods 'Evaluation process'

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