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Dataset

SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres

Tumour-normal data used in Additional file 2 Table S2.

Evaluation results

32 evaluations · 704 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		81.7% F1 (INDELs, average over the 21 replicate 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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'Average', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		80.5% F1 (INDELs, tumour WGS_EA_T_1 with normal WGS_EA_N_1)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_EA_T_1 vs WGS_EA_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		78.8% F1 (INDELs, tumour WGS_FD_T_1 with normal WGS_FD_N_1)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_FD_T_1 vs WGS_FD_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		78.5% F1 (INDELs, tumour WGS_FD_T_2 with normal WGS_FD_N_2)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_FD_T_2 vs WGS_FD_N_2', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		78.9% F1 (INDELs, tumour WGS_FD_T_3 with normal WGS_FD_N_3)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_FD_T_3 vs WGS_FD_N_3', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		86.3% F1 (INDELs, tumour WGS_IL_T_1 with normal WGS_IL_N_1)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_IL_T_1 vs WGS_IL_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		83.2% F1 (INDELs, tumour WGS_IL_T_2 with normal WGS_IL_N_2)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_IL_T_2 vs WGS_IL_N_2', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		83.9% F1 (INDELs, tumour WGS_IL_T_3 with normal WGS_IL_N_3)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_IL_T_3 vs WGS_IL_N_3', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		82.6% F1 (INDELs, tumour WGS_LL_T_1 with normal WGS_LL_N_1)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_LL_T_1 vs WGS_LL_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		83% F1 (INDELs, tumour WGS_NC_T_1 with normal WGS_NC_N_1)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NC_T_1 vs WGS_NC_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		81.1% F1 (INDELs, tumour WGS_NS_T_1 with normal WGS_NS_N_1)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NS_T_1 vs WGS_NS_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		80.9% F1 (INDELs, tumour WGS_NS_T_2 with normal WGS_NS_N_2)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NS_T_2 vs WGS_NS_N_2', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		80.2% F1 (INDELs, tumour WGS_NS_T_3 with normal WGS_NS_N_3)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NS_T_3 vs WGS_NS_N_3', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		81.6% F1 (INDELs, tumour WGS_NS_T_4 with normal WGS_NS_N_4)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NS_T_4 vs WGS_NS_N_4', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		79.4% F1 (INDELs, tumour WGS_NS_T_5 with normal WGS_NS_N_5)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NS_T_5 vs WGS_NS_N_5', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		81.4% F1 (INDELs, tumour WGS_NS_T_6 with normal WGS_NS_N_6)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NS_T_6 vs WGS_NS_N_6', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		80.3% F1 (INDELs, tumour WGS_NS_T_7 with normal WGS_NS_N_7)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NS_T_7 vs WGS_NS_N_7', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		79.9% F1 (INDELs, tumour WGS_NS_T_8 with normal WGS_NS_N_8)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NS_T_8 vs WGS_NS_N_8', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		81.1% F1 (INDELs, tumour WGS_NS_T_9 with normal WGS_NS_N_9)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NS_T_9 vs WGS_NS_N_9', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		84.6% F1 (INDELs, tumour WGS_NV_T_1 with normal WGS_NV_N_1)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NV_T_1 vs WGS_NV_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		83.8% F1 (INDELs, tumour WGS_NV_T_2 with normal WGS_NV_N_2)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NV_T_2 vs WGS_NV_N_2', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, indel F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		85.2% F1 (INDELs, tumour WGS_NV_T_3 with normal WGS_NV_N_3)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, INDELs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-indel

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 S2, INDELs section, row 'WGS_NV_T_3 vs WGS_NV_N_3', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, SNV F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		92.3% F1 (SNVs, average over the 21 replicate 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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, SNVs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-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 S2, SNVs section, row 'Average', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, SNV F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		93.8% F1 (SNVs, tumour WGS_EA_T_1 with normal WGS_EA_N_1)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, SNVs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-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 S2, SNVs section, row 'WGS_EA_T_1 vs WGS_EA_N_1', column 'DRAGEN'
Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022)Protocol: SEQC2 HCC1395 sequencing centre and platform, SNV F1 (Sahraeian et al. 2022 Table S2)
Dataset: SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres		91.3% F1 (SNVs, tumour WGS_FD_T_1 with normal WGS_FD_N_1)
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 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, SNVs (Sahraeian et al. 2022)

somatic-neusomatic-20261010-protocol-sahraeian2022-wgs-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 S2, SNVs section, row 'WGS_FD_T_1 vs WGS_FD_N_1', column 'DRAGEN'

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

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Readiness checks, gaps and artifacts

Release 2026-10-10-457d7eaef7d6 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

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Missing or unresolved evidence

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  • File checksums match the recorded files: not yet verified
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  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

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  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
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Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
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Verified: Not verified

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Dataset and evaluation context

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Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

14 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-457d7eaef7d6
Property and statementOriginal source and locationReview and provenance
Accession
NCBI SRA SRP162370
Context-only references		Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Genome Biology 23:12, published 2022-01-07; PMC8740374 full-text XML
Retrieved: 2026-10-10T06:04:11Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.accession

Source artifact SHA-256: 78dbe540c2558585bc7537e0e6563706fdaa329b2708e5dc82b77074379b4a6e

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Accession
NCBI SRA SRP162370
Context-only references		Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf)

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: 13059_2021_2592_MOESM2_ESM.pdf
Retrieved: 2026-10-10T06:04:16Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.accession

Source artifact SHA-256: 10a109d80f6f49446ea84bd9f7f6b31c20d634516c8666376ac8a8f51f3236d0

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Assay
Paired tumour-normal whole-genome sequencing, Trimmomatic, BWA-MEM 0.7.15, Picard MarkDuplicates
Context-only references		Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Genome Biology 23:12, published 2022-01-07; PMC8740374 full-text XML
Retrieved: 2026-10-10T06:04:11Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.assay

Source artifact SHA-256: 78dbe540c2558585bc7537e0e6563706fdaa329b2708e5dc82b77074379b4a6e

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Assay
Paired tumour-normal whole-genome sequencing, Trimmomatic, BWA-MEM 0.7.15, Picard MarkDuplicates
Context-only references		Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf)

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: 13059_2021_2592_MOESM2_ESM.pdf
Retrieved: 2026-10-10T06:04:16Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.assay

Source artifact SHA-256: 10a109d80f6f49446ea84bd9f7f6b31c20d634516c8666376ac8a8f51f3236d0

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Population
21 tumour-normal WGS replicate pairs (labels WGS_<site>_T/N_<n>, site codes EA, FD, IL, LL, NC, NS, NV) on HiSeq X Ten, HiSeq 4000 and NovaSeq. Results say six sequencing centres; seven site codes appear because IL and NV are probably both Illumina (HiSeq and NovaSeq; Methods describe NovaSeq replicates 'from Illumina'), which the source does not state outright.
Context-only references		Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Genome Biology 23:12, published 2022-01-07; PMC8740374 full-text XML
Retrieved: 2026-10-10T06:04:11Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.population

Source artifact SHA-256: 78dbe540c2558585bc7537e0e6563706fdaa329b2708e5dc82b77074379b4a6e

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Population
21 tumour-normal WGS replicate pairs (labels WGS_<site>_T/N_<n>, site codes EA, FD, IL, LL, NC, NS, NV) on HiSeq X Ten, HiSeq 4000 and NovaSeq. Results say six sequencing centres; seven site codes appear because IL and NV are probably both Illumina (HiSeq and NovaSeq; Methods describe NovaSeq replicates 'from Illumina'), which the source does not state outright.
Context-only references		Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf)

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: 13059_2021_2592_MOESM2_ESM.pdf
Retrieved: 2026-10-10T06:04:16Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.population

Source artifact SHA-256: 10a109d80f6f49446ea84bd9f7f6b31c20d634516c8666376ac8a8f51f3236d0

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Source location
Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'
Context-only references		Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Genome Biology 23:12, published 2022-01-07; PMC8740374 full-text XML
Retrieved: 2026-10-10T06:04:11Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.source_locator

Source artifact SHA-256: 78dbe540c2558585bc7537e0e6563706fdaa329b2708e5dc82b77074379b4a6e

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Source location
Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'
Context-only references		Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf)

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: 13059_2021_2592_MOESM2_ESM.pdf
Retrieved: 2026-10-10T06:04:16Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.source_locator

Source artifact SHA-256: 10a109d80f6f49446ea84bd9f7f6b31c20d634516c8666376ac8a8f51f3236d0

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Split
Evaluation region: the 50% of the SEQC2 high-confidence genome held out from SEQC-WGS-GT-50 training
Context-only references		Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: Genome Biology 23:12, published 2022-01-07; PMC8740374 full-text XML
Retrieved: 2026-10-10T06:04:11Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.split

Source artifact SHA-256: 78dbe540c2558585bc7537e0e6563706fdaa329b2708e5dc82b77074379b4a6e

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Split
Evaluation region: the 50% of the SEQC2 high-confidence genome held out from SEQC-WGS-GT-50 training
Context-only references		Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf)

Original source ↗

Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: 13059_2021_2592_MOESM2_ESM.pdf
Retrieved: 2026-10-10T06:04:16Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.split

Source artifact SHA-256: 10a109d80f6f49446ea84bd9f7f6b31c20d634516c8666376ac8a8f51f3236d0

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

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Sources and history

Release 2026-10-10-457d7eaef7d6 · Record review: source checked

2 source records and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: somatic-neusomatic-20261010-data-sahraeian2022-wgs

areas
dna-genomes
contexts
clinical_research
population
21 tumour-normal WGS replicate pairs (labels WGS_<site>_T/N_<n>, site codes EA, FD, IL, LL, NC, NS, NV) on HiSeq X Ten, HiSeq 4000 and NovaSeq. Results say six sequencing centres; seven site codes appear because IL and NV are probably both Illumina (HiSeq and NovaSeq; Methods describe NovaSeq replicates 'from Illumina'), which the source does not state outright.
split
Evaluation region: the 50% of the SEQC2 high-confidence genome held out from SEQC-WGS-GT-50 training
assay
Paired tumour-normal whole-genome sequencing, Trimmomatic, BWA-MEM 0.7.15, Picard MarkDuplicates
accession
NCBI SRA SRP162370
source locator
Additional file 2 Table S2 row labels; Results; Methods 'SEQC2 tumor-normal sequencing data and ground truth' and 'Evaluation process'
missing metadata
version: reason: unreported; note: Truth set is SEQC2 v1.0; data release not otherwise stated
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