{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T15:13:47Z","timestamp":1778253227720,"version":"3.51.4"},"reference-count":43,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["FWO\u2010TBM T003022N"],"award-info":[{"award-number":["FWO\u2010TBM T003022N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["febs.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Oncology"],"published-print":{"date-parts":[[2026,5]]},"abstract":"<jats:p>Copy number variations (CNVs) play a crucial role in cancer diagnostics and prognostics, potentially impacting treatment decisions. Ultra\u2010low\u2010pass whole\u2010genome sequencing (ULP\u2010WGS) has emerged as a promising alternative to array\u2010based methods for CNV detection, especially in formalin\u2010fixed paraffin\u2010embedded (FFPE) samples. However, sequencing biases and sample heterogeneity necessitate the optimization of CNV detection tools for FFPE sample\u2010derived data. This study evaluates three open\u2010source CNV callers (CNVpytor, ichorCNA, and WisecondorX) using ULP\u2010WGS and compares their performance against a single nucleotide polymorphism (SNP) array. Our results demonstrate that under optimal experimental conditions, ichorCNA and WisecondorX achieved equal detection of true positive results, with reduced false positive results compared to the SNP array. The SNP array detection pattern differed somewhat from that of the CNV callers, while ichorCNA and WisecondorX had the most comparable detection pattern. We highlight the importance of (pre\u2010)analytical parameters such as neoplastic cell content, sequencing coverage, and bin size selection on CNV detection accuracy. Our findings support the adoption of ULP\u2010WGS\u2010based CNV detection as a robust alternative to SNP arrays, with WisecondorX emerging as the most suitable tool for clinical implementation.<\/jats:p>","DOI":"10.1002\/1878-0261.70192","type":"journal-article","created":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T07:38:58Z","timestamp":1766561938000},"page":"1270-1283","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Crucial parameters for precise copy number variation detection in formalin\u2010fixed paraffin\u2010embedded solid cancer samples"],"prefix":"10.1002","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9691-6635","authenticated-orcid":false,"given":"Hanne","family":"Goris","sequence":"first","affiliation":[{"name":"Department of Pathology Antwerp University Hospital  Belgium"},{"name":"Center for Oncological Research (CORE), Molecular Imaging, Pathology, Radiotherapy &amp; Oncology (MIPRO) University of Antwerp  Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vasiliki","family":"Siozopoulou","sequence":"additional","affiliation":[{"name":"Center for Oncological Research (CORE), Molecular Imaging, Pathology, Radiotherapy &amp; Oncology (MIPRO) University of Antwerp  Belgium"},{"name":"Department of Pathology Ziekenhuis aan de Stroom  Antwerp Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L\u00e9on C","family":"van Kempen","sequence":"additional","affiliation":[{"name":"Department of Pathology Antwerp University Hospital  Belgium"},{"name":"Center for Oncological Research (CORE), Molecular Imaging, Pathology, Radiotherapy &amp; Oncology (MIPRO) University of Antwerp  Belgium"},{"name":"Department of Pathology, Maastricht University Maastricht University Medical Center  The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Sieben","sequence":"additional","affiliation":[{"name":"Department of Pathology Antwerp University Hospital  Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ella","family":"Roelant","sequence":"additional","affiliation":[{"name":"Clinical Trial Center (CTC) CRC Antwerp, Antwerp University Hospital University of Antwerp  Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stig","family":"Hellemans","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Adrem Data Lab University of Antwerp  Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elyne","family":"Backx","sequence":"additional","affiliation":[{"name":"Department of Pathology Antwerp University Hospital  Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laure","family":"Sorber","sequence":"additional","affiliation":[{"name":"Department of Pathology Antwerp University Hospital  Belgium"},{"name":"Center for Oncological Research (CORE), Molecular Imaging, Pathology, Radiotherapy &amp; Oncology (MIPRO) University of Antwerp  Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Koen","family":"De Winne","sequence":"additional","affiliation":[{"name":"Department of Pathology Antwerp University Hospital  Belgium"},{"name":"Center for Oncological Research (CORE), Molecular Imaging, Pathology, Radiotherapy &amp; Oncology (MIPRO) University of Antwerp  Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Senada","family":"Koljenovi\u0107","sequence":"additional","affiliation":[{"name":"Department of Pathology Antwerp University Hospital  Belgium"},{"name":"Center for Oncological Research (CORE), Molecular Imaging, Pathology, Radiotherapy &amp; Oncology (MIPRO) University of Antwerp  Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9122-0639","authenticated-orcid":false,"given":"Karen","family":"Zwaenepoel","sequence":"additional","affiliation":[{"name":"Department of Pathology Antwerp University Hospital  Belgium"},{"name":"Center for Oncological Research (CORE), Molecular Imaging, Pathology, Radiotherapy &amp; 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