{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T21:49:58Z","timestamp":1785880198793,"version":"3.56.0"},"reference-count":47,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T00:00:00Z","timestamp":1780531200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009272","name":"Chordoma Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009272","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Neoplasia"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.neo.2026.101325","type":"journal-article","created":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T07:03:51Z","timestamp":1781247831000},"page":"101325","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"special_numbering":"C","title":["The copy-number events in skull base chordoma stratify tumours into four biologically coherent groups"],"prefix":"10.1016","volume":"79","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9396-7610","authenticated-orcid":false,"given":"Szymon","family":"Baluszek","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paulina","family":"Kober","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Renata","family":"Woroniecka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Ma\u0142awska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Micha\u0142","family":"W\u0105grodzki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacek","family":"Kunicki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomasz","family":"Mandat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beata","family":"Grygalewicz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mateusz","family":"Bujko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.neo.2026.101325_bib0001","article-title":"decoupleR: ensemble of computational methods to infer biological activities from omics data","volume":"2","author":"Badia-i-Mompel","year":"2022","journal-title":"Bioinform. Adv."},{"key":"10.1016\/j.neo.2026.101325_bib0002","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-021-21026-5","article-title":"Whole genome sequencing of skull-base chordoma reveals genomic alterations associated with recurrence and chordoma-specific survival","volume":"12","author":"Bai","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neo.2026.101325_bib0003","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1158\/1078-0432.CCR-22-1865","article-title":"Gene expression profiling identifies two chordoma subtypes associated with distinct molecular mechanisms and clinical outcomes","volume":"29","author":"Bai","year":"2023","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.neo.2026.101325_bib0004","doi-asserted-by":"crossref","first-page":"3043","DOI":"10.1007\/s00586-018-5764-0","article-title":"Chordoma: a systematic review of the epidemiology and clinical prognostic factors predicting progression-free and overall survival","volume":"27","author":"Bakker","year":"2018","journal-title":"Eur. Spine J."},{"key":"10.1016\/j.neo.2026.101325_bib0005","doi-asserted-by":"crossref","DOI":"10.1186\/s40478-023-01610-0","article-title":"DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment","volume":"11","author":"Baluszek","year":"2023","journal-title":"Acta Neuropathol. Commun."},{"key":"10.1016\/j.neo.2026.101325_bib0006","doi-asserted-by":"crossref","unstructured":"Baluszek S.P., Kober P., W\u0105grodzki M., Kunicki J., Wojta\u015b B., Szadkowska P., Kami\u0144ska B., Passeri T., Mandat T., Bujko M. (2025) TP53 Mutations as drivers of chordoma progression and hallmarks of aggressive chordoma. doi: 10.21203\/rs.3.rs-7374485\/v1.","DOI":"10.21203\/rs.3.rs-7374485\/v1"},{"key":"10.1016\/j.neo.2026.101325_bib0007","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1007\/s00428-017-2224-x","article-title":"Transcriptome comparison identifies potential biomarkers of spine and skull base chordomas","volume":"472","author":"Bell","year":"2018","journal-title":"Virchows Arch."},{"key":"10.1016\/j.neo.2026.101325_bib0008","series-title":"Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining","first-page":"785","article-title":"XGBoost: a scalable tree boosting system","author":"Chen","year":"2016"},{"key":"10.1016\/j.neo.2026.101325_bib0009","doi-asserted-by":"crossref","first-page":"4540","DOI":"10.1158\/0008-5472.CAN-20-1387","article-title":"Inhibition of histone H3K27 demethylases inactivates brachyury (TBXT) and promotes chordoma cell death","volume":"80","author":"Cottone","year":"2020","journal-title":"Cancer Res."},{"key":"10.1016\/j.neo.2026.101325_bib0010","doi-asserted-by":"crossref","unstructured":"DeBruine Z.J., Pospisilik J.A., Triche T.J. (2021) Fast and interpretable non-negative matrix factorization for atlas-scale single cell data. doi: 10.1101\/2021.09.01.458620.","DOI":"10.1101\/2021.09.01.458620"},{"key":"10.1016\/j.neo.2026.101325_bib0011","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1111\/j.1654-1103.2003.tb02228.x","article-title":"VEGAN, a package of R functions for community ecology","volume":"14","author":"Dixon","year":"2003","journal-title":"J. Veg. Sci."},{"key":"10.1016\/j.neo.2026.101325_bib0012","unstructured":"Dolgalev I. (2025) msigdbr: mSigDB gene sets for multiple organisms in a tidy data format."},{"key":"10.1016\/j.neo.2026.101325_bib0013","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.5858\/2009-0380-OA.1","article-title":"The prognostic value of ki-67, p53, epidermal growth facto r receptor, 1p36, 9p21, 10q23, and 17p13 in Skull base Chordomas","volume":"134","author":"Horbinski","year":"2010","journal-title":"Archi. Pathol. Lab. Med."},{"key":"10.1016\/j.neo.2026.101325_bib0014","doi-asserted-by":"crossref","DOI":"10.1002\/ctm2.1429","article-title":"Unravelling the role of immune cells and FN1 in the recurrence and therapeutic process of skull base chordoma","volume":"13","author":"Huo","year":"2023","journal-title":"Clin. Transl. Med."},{"key":"10.1016\/j.neo.2026.101325_bib0015","doi-asserted-by":"crossref","DOI":"10.1186\/s40478-024-01833-9","article-title":"Genomic profiles and clinical presentation of chordoma","volume":"12","author":"Koka","year":"2024","journal-title":"Acta Neuropathol. Commun."},{"key":"10.1016\/j.neo.2026.101325_bib0016","doi-asserted-by":"crossref","unstructured":"Korotkevich G., Sukhov V., Budin N., Shpak B., Artyomov M.N., Sergushichev A. (2016) Fast gene set enrichment analysis. doi: 10.1101\/060012.","DOI":"10.1101\/060012"},{"key":"10.1016\/j.neo.2026.101325_bib0017","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1038\/labinvest.3700218","article-title":"Loss of heterozygosity on chromosome 22q in gastrointestinal stromal tumors (GISTs): a study on 50 cases","volume":"85","author":"Lasota","year":"2005","journal-title":"Lab. Investig."},{"key":"10.1016\/j.neo.2026.101325_bib0018","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0018846","article-title":"Recurrent chromosomal copy number alterations in sporadic chordomas","volume":"6","author":"Le","year":"2011","journal-title":"PLoS. One"},{"key":"10.1016\/j.neo.2026.101325_bib0019","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neo.2026.101325_bib0020","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.neo.2026.101325_bib0021","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1093\/bioinformatics\/btz605","article-title":"gwasrapidd: an R package to query, download and wrangle GWAS catalog data","volume":"36","author":"Magno","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neo.2026.101325_bib0022","first-page":"1","article-title":"Chordoma: incidence and survival patterns in the United States, 1973\u20131995","volume":"12","author":"McMaster","year":"2001","journal-title":"Cancer Causes Control"},{"key":"10.1016\/j.neo.2026.101325_bib0023","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-30453-x","article-title":"Clinical sequencing of soft tissue and bone sarcomas delineates diverse genomic landscapes and potential therapeutic targets","volume":"13","author":"Nacev","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neo.2026.101325_bib0024","first-page":"1132","article-title":"A complex with chromatin modifiers that occupies E2F- and myc-responsive genes in G 0 cells","volume":"296","author":"Ogawa","year":"2002","journal-title":"Science (1979)"},{"key":"10.1016\/j.neo.2026.101325_bib0025","doi-asserted-by":"crossref","first-page":"2586","DOI":"10.1093\/bioinformatics\/btn465","article-title":"Gene set enrichment analysis using linear models and diagnostics","volume":"24","author":"Oron","year":"2008","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neo.2026.101325_bib0026","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.3171\/2023.1.JNS222180","article-title":"The mutational landscape of skull base and spinal chordomas and the identification of potential prognostic and theranostic biomarkers","volume":"139","author":"Passeri","year":"2023","journal-title":"J. Neurosurg."},{"key":"10.1016\/j.neo.2026.101325_bib0027","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1002\/ijc.11421","article-title":"Mapping of candidate region for chordoma development to 1p36.13 by LOH analysis","volume":"107","author":"Riva","year":"2003","journal-title":"Int. J. Cancer"},{"key":"10.1016\/j.neo.2026.101325_bib0028","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1007\/s13353-025-00951-x","article-title":"Pivotal role of biallelic frequency analysis in identifying copy number alterations using genome-wide methods in tumors with a high level of aneuploidy","volume":"67","author":"Rymuza","year":"2026","journal-title":"J. Appl. Genet."},{"key":"10.1016\/j.neo.2026.101325_bib0029","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-017-02391-6","article-title":"Perturbation-response genes reveal signaling footprints in cancer gene expression","volume":"9","author":"Schubert","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neo.2026.101325_bib0030","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neo.2026.101325_bib0031","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-017-01026-0","article-title":"The driver landscape of sporadic chordoma","volume":"8","author":"Tarpey","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neo.2026.101325_bib0032","doi-asserted-by":"crossref","first-page":"D941","DOI":"10.1093\/nar\/gky1015","article-title":"COSMIC: the catalogue of somatic mutations In cancer","volume":"47","author":"Tate","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neo.2026.101325_bib0033","doi-asserted-by":"crossref","DOI":"10.1016\/j.esmoop.2025.105498","article-title":"CDK4\/6 inhibition in advanced chordoma: final results of the NCT PMO-1601 trial","volume":"10","author":"Teleanu","year":"2025","journal-title":"ESMo Open."},{"key":"10.1016\/j.neo.2026.101325_bib0034","unstructured":"Volker Hovestadt M.Z. (2017) conumee."},{"key":"10.1016\/j.neo.2026.101325_bib0035","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1002\/path.1969","article-title":"Brachyury, a crucial regulator of notochordal development, is a novel biomarker for chordomas","volume":"209","author":"Vujovic","year":"2006","journal-title":"J. Pathol."},{"key":"10.1016\/j.neo.2026.101325_bib0036","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1016\/j.ajpath.2022.12.012","article-title":"SMARCB1 Loss in poorly differentiated chordomas drives tumor progression","volume":"193","author":"Walhart","year":"2023","journal-title":"Am. J. Pathol."},{"key":"10.1016\/j.neo.2026.101325_bib0037","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1007\/s11060-010-0250-5","article-title":"Gain of chromosome 7 by chromogenic in situ hybridization (CISH) in chordomas is correlated to c-MET expression","volume":"101","author":"Walter","year":"2011","journal-title":"J. Neurooncol."},{"key":"10.1016\/j.neo.2026.101325_bib0038","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic. Acids. Res."},{"key":"10.1016\/j.neo.2026.101325_bib0039","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1002\/gcc.22362","article-title":"Genomic aberrations frequently alter chromatin regulatory genes in chordoma","volume":"55","author":"Wang","year":"2016","journal-title":"Genes Chromosomes Cancer"},{"key":"10.1016\/j.neo.2026.101325_bib0040","doi-asserted-by":"crossref","first-page":"284","DOI":"10.3390\/cancers11030284","article-title":"Gliosarcoma is driven by alterations in PI3K\/akt, RAS\/MAPK pathways and characterized by collagen gene expression signature","volume":"11","author":"Wojtas","year":"2019","journal-title":"Cancers"},{"key":"10.1016\/j.neo.2026.101325_bib0041","doi-asserted-by":"crossref","first-page":"4649","DOI":"10.2147\/OTT.S252990","article-title":"Deficiency of PTEN and CDKN2A tumor-suppressor genes in conventional and chondroid chordomas: molecular characteristics and clinical relevance","volume":"Volume 13","author":"Yang","year":"2020","journal-title":"OncoTargets Ther."},{"key":"10.1016\/j.neo.2026.101325_bib0042","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1038\/ng.454","article-title":"T (brachyury) gene duplication confers major susceptibility to familial chordoma","volume":"41","author":"Yang","year":"2009","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neo.2026.101325_bib0043","doi-asserted-by":"crossref","DOI":"10.1016\/j.xcrm.2024.101757","article-title":"Clinical-proteomic classification and precision treatment strategy of chordoma","volume":"5","author":"Yin","year":"2024","journal-title":"Cell Reports Med."},{"key":"10.1016\/j.neo.2026.101325_bib0044","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms3612","article-title":"Inferring tumour purity and stromal and immune cell admixture from expression data","volume":"4","author":"Yoshihara","year":"2013","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neo.2026.101325_bib0045","article-title":"Proteogenomic characterization of skull-base chordoma","volume":"15","author":"Zhang","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neo.2026.101325_bib0046","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.humpath.2020.07.002","article-title":"Chromosome 3p loss of heterozygosity and reduced expression of H3K36me3 correlate with longer relapse-free survival in sacral conventional chordoma","volume":"104","author":"Zhu","year":"2020","journal-title":"Hum. Pathol."},{"key":"10.1016\/j.neo.2026.101325_bib0047","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1093\/neuonc\/noab235","article-title":"DNA methylation-based prognostic subtypes of chordoma tumors in tissue and plasma","volume":"24","author":"Zuccato","year":"2022","journal-title":"Neuro Oncol."}],"container-title":["Neoplasia"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476558626000552?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476558626000552?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T21:24:37Z","timestamp":1785878677000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476558626000552"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":47,"alternative-id":["S1476558626000552"],"URL":"https:\/\/doi.org\/10.1016\/j.neo.2026.101325","relation":{},"ISSN":["1476-5586"],"issn-type":[{"value":"1476-5586","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"The copy-number events in skull base chordoma stratify tumours into four biologically coherent groups","name":"articletitle","label":"Article Title"},{"value":"Neoplasia","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.neo.2026.101325","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"101325"}}