DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35924981", "kind": "science-record", "revision": 3, "content_hash": "sha256:0f453b2f448e7a95017100225287e526415d7d02a21b7a50b150a77f87659274", "created_at": "2026-11-01T18:15:01Z", "updated_at": "2026-11-01T21:28:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference.", "doi": "10.1093/bioinformatics/btac542", "pmid": "35924981", "authors": ["Vonn Walter", "Hyo Young Choi", "Xiaobei Zhao", "Yan Gao", "Jeremiah Holt", "D Neil Hayes"], "journal": "Bioinformatics (Oxford, England)", "year": 2022, "abstract": "MOTIVATION: Somatic DNA copy number alterations (CNAs) arise in tumor tissue because of underlying genomic instability. Recurrent CNAs that occur in the same genomic region across multiple independent samples are of interest to researchers because they may contain genes that contribute to the cancer phenotype. However, differences in copy number states between cancers are also commonly of interest, for example when comparing tumors with distinct morphologies in the same anatomic location. Current methodologies are limited by their inability to perform direct comparisons of CNAs between tumor cohorts, and thus they cannot formally assess the statistical significance of observed copy number differences or identify regions of the genome where these differences occur.\nRESULTS: We introduce the DiNAMIC.Duo R package that can be used to identify recurrent CNAs in a single cohort or recurrent copy number differences between two cohorts, including when neither cohort is copy neutral. The package utilizes Python scripts for computational efficiency and provides functionality for producing figures and summary output files.\nAVAILABILITY AND IMPLEMENTATION: The DiNAMIC.Duo R package is available from CRAN at https://cran.r-project.org/web/packages/DiNAMIC.Duo/index.html. This article uses publicly available data from the Broad Institute TCGA Genome Data Analysis Center, https://doi.org/10.7908/C11G0KM9.\nSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.", "claims": [{"id": "claim-method", "statement": "Additionally, because maxi(X¯i-Y¯i) is invariant under constant cyclic shifts, our theoretical study of cyclic shift testing (Walter et al., 2015) implies that DiNAMIC.Duo’s P-values are asymptotically consistent.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35924981", "locator": "sections[2] \"2 DiNAMIC.Duo workflow and outputs\" paragraph 3", "quote": "Additionally, because maxi(X¯i-Y¯i) is invariant under constant cyclic shifts, our theoretical study of cyclic shift testing (Walter et al., 2015) implies that DiNAMIC.Duo’s P-values are asymptotically consistent."}], "state": "complete"}, {"id": "claim-data-access", "statement": "This article uses publicly available data from the Broad Institute TCGA Genome Data Analysis Center, https://doi.org/10.7908/C11G0KM9.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35924981", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "This article uses publicly available data from the Broad Institute TCGA Genome Data Analysis Center, https://doi.org/10.7908/C11G0KM9."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "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:35924981"], "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_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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