F1 (SNVs, tumour WGS_NS_T_9 with normal WGS_NS_N_9) of Lancet 1.0.7 (Sahraeian et al. 2022) on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres
83.6% F1 (SNVs, tumour WGS_NS_T_9 with normal WGS_NS_N_9)
Methods
- Tested configuration
- Lancet 1.0.7 (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
- Procedure
- SEQC2 HCC1395 sequencing centre and platform, SNV F1 (Sahraeian et al. 2022 Table S2)
- Evaluation
- Lancet on SEQC2 HCC1395/HCC1395BL WGS replicate pairs from multiple sequencing centres, SNVs (Sahraeian et al. 2022)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedAchieving 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_NS_T_9 vs WGS_NS_N_9', column 'Lancet'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Held-out 50% of the high-confidence genome
- Adaptation
- Not reported
- Scoring implementation
- F1 (%) of PASS calls against the SEQC2 truth set, exact match
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 83.6 Individual claims | Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample Additional file 2 Table S2, SNVs section, row 'WGS_NS_T_9 vs WGS_NS_N_9', column 'Lancet' 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 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-10 independent paper Audit detailsParsed from the pinned PDF word boxes (pdftotext -bbox, pdftotext version 26.08.0) by extract/extract_neusomatic.py; columns fixed by position (see retrieval-log.md); column means match the printed Average row. Pending independent review. Independent review 2026-10-10: value, row and column match the source. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 83.6 Individual claims | 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_NS_T_9 vs WGS_NS_N_9', column 'Lancet' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2021_2592_MOESM2_ESM.pdf | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-10 independent paper Audit detailsParsed from the pinned PDF word boxes (pdftotext -bbox, pdftotext version 26.08.0) by extract/extract_neusomatic.py; columns fixed by position (see retrieval-log.md); column means match the printed Average row. Pending independent review. Independent review 2026-10-10: value, row and column match the source. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-10-457d7eaef7d6 · Record review: source checked
2 source records and release history
- Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample · Original source · Genome Biology 23:12, published 2022-01-07; PMC8740374 full-text XML
- Sahraeian et al. 2022, Additional file 2: Supplementary Tables S1-S10 (13059_2021_2592_MOESM2_ESM.pdf) · Original source · 13059_2021_2592_MOESM2_ESM.pdf
Technical metadata and extraction receipts
Stable ID: somatic-neusomatic-20261010-result-sahraeian2022-lancet-wgs-snv-wgs-ns-t-9-wgs-ns-n-9
- metric
- f1-score
- metric direction
- higher
- unit
- percent
- metric qualifier
- SNVs, tumour WGS_NS_T_9 with normal WGS_NS_N_9
- printed value
- 83.6
- numeric value
- 83.6
- source locator
- Additional file 2 Table S2, SNVs section, row 'WGS_NS_T_9 vs WGS_NS_N_9', column 'Lancet'
- missing metadata
- uncertainty: reason: unreported
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the PDF and matched its SHA-256. Read the word boxes (pdftotext -bbox) with a parser written for this review: columns fixed from the x-centres of the numbers, each rotated header assigned to the nearest column, and the NeuSomatic-S and NeuSomatic model groups split at the second DREAM3 header; the extractor's scripts were not run. Column identity was then checked independently against the article prose (Table S2 NeuSomatic SEQC-WGS-GT50-SpikeWGS10 averages 94.6 and 87.9, the 3.7-point indel lead over Octopus-RF, the Table S3 normal-contamination drops for MuTect2, MuSE, Lancet and Strelka2, and the Table S4 indel order and 0.6-point SNV lead) and against the SNV-only columns. Every printed Average equals the mean of its rows within 0.05.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-10; artifact sha256: 10a109d80f6f49446ea84bd9f7f6b31c20d634516c8666376ac8a8f51f3236d0; retrieval url: https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-021-02592-9/MediaObjects/13059_2021_2592_MOESM2_ESM.pdf; note: Parsed from the pinned PDF word boxes (pdftotext -bbox, pdftotext version 26.08.0) by extract/extract_neusomatic.py; columns fixed by position (see retrieval-log.md); column means match the printed Average row. Pending independent review. Independent review 2026-10-10: value, row and column match the source.