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.
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
| Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) 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 | 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 hwang2026-wes-cnv Context-only references | Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) 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 | 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 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) 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 | 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
| Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) 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 | 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 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) 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 | 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-hwang2026-protocol-pre-filter Context-only references | Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) 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 | 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 recall Context-only references | Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) 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 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations3 values
| Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) 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 | 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 records31 values
| Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) 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 | 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: 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) 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 | 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
- Improving CNV Detection Performance Except for Software-Specific Problematic Regions (Hwang et al., Genes 2026) · Original source · Genes 17(1):105, published 2026-01-19; PMC12841491 full-text XML
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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