{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T08:08:08Z","timestamp":1778659688004,"version":"3.51.4"},"reference-count":36,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T00:00:00Z","timestamp":1716336000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004097","name":"Fondation ARC pour la Recherche sur Le Cancer","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004097","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004622","name":"KWF Kankerbestrijding","doi-asserted-by":"publisher","award":["10382"],"award-info":[{"award-number":["10382"]}],"id":[{"id":"10.13039\/501100004622","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004622","name":"KWF Kankerbestrijding","doi-asserted-by":"publisher","award":["10781"],"award-info":[{"award-number":["10781"]}],"id":[{"id":"10.13039\/501100004622","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Experimental and Molecular Pathology"],"published-print":{"date-parts":[[2024,6]]},"DOI":"10.1016\/j.yexmp.2024.104906","type":"journal-article","created":{"date-parts":[[2024,5,30]],"date-time":"2024-05-30T18:50:12Z","timestamp":1717095012000},"page":"104906","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"special_numbering":"C","title":["Accurate detection of copy number aberrations in FFPE samples using the mFAST-SeqS approach"],"prefix":"10.1016","volume":"137","author":[{"given":"Aude","family":"Jary","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongsoo","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kirsten","family":"Rozemeijer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul P.","family":"Eijk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramon P.","family":"van der Zee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maaike C.G.","family":"Bleeker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saskia M.","family":"Wilting","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Renske D.M.","family":"Steenbergen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.yexmp.2024.104906_bb0005","doi-asserted-by":"crossref","first-page":"2798","DOI":"10.1158\/1078-0432.CCR-20-3954","article-title":"Detection of aneuploidy in cerebrospinal fluid from patients with breast cancer can improve diagnosis of leptomeningeal metastases","volume":"27","author":"Angus","year":"2021","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.yexmp.2024.104906_bb0010","first-page":"1599","article-title":"HPV-16 E6 upregulation of DNMT1 through repression of tumor suppressor p53","volume":"24","author":"Au Yeung","year":"2010","journal-title":"Oncol. Rep."},{"key":"10.1016\/j.yexmp.2024.104906_bb0015","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1373\/clinchem.2014.234286","article-title":"Rapid identification of plasma DNA samples with increased ctDNA levels by a modified FAST-SeqS approach","volume":"61","author":"Belic","year":"2015","journal-title":"Clin. Chem."},{"key":"10.1016\/j.yexmp.2024.104906_bb0020","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1007\/978-3-319-42044-8_28","article-title":"mFast-SeqS as a monitoring and pre-screening tool for tumor-specific aneuploidy in plasma DNA","volume":"924","author":"Belic","year":"2016","journal-title":"Adv. Exp. Med. Biol."},{"key":"10.1016\/j.yexmp.2024.104906_bb0025","doi-asserted-by":"crossref","first-page":"E579","DOI":"10.1002\/ijc.26496","article-title":"Chromosomal profiles of high-grade cervical intraepithelial neoplasia relate to duration of preceding high-risk human papillomavirus infection","volume":"131","author":"Bierkens","year":"2012","journal-title":"Int. J. Cancer"},{"key":"10.1016\/j.yexmp.2024.104906_bb0030","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1038\/sj.onc.1209950","article-title":"Viral oncoproteins target the DNA methyltransferases","volume":"26","author":"Burgers","year":"2007","journal-title":"Oncogene"},{"key":"10.1016\/j.yexmp.2024.104906_bb0035","doi-asserted-by":"crossref","first-page":"464","DOI":"10.18632\/oncotarget.23066","article-title":"Exome sequencing reveals aberrant signalling pathways as hallmark of treatment-naive anal squamous cell carcinoma","volume":"9","author":"Cacheux","year":"2018","journal-title":"Oncotarget"},{"key":"10.1016\/j.yexmp.2024.104906_bb0040","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s40246-019-0220-8","article-title":"Next-generation sequencing in liquid biopsy: cancer screening and early detection","volume":"13","author":"Chen","year":"2019","journal-title":"Hum. Genom."},{"key":"10.1016\/j.yexmp.2024.104906_bb0045","doi-asserted-by":"crossref","first-page":"1871","DOI":"10.1073\/pnas.1717846115","article-title":"Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs)","volume":"115","author":"Douville","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.yexmp.2024.104906_bb0050","doi-asserted-by":"crossref","first-page":"4858","DOI":"10.1073\/pnas.1910041117","article-title":"Assessing aneuploidy with repetitive element sequencing","volume":"117","author":"Douville","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.yexmp.2024.104906_bb0055","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1002\/ijc.11691","article-title":"Mechanisms of genomic instability in human cancer: insights from studies with human papillomavirus oncoproteins","volume":"109","author":"Duensing","year":"2004","journal-title":"Int. J. Cancer"},{"key":"10.1016\/j.yexmp.2024.104906_bb0060","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/2049-2618-2-6","article-title":"An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform","volume":"2","author":"Fadrosh","year":"2014","journal-title":"Microbiome"},{"key":"10.1016\/j.yexmp.2024.104906_bb0065","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1097\/01.qai.0000179460.61987.33","article-title":"High-resolution analysis of genomic alterations and human papillomavirus integration in anal intraepithelial neoplasia","volume":"40","author":"Gagne","year":"2005","journal-title":"J. Acquir. Immune Defic. Syndr."},{"key":"10.1016\/j.yexmp.2024.104906_bb0070","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.jmoldx.2014.09.008","article-title":"Assessing copy number alterations in targeted, amplicon-based next-generation sequencing data","volume":"17","author":"Grasso","year":"2015","journal-title":"J. Mol. Diagn."},{"key":"10.1016\/j.yexmp.2024.104906_bb0075","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1038\/bjc.1997.547","article-title":"A recurrent pattern of chromosomal aberrations and immunophenotypic appearance defines anal squamous cell carcinomas","volume":"76","author":"Heselmeyer","year":"1997","journal-title":"Br. J. Cancer"},{"key":"10.1016\/j.yexmp.2024.104906_bb0080","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/modpathol.3880321","article-title":"Loss in 3p and 4p and gain of 3q are concomitant aberrations in squamous cell carcinoma of the vulva","volume":"14","author":"Jee","year":"2001","journal-title":"Mod. Pathol."},{"key":"10.1016\/j.yexmp.2024.104906_bb0085","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0041162","article-title":"FAST-SeqS: a simple and efficient method for the detection of aneuploidy by massively parallel sequencing","volume":"7","author":"Kinde","year":"2012","journal-title":"PLoS One"},{"key":"10.1016\/j.yexmp.2024.104906_bb0090","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with burrows-wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.yexmp.2024.104906_bb0095","doi-asserted-by":"crossref","first-page":"2086","DOI":"10.1002\/1878-0261.13196","article-title":"Genome-wide aneuploidy detected by mFast-SeqS in circulating cell-free DNA is associated with poor response to pembrolizumab in patients with advanced urothelial cancer","volume":"16","author":"Mendelaar","year":"2022","journal-title":"Mol. Oncol."},{"key":"10.1016\/j.yexmp.2024.104906_bb0100","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/nrc2886","article-title":"Human papillomavirus oncoproteins: pathways to transformation","volume":"10","author":"Moody","year":"2010","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.yexmp.2024.104906_bb0105","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1139\/O08-003","article-title":"From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors","volume":"86","author":"Morozova","year":"2008","journal-title":"Biochem. Cell Biol."},{"key":"10.1016\/j.yexmp.2024.104906_bb0110","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/s41588-019-0562-0","article-title":"Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition","volume":"52","author":"Rodriguez-Martin","year":"2020","journal-title":"Nat. Genet."},{"key":"10.1016\/j.yexmp.2024.104906_bb0115","doi-asserted-by":"crossref","first-page":"2022","DOI":"10.1101\/gr.175141.114","article-title":"DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly","volume":"24","author":"Scheinin","year":"2014","journal-title":"Genome Res."},{"key":"10.1016\/j.yexmp.2024.104906_bb0120","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.1101\/gr.149400","article-title":"Reading between the LINEs: human genomic variation induced by LINE-1 Retrotransposition","volume":"10","author":"Sheen","year":"2000","journal-title":"Genome Res."},{"key":"10.1016\/j.yexmp.2024.104906_bb0125","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/nrc3728","article-title":"Clinical implications of (epi)genetic changes in HPV-induced cervical precancerous lesions","volume":"14","author":"Steenbergen","year":"2014","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.yexmp.2024.104906_bb0130","doi-asserted-by":"crossref","first-page":"11","DOI":"10.2217\/epi-2022-0453","article-title":"Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing","volume":"15","author":"Sun","year":"2023","journal-title":"Epigenomics"},{"key":"10.1016\/j.yexmp.2024.104906_bb0135","doi-asserted-by":"crossref","first-page":"4542","DOI":"10.1002\/cam4.1633","article-title":"Molecular heterogeneity in human papillomavirus-dependent and -independent vulvar carcinogenesis","volume":"7","author":"Swarts","year":"2018","journal-title":"Cancer Med."},{"key":"10.1016\/j.yexmp.2024.104906_bb0140","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.ejca.2013.08.022","article-title":"Chromosomal gains and losses in human papillomavirus-associated neoplasia of the lower genital tract - a systematic review and meta-analysis","volume":"50","author":"Thomas","year":"2014","journal-title":"Eur. J. Cancer"},{"key":"10.1016\/j.yexmp.2024.104906_bb0145","doi-asserted-by":"crossref","DOI":"10.1002\/ijc.33459","article-title":"DNA methylation markers for cancer risk prediction of vulvar intraepithelial neoplasia","author":"Thuijs","year":"2021","journal-title":"Int. J. Cancer"},{"key":"10.1016\/j.yexmp.2024.104906_bb0150","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1093\/carcin\/bgz094","article-title":"Risk stratification of cervical lesions using capture sequencing and machine learning method based on HPV and human integrated genomic profiles","volume":"40","author":"Tian","year":"2019","journal-title":"Carcinogenesis"},{"key":"10.1016\/j.yexmp.2024.104906_bb0155","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1093\/bioinformatics\/btm030","article-title":"CGHcall: calling aberrations for array CGH tumor profiles","volume":"23","author":"van de Wiel","year":"2007","journal-title":"Bioinformatics"},{"key":"10.1016\/j.yexmp.2024.104906_bb0160","doi-asserted-by":"crossref","first-page":"2154","DOI":"10.1093\/cid\/ciaa397","article-title":"Cancer risk stratification of anal intraepithelial neoplasia in human immunodeficiency virus-positive men by validated methylation markers associated with progression to cancer","volume":"72","author":"van der Zee","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.yexmp.2024.104906_bb0165","doi-asserted-by":"crossref","DOI":"10.1002\/1878-0261.12926","article-title":"DNA methylation markers have universal prognostic value for anal cancer risk in HIV-negative and HIV-positive individuals","author":"van der Zee","year":"2021","journal-title":"Mol. Oncol."},{"key":"10.1016\/j.yexmp.2024.104906_bb0170","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1080\/15592294.2018.1507197","article-title":"Host-cell DNA methylation patterns during high-risk HPV-induced carcinogenesis reveal a heterogeneous nature of cervical pre-cancer","volume":"13","author":"Verlaat","year":"2018","journal-title":"Epigenetics"},{"key":"10.1016\/j.yexmp.2024.104906_bb0175","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.pvr.2016.04.003","article-title":"Molecular events leading to HPV-induced high grade neoplasia","volume":"2","author":"Wilting","year":"2016","journal-title":"Papillomavirus Res."},{"key":"10.1016\/j.yexmp.2024.104906_bb0180","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1158\/0008-5472.CAN-08-2478","article-title":"Chromosomal signatures of a subset of high-grade premalignant cervical lesions closely resemble invasive carcinomas","volume":"69","author":"Wilting","year":"2009","journal-title":"Cancer Res."}],"container-title":["Experimental and Molecular Pathology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S001448002400025X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S001448002400025X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T07:12:18Z","timestamp":1778656338000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S001448002400025X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6]]},"references-count":36,"alternative-id":["S001448002400025X"],"URL":"https:\/\/doi.org\/10.1016\/j.yexmp.2024.104906","relation":{},"ISSN":["0014-4800"],"issn-type":[{"value":"0014-4800","type":"print"}],"subject":[],"published":{"date-parts":[[2024,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Accurate detection of copy number aberrations in FFPE samples using the mFAST-SeqS approach","name":"articletitle","label":"Article Title"},{"value":"Experimental and Molecular Pathology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.yexmp.2024.104906","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"104906"}}