Configuration

NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)

NeuSomatic-S DREAM3 as run in the cited comparison.

Overview

NeuSomatic: Neural-network somatic SNV and indel caller; in one linked comparison it was run in ensemble mode over other callers' output.

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

Evaluations and results

6 evaluations · 154 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: NeuSomatic-S DREAM3 model (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)	54.4% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	68.1% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	69.1% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	60.3% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	62.9% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	51.2% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	15% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	73.8% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	88.6% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	90.1% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	85.4% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	86.6% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	75.4% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (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)	16.6% 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 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 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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% F1 (INDELs, average over the 47 purity-coverage pairs as printed) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'Average', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	26.6% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_10%T vs SPP_100x_100%N', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	74.4% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_100%T vs SPP_100x_100%N', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	57.1% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_20%T vs SPP_100x_100%N', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	12.2% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_5%T vs SPP_100x_100%N', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	73.8% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_50%T vs SPP_100x_100%N', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	78.3% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_100x_75%T vs SPP_100x_100%N', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	8.7% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_10%T vs SPP_10x_100%N', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	26.3% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_100%T vs SPP_10x_100%N', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	15.9% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_20%T vs SPP_10x_100%N', column 'NeuSomatic-S DREAM3'
Configuration: NeuSomatic-S DREAM3 model (Sahraeian et al. 2022)	Protocol: SEQC2 HCC1395 tumour purity, coverage and normal contamination, indel 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	4.4% F1 (INDELs, 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	Author-reported evaluation · Source checked Methods, coverage and source NeuSomatic-S DREAM3 on SEQC2 tumour-normal titration, INDELs (Sahraeian et al. 2022) somatic-neusomatic-20261010-protocol-sahraeian2022-titration-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 S3, INDELs section, row 'SPP_10x_5%T vs SPP_10x_100%N', column 'NeuSomatic-S DREAM3'

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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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Stable ID: somatic-neusomatic-20261010-config-sahraeian2022-neusomatic-s-dream3

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: NeuSomatic-S DREAM3
foundation model eligible: false
version: 0.1.4
checkpoint: DREAM3 model (standalone mode), as named in Additional file 2 Table S1
training overlap: ICGC-TCGA DREAM Challenge Stage 3 in silico tumour-normal data (spiked SNVs and indels, five purity settings, 50% of the genome); trained by the NeuSomatic developers in earlier work. No SEQC2 data.
protocol: Standalone mode: alignment-scanning candidates only; preprocessing -scan_maf 0.01 -min_mapq 10 -snp_min_af 0.03 -snp_min_bq 15 -snp_min_ao 3 -ins_min_af 0.02 -del_min_af 0.02
source locator: Methods 'Somatic mutation detection algorithms'; Additional file 2 Table S1 and Tables S2-S4 column headers

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