Relevance of ACMG five-category CNV pathogenicity classification against expert labels (Zhang et al. Table 3) to "Select a copy-number variant detection and characterisation workflow"
- Use case
- Select a copy-number variant detection and characterisation workflow
- Assessed by
- ACMG five-category CNV pathogenicity classification against expert labels (Zhang et al. Table 3)
- Relevance
- Proxy evidence
- Endpoint
- Accuracy, sensitivity, specificity, PPV, FPR, F1 and MCC of AnnotSV, ClassifyCNV, dbCNV, MarCNV-ISV and X-CNV against expert ACMG classifications
Proxy: automated pathogenicity classification of already detected CNVs bears on the characterisation and analyst-assessment part of the question, but no detection from sequencing reads is evaluated and the reference is expert ACMG labelling.
5 reviewed evaluations
- AnnotSV on the expert-classified ACMG CNV benchmark (five category)
- ClassifyCNV on the expert-classified ACMG CNV benchmark (five category)
- dbCNV on the expert-classified ACMG CNV benchmark (five category)
- MarCNV-ISV on the expert-classified ACMG CNV benchmark (five category)
- X-CNV on the expert-classified ACMG CNV benchmark (five category)
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.
19 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations1 values
| Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison group zhang2026-cnv-classification Context-only references | Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison title Automated ACMG CNV classification tools against expert labels (Zhang et al. 2026) Context-only references | Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Accuracy, sensitivity, specificity, PPV, FPR, F1 and MCC of AnnotSV, ClassifyCNV, dbCNV, MarCNV-ISV and X-CNV against expert ACMG classifications Context-only references | Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field links:assessed_by:cnv-20261011-zhang2026-protocol-five-category Context-only references | Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Headline metric accuracy Context-only references | Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations6 values
| Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records43 values
| Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Rationale Proxy: automated pathogenicity classification of already detected CNVs bears on the characterisation and analyst-assessment part of the question, but no detection from sequencing reads is evaluated and the reference is expert ACMG labelling. Context-only references | Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics' Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- Can automated copy number variation pathogenicity prediction tools replace manual review under the ACMG framework? A clinical validation (Zhang, Zhang and Chen, Global Medical Genetics 2026) · Original source · Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Technical metadata and extraction receipts
Stable ID: use-case-mapping-cnv-20261011-zhang2026-five-category
- field
- links:assessed_by:cnv-20261011-zhang2026-protocol-five-category
- value
- cnv-20261011-zhang2026-protocol-five-category
- relevance
- proxy
- endpoint
- Accuracy, sensitivity, specificity, PPV, FPR, F1 and MCC of AnnotSV, ClassifyCNV, dbCNV, MarCNV-ISV and X-CNV against expert ACMG classifications
- rationale
- Proxy: automated pathogenicity classification of already detected CNVs bears on the characterisation and analyst-assessment part of the question, but no detection from sequencing reads is evaluated and the reference is expert ACMG labelling.
- constraints
- Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with detection results from other protocols; the endpoint is classification, not detection.
- limitations
- How the five-class metrics are averaged across classes is not stated.; Reference labels are expert ACMG classifications, a semi-quantitative standard with known inter-reviewer variability (Discussion paragraph 5).; The set is enriched for pregnancy-loss and prenatal cases and is imbalanced (benign is about half of the duplications), which the authors say affects the metrics (Discussion paragraphs 5 and 6).; Classification of already detected CNVs from their coordinates; no read data or detection step is evaluated.; Some training sets of the evaluated tools (ClinVar, ClinGen, DGV) may overlap the published cohorts used as reference; the paper does not test this.; Two of the three authors (X. Zhang and D. Chen) are authors of dbCNV (reference 24), developed in the same laboratory, so the dbCNV rows are author_reported. dbCNV's original test set was that laboratory's internal dataset, and this benchmark includes the laboratory's internal CNV-seq cases (December 2019 to November 2025); overlap is not tested. The paper declares no competing interests.
- citation locators
- source id: cnv-20261011-zhang2026-source-article; locator: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics'
- source locator
- cnv-20261011-zhang2026-source-article: Table 3; Methods 'Data analysis'; Results 'Comparative analysis of clinical metrics'
- headline metric
- accuracy
- comparison group
- zhang2026-cnv-classification
- comparison title
- Automated ACMG CNV classification tools against expert labels (Zhang et al. 2026)
- stratum label
- Five-category classification
- stratum order
- 1
- reason
- Recorded from the 2026-10-11 use-case literature pass (data/omics/use-case-coverage-cnv-20261011-zhang2026). Independently reviewed in docs/reviews/use-cases/splicing-cnv-use-cases-2026-10-12.md.
- review
- method: source-hash-verification; independent-cell-check; automated-source-review; scope-review; reviewer: claude; reviewer note: Independent Claude review agent reviewer-scnv; did not extract this batch; no human review claimed; date: 2026-10-12; artifact sha256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13018948/fullTextXML; method note: Drafted by the collector agent uc-splicing-cnv from the pinned source.; note: Checked by reviewer-scnv against the pinned source; verdict in docs/reviews/use-cases/splicing-cnv-use-cases-2026-10-12.md and in this batch's review.md.
- reviewed evaluations
- cnv-20261011-zhang2026-eval-five-category-annotsv; cnv-20261011-zhang2026-eval-five-category-classifycnv; cnv-20261011-zhang2026-eval-five-category-dbcnv; cnv-20261011-zhang2026-eval-five-category-marcnv-isv; cnv-20261011-zhang2026-eval-five-category-x-cnv
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