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Evidence claim

Relevance of Three-category CNV classification, per-class agreement on duplications (Zhang et al. Table 4, DUP) to "Select a copy-number variant detection and characterisation workflow"

Use case
Select a copy-number variant detection and characterisation workflow
Assessed by
Three-category CNV classification, per-class agreement on duplications (Zhang et al. Table 4, DUP)
Relevance
Proxy evidence
Endpoint
Per-class agreement of AnnotSV, ClassifyCNV, dbCNV, MarCNV-ISV and X-CNV against expert ACMG classifications (2,125 duplications)

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

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

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statementOriginal source and locationReview and provenance
Citation locations
1 values
  • source id
    cnv-20261011-zhang2026-source-article
    locator
    Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'
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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.citation_locators

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.comparison_group

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.comparison_title

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

Constraints
2 values
  • 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.
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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.constraints

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

Endpoint
Per-class agreement of AnnotSV, ClassifyCNV, dbCNV, MarCNV-ISV and X-CNV against expert ACMG classifications (2,125 duplications)
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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.endpoint

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

Claimed field
links:assessed_by:cnv-20261011-zhang2026-protocol-three-category-duplications
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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.field

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

Headline metric
recall
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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.headline_metric

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

Limitations
5 values
  • 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.
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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.limitations

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

Pinned records
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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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.pins

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

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)

Original source ↗

cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'

Version: Global Medical Genetics 13:100096 (2026), published online 2026-03-06; PMC13018948 full-text XML
Retrieved: 2026-10-11T21:36:59Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.rationale

Source artifact SHA-256: a0810a8bff1ab3d2603a4832a56291cc182c8530aa8dffc6ac5318abd989ada0

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

Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: use-case-mapping-cnv-20261011-zhang2026-three-category-duplications

field
links:assessed_by:cnv-20261011-zhang2026-protocol-three-category-duplications
value
cnv-20261011-zhang2026-protocol-three-category-duplications
relevance
proxy
endpoint
Per-class agreement of AnnotSV, ClassifyCNV, dbCNV, MarCNV-ISV and X-CNV against expert ACMG classifications (2,125 duplications)
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
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 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'
source locator
cnv-20261011-zhang2026-source-article: Table 4 rows 'DUP' B, VUS, P; Results 'Analysis of three-category performance'
headline metric
recall
comparison group
zhang2026-cnv-classification
comparison title
Automated ACMG CNV classification tools against expert labels (Zhang et al. 2026)
stratum label
Three-category, duplications
stratum order
2
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-three-category-duplications-annotsv; cnv-20261011-zhang2026-eval-three-category-duplications-classifycnv; cnv-20261011-zhang2026-eval-three-category-duplications-dbcnv; cnv-20261011-zhang2026-eval-three-category-duplications-marcnv-isv; cnv-20261011-zhang2026-eval-three-category-duplications-x-cnv
pins
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