{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T04:30:57Z","timestamp":1786681857218,"version":"build-2736575974"},"reference-count":57,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["24-14-00439"],"award-info":[{"award-number":["24-14-00439"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Endocrinol."],"abstract":"\n Background<\/jats:title>\n Copy number alterations (CNAs) drive cancer by amplifying oncogenes and deleting tumor suppressor genes. Although CNA patterns are well-studied in common cancers, they remain poorly characterized in rare tumors.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n In this study, we employed an allele-specific copy number analysis using ASCAT on 25 head and neck paragangliomas (HNPGLs) with high tumor cell purity (\u226570%) and available clinicopathologic and mutation data.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n The majority of HNPGLs exhibited a near-diploid state. The recurrent somatic CNAs were predominantly hemizygous deletions, frequently affecting chromosomal regions 7q11, 1p36, 1p34, and 1p21.1-1p13.2, and involving key tumor suppressor genes associated with paragangliomas\/pheochromocytomas (PPGLs), including\n SDHB<\/jats:italic>\n ,\n SDHD<\/jats:italic>\n ,\n ATRX<\/jats:italic>\n ,\n SDHAF2<\/jats:italic>\n ,\n FH<\/jats:italic>\n ,\n MEN1<\/jats:italic>\n ,\n SDHA<\/jats:italic>\n , and\n VHL<\/jats:italic>\n . Frequent homozygous and hemizygous deletions were also observed in the tumor suppressor genes\n BCL10<\/jats:italic>\n ,\n PHF6<\/jats:italic>\n ,\n RPL5<\/jats:italic>\n , and\n STAG2<\/jats:italic>\n . Whole-gene amplifications were identified in several PPGL-associated oncogenes, such as\n BRAF<\/jats:italic>\n ,\n IDH1<\/jats:italic>\n ,\n PDGFRA<\/jats:italic>\n , and\n KIT<\/jats:italic>\n . Additionally, we identified concurrent mutations and allelic imbalances, suggestive of potential wild type allele loss in several novel tumor suppressor genes (\n CARS<\/jats:italic>\n and\n PRDM2<\/jats:italic>\n ), which may point to a role in tumor pathogenesis.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n Collectively, our study reveals a complex landscape of somatic CNAs in HNPGLs. The presence of recurrent alterations in hotspot genomic loci and PPGLs-associated genes suggests that genomic instability may be a significant contributing factor to tumor development and progression.<\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fendo.2026.1841009","type":"journal-article","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T04:23:10Z","timestamp":1786681390000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Complex landscape of somatic copy number alterations in head and neck paragangliomas"],"prefix":"10.3389","volume":"17","author":[{"given":"Vladislav S.","family":"Pavlov","sequence":"first","affiliation":[{"name":"Engelhardt Institute of Molecular Biology, Russian Academy of Sciences","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria S.","family":"Fedorova","sequence":"additional","affiliation":[{"name":"Engelhardt Institute of Molecular 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