rewirebio.iobenchmarks
Evidence claim

Relevance of Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter) to "Select a copy-number variant detection and characterisation workflow"

Use case
Select a copy-number variant detection and characterisation workflow
Assessed by
Exon-level CNV detection in clinical exomes against CMA truth, default calls (Hwang et al. Table 4, pre-filter)
Relevance
Proxy evidence
Endpoint
Exon-level TP, FP and FN counts with sensitivity and PPV of ExomeDepth, CNVkit, CoNIFER and cn.MOPS against CMA CNVs in clinical exomes

Proxy: germline CNV detection accuracy against an orthogonal array truth set, but from exome rather than whole-genome data and scored per exon; it covers duplications as well as deletions.

4 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-hwang2026-source-article
    locator
    Table 4; Methods 2.2 to 2.5; Results 3.3
Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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

Inspected artifact

Comparison group
hwang2026-wes-cnv
Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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

Inspected artifact

Comparison title
Exome CNV callers against CMA truth, before and after removing problematic regions (Hwang et al. 2026)
Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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 any other protocol's results; inputs, truth and matching rules differ.
Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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

Inspected artifact

Endpoint
Exon-level TP, FP and FN counts with sensitivity and PPV of ExomeDepth, CNVkit, CoNIFER and cn.MOPS against CMA CNVs in clinical exomes
Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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

Inspected artifact

Claimed field
links:assessed_by:cnv-20261011-hwang2026-protocol-pre-filter
Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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

Inspected artifact

Headline metric
recall
Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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

Inspected artifact

Limitations
3 values
  • Exome input, not the whole-genome input this use case names.
  • Exon-level scoring against CMA-derived truth: CMA misses small CNVs and only CNVs overlapping exome baits were kept, so precision counts any exon call outside that truth as false.
  • 39 individuals from one centre; no uncertainty intervals are printed.
Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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

Inspected artifact

Pinned records
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Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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

Inspected artifact

Rationale
Proxy: germline CNV detection accuracy against an orthogonal array truth set, but from exome rather than whole-genome data and scored per exon; it covers duplications as well as deletions.
Context-only references
Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026)

Original source ↗

cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3

Version: Genes 17(1):105, published 2026-01-19; PMC12841491 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d

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-hwang2026-pre-filter

field
links:assessed_by:cnv-20261011-hwang2026-protocol-pre-filter
value
cnv-20261011-hwang2026-protocol-pre-filter
relevance
proxy
endpoint
Exon-level TP, FP and FN counts with sensitivity and PPV of ExomeDepth, CNVkit, CoNIFER and cn.MOPS against CMA CNVs in clinical exomes
rationale
Proxy: germline CNV detection accuracy against an orthogonal array truth set, but from exome rather than whole-genome data and scored per exon; it covers duplications as well as deletions.
constraints
Inspect every linked evaluation's source locator before citing a result.; Do not combine this mapping's evaluations with any other protocol's results; inputs, truth and matching rules differ.
limitations
Exome input, not the whole-genome input this use case names.; Exon-level scoring against CMA-derived truth: CMA misses small CNVs and only CNVs overlapping exome baits were kept, so precision counts any exon call outside that truth as false.; 39 individuals from one centre; no uncertainty intervals are printed.
citation locators
source id: cnv-20261011-hwang2026-source-article; locator: Table 4; Methods 2.2 to 2.5; Results 3.3
source locator
cnv-20261011-hwang2026-source-article: Table 4; Methods 2.2 to 2.5; Results 3.3
headline metric
recall
comparison group
hwang2026-wes-cnv
comparison title
Exome CNV callers against CMA truth, before and after removing problematic regions (Hwang et al. 2026)
stratum label
Default calls
stratum order
1
reason
Recorded from the 2026-10-11 use-case literature pass (data/omics/use-case-coverage-cnv-20261011-hwang2026). 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: ff82a186d0adcf319b603a1100427ec0f6ed95becf040b512d0aef5e515bdc5d; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12841491/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-hwang2026-eval-pre-filter-cn-mops; cnv-20261011-hwang2026-eval-pre-filter-cnvkit; cnv-20261011-hwang2026-eval-pre-filter-conifer; cnv-20261011-hwang2026-eval-pre-filter-exomedepth
pins
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