Application of qualifying variants for genomic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41570118", "kind": "science-record", "revision": 3, "content_hash": "sha256:40ae8ba44f99df8f7987b7af7ad047ad02da8cb87abd2ba186928d3050437114", "created_at": "2026-11-01T20:31:32Z", "updated_at": "2026-11-01T22:15:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Application of qualifying variants for genomic analysis.", "doi": "10.1093/bioinformatics/btaf676", "pmid": "41570118", "authors": ["Dylan Lawless", "Ali Saadat", "Mariam Ait Oumelloul", "Simon Boutry", "Veronika Stadler", "Sabine Österle", "Jan Armida", "David Haerry", "D Sean Froese", "Luregn J Schlapbach", "Jacques Fellay"], "journal": "Bioinformatics (Oxford, England)", "year": 2026, "abstract": "MOTIVATION: Qualifying variants (QVs) are genomic alterations selected by defined criteria within analysis pipelines. Although crucial for both research and clinical diagnostics, QVs are often seen as simple filters rather than dynamic elements that influence the entire workflow. In practice these rules are embedded within pipelines, which hinders transparency, audit, and reuse across tools. A unified, portable specification for QV criteria is needed.\nRESULTS: Our aim is to embed the concept of a \"QV\" into the genomic analysis vernacular, moving beyond its treatment as a single filtering step. By decoupling QV criteria from pipeline variables and code, the framework enables clearer discussion, application, and reuse. It provides a flexible reference model for integrating QVs into analysis pipelines, improving reproducibility, interpretability, and interdisciplinary communication. Validation across diverse applications confirmed that QV based workflows match conventional methods while offering greater clarity and scalability.\nAVAILABILITY: The source code and data are accessible at the Zenodo repository https://doi.org/10.5281/zenodo.17414191. Manuscript files are available at https://github.com/DylanLawless/qvApp2025lawless. The QV framework is available under the MIT licence, and the dataset will be maintained for at least two years following publication.", "claims": [{"id": "claim-data-access", "statement": "The source code and data are accessible at the Zenodo repository https://doi.org/10.5281/zenodo.17414191. Manuscript files are available at https://github.com/DylanLawless/qvApp2025lawless. The QV framework is available under the MIT licence.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41570118", "locator": "sections[25] \"Data availability\" paragraph 2", "quote": "The source code and data are accessible at the Zenodo repository https://doi.org/10.5281/zenodo.17414191. Manuscript files are available at https://github.com/DylanLawless/qvApp2025lawless. The QV framework is available under the MIT licence."}], "state": "complete"}, {"id": "claim-target-result", "statement": "As shown in Fig. 1, available as supplementary data at Bioinformatics online, the outputs from both methods were identical, demonstrating a 100% match.", "kind": "quantitative", "target": {"value": 100.0, "unit": "per cent", "tolerance": null, "source": "As shown in Fig. 1, available as supplementary data at Bioinformatics online, the outputs from both methods were identical, demonstrating a 100% match."}, "evidence": [{"asset": "source:pmid:41570118", "locator": "sections[11] \"3.1 Validation rare disease cohort case study\" paragraph 2", "quote": "As shown in Fig. 1, available as supplementary data at Bioinformatics online, the outputs from both methods were identical, demonstrating a 100% match."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "As shown in Fig. 1, available as supplementary data at Bioinformatics online, the outputs from both methods were identical, demonstrating a 100% match.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41570118"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJNA200694"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PRJNA200694"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41570118", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/bioinformatics/btaf676", "sha256": "sha256:d1a6c2337ede8d0585201c79453d45abe1e29655e6c59042c6ffdfb8643b38c0", "bytes": 23304, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/bioinformatics/btaf676", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12926777", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PRJNA200694", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PRJNA200694", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA200694", "version": null, "note": "The source code and data are accessible at the Zenodo repository https://doi.org/10.5281/zenodo.17414191. 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