Evidence claim

Relevance of Exon-level CNV detection in clinical exomes against CMA truth, after removing tool-specific problematic regions (Hwang et al. Table 4, post-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, after removing tool-specific problematic regions (Hwang et al. Table 4, post-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, after the problematic-region filter

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 statement	Original source and location	Review 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, after the problematic-region 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.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-post-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 5 values The filter is the authors' method and is defined on the same 180-sample cohort, including the 39 evaluated exomes. The reference truth set shrinks after filtering (Table 4 row 'Reference Truth set'), so post-filter sensitivity is on fewer exons. 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
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62dbd731fa496efc47270018e12eb618138dce3cc651f271ad5b0fc0045d2c92 record id cnv-20261011-hwang2026-source-article fields status attributes.artifact_sha256 sha256 33f5227b8d66ed68dc50ac7f888035552a9445a6ed4d118017989976041478d5 record id use-case-cnv-detection-characterisation fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 e86232bbdd2e9f2de3ba90f86e72b53bdd8368f9c0ddc74b7ee5870155f0a0d0 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

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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

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-cnv-20261011-hwang2026-post-filter

field: links:assessed_by:cnv-20261011-hwang2026-protocol-post-filter
value: cnv-20261011-hwang2026-protocol-post-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, after the problematic-region filter
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: The filter is the authors' method and is defined on the same 180-sample cohort, including the 39 evaluated exomes.; The reference truth set shrinks after filtering (Table 4 row 'Reference Truth set'), so post-filter sensitivity is on fewer exons.; 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: After problematic-region filter
stratum order: 2
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-post-filter-cn-mops; cnv-20261011-hwang2026-eval-post-filter-cnvkit; cnv-20261011-hwang2026-eval-post-filter-conifer; cnv-20261011-hwang2026-eval-post-filter-exomedepth
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