| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 72.5% F1 (INDELs, average over the 6 library pairs as printed) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'Average', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 83.3% F1 (INDELs, tumour LBP_Nextera_T_100ng with normal LBP_Nextera_N_100ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_Nextera_T_100ng vs LBP_Nextera_N_100ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 83.2% F1 (INDELs, tumour LBP_Nextera_T_10ng with normal LBP_Nextera_N_10ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_Nextera_T_10ng vs LBP_Nextera_N_10ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 79.3% F1 (INDELs, tumour LBP_Nextera_T_1ng with normal LBP_Nextera_N_1ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_Nextera_T_1ng vs LBP_Nextera_N_1ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 82.3% F1 (INDELs, tumour LBP_TruSeq_T_100ng with normal LBP_TruSeq_N_100ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_TruSeq_T_100ng vs LBP_TruSeq_N_100ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 75.1% F1 (INDELs, tumour LBP_TruSeq_T_10ng with normal LBP_TruSeq_N_10ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_TruSeq_T_10ng vs LBP_TruSeq_N_10ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 31.5% F1 (INDELs, tumour LBP_TruSeq_T_1ng with normal LBP_TruSeq_N_1ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_TruSeq_T_1ng vs LBP_TruSeq_N_1ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 80.5% F1 (SNVs, average over the 6 library pairs as printed) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'Average', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 92.6% F1 (SNVs, tumour LBP_Nextera_T_100ng with normal LBP_Nextera_N_100ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'LBP_Nextera_T_100ng vs LBP_Nextera_N_100ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 93.1% F1 (SNVs, tumour LBP_Nextera_T_10ng with normal LBP_Nextera_N_10ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'LBP_Nextera_T_10ng vs LBP_Nextera_N_10ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 89.9% F1 (SNVs, tumour LBP_Nextera_T_1ng with normal LBP_Nextera_N_1ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'LBP_Nextera_T_1ng vs LBP_Nextera_N_1ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 90.5% F1 (SNVs, tumour LBP_TruSeq_T_100ng with normal LBP_TruSeq_N_100ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'LBP_TruSeq_T_100ng vs LBP_TruSeq_N_100ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 86.4% F1 (SNVs, tumour LBP_TruSeq_T_10ng with normal LBP_TruSeq_N_10ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'LBP_TruSeq_T_10ng vs LBP_TruSeq_N_10ng', column 'DRAGEN' |
|---|
| Configuration: DRAGEN v3.7.5 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 30.5% F1 (SNVs, tumour LBP_TruSeq_T_1ng with normal LBP_TruSeq_N_1ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDRAGEN on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'LBP_TruSeq_T_1ng vs LBP_TruSeq_N_1ng', column 'DRAGEN' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 67.4% F1 (INDELs, average over the 6 library pairs as printed) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'Average', column 'Lancet' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 80.3% F1 (INDELs, tumour LBP_Nextera_T_100ng with normal LBP_Nextera_N_100ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_Nextera_T_100ng vs LBP_Nextera_N_100ng', column 'Lancet' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 80.2% F1 (INDELs, tumour LBP_Nextera_T_10ng with normal LBP_Nextera_N_10ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_Nextera_T_10ng vs LBP_Nextera_N_10ng', column 'Lancet' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 76.2% F1 (INDELs, tumour LBP_Nextera_T_1ng with normal LBP_Nextera_N_1ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_Nextera_T_1ng vs LBP_Nextera_N_1ng', column 'Lancet' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 78.1% F1 (INDELs, tumour LBP_TruSeq_T_100ng with normal LBP_TruSeq_N_100ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_TruSeq_T_100ng vs LBP_TruSeq_N_100ng', column 'Lancet' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 72.7% F1 (INDELs, tumour LBP_TruSeq_T_10ng with normal LBP_TruSeq_N_10ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_TruSeq_T_10ng vs LBP_TruSeq_N_10ng', column 'Lancet' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, indel F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 17% F1 (INDELs, tumour LBP_TruSeq_T_1ng with normal LBP_TruSeq_N_1ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, INDELs section, row 'LBP_TruSeq_T_1ng vs LBP_TruSeq_N_1ng', column 'Lancet' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 75.1% F1 (SNVs, average over the 6 library pairs as printed) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'Average', column 'Lancet' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 88.7% F1 (SNVs, tumour LBP_Nextera_T_100ng with normal LBP_Nextera_N_100ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'LBP_Nextera_T_100ng vs LBP_Nextera_N_100ng', column 'Lancet' |
|---|
| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 90.3% F1 (SNVs, tumour LBP_Nextera_T_10ng with normal LBP_Nextera_N_10ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'LBP_Nextera_T_10ng vs LBP_Nextera_N_10ng', column 'Lancet' |
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| Configuration: Lancet 1.0.7 (Sahraeian et al. 2022) | Protocol: SEQC2 HCC1395 library preparation and DNA input, SNV F1 (Sahraeian et al. 2022 Table S4)
Dataset: SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA) | 85.6% F1 (SNVs, tumour LBP_Nextera_T_1ng with normal LBP_Nextera_N_1ng) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceLancet on SEQC2 HCC1395/HCC1395BL library-preparation replicates (TruSeq-Nano and Nextera Flex, 1-100 ng DNA), SNVs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-library-prep-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 S4, SNVs section, row 'LBP_Nextera_T_1ng vs LBP_Nextera_N_1ng', column 'Lancet' |
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