{"entity": "researcher", "timestamp": "2026-07-13T09:46:54.647Z", "family": "Ivanov \u00d6fverholm", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-6907-8004", "affiliations": ["Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.", "Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/0ba94eeea4d24e9c8c354fe1256fd0ce.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/0ba94eeea4d24e9c8c354fe1256fd0ce"}}, "publications": [{"entity": "publication", "iuid": "9e68a455ebfb445fb36a31627cb0b31b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e68a455ebfb445fb36a31627cb0b31b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e68a455ebfb445fb36a31627cb0b31b"}}, "title": "Prospective Screening of Cancer Syndromes in Patients with Mesenchymal Tumors.", "authors": [{"family": "\u00d6fverholm", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-6907-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba94eeea4d24e9c8c354fe1256fd0ce.json"}}, {"family": "Lin", "given": "Yingbo", "initials": "Y", "orcid": "0000-0001-7190-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dfabc46c47741b9ace94b082d60184d.json"}}, {"family": "Mondini", "given": "Julia", "initials": "J"}, {"family": "Hardingz", "given": "John", "initials": "J"}, {"family": "Br\u00e4nstr\u00f6m", "given": "Robert", "initials": "R", "orcid": "0000-0001-6245-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5818dd9c4e4b9eae136c135d411c66.json"}}, {"family": "Tsagkozis", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-6631-2053", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae792176785f4fb3b5a1eb36478570f7.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Gellerbring", "given": "Anna", "initials": "A"}, {"family": "Lindberg", "given": "Johan", "initials": "J"}, {"family": "Chellappa", "given": "Venkatesh", "initials": "V"}, {"family": "Mayrhofer", "given": "Markus", "initials": "M"}, {"family": "Haglund", "given": "Cecilia", "initials": "C"}, {"family": "Haglund de Flon", "given": "Felix", "initials": "F"}, {"family": "Wallander", "given": "Karin", "initials": "K", "orcid": "0000-0001-8166-9678", "researcher": {"href": "https://publications.scilifelab.se/researcher/db174787efd74dc1b84f1bf56b74a22d.json"}}], "type": "journal article", "published": "2024-11-13", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "16", "issue": "22", "pages": "3816", "issn-l": "2072-6694"}, "abstract": "The etiology of most mesenchymal tumors is unknown, and knowledge about syndromes with an increased risk of tumors in bone or soft tissue is sparse.\n\nWe present a prospective germline analysis of 312 patients with tumors suspected of being sarcomas at a tertiary sarcoma center. Germline and tumor whole genome sequencing, tumor transcriptome, and methylome analyses were performed.\n\nGermline pathogenic or likely pathogenic variants associated with an increased risk of tumors were detected in 24 patients (8%), of which 11 (4%) harbored a detectable second hit in the tumor. Second hits were confirmed in genes with (NF1, RB1, TP53, EXT2, and SDHC) and without (ATM, CDC73, MLH1, MSH6, POLG, and KCNQ1) known association with mesenchymal tumor predisposition. Sarcomas from two Lynch syndrome patients showed mismatch repair deficiency, predicting a treatment response to immune checkpoint inhibitors (Level 1 biomarker according to the FDA (Federal Drug Administration) and ESMO (European Society for Medical Oncology)). None of the three CHEK2 carriers had a second hit in the tumor, suggesting a weak link to sarcoma.\n\nWe conclude that second-hit analyses can be used in standard of care to identify syndrome-related tumors. This approach can help distinguish true manifestations of tumor syndromes from unrelated germline findings and enhance the understanding of germline predisposition in soft tissue tumors. Prospective screening using germline whole genome sequencing should be considered when comprehensive somatic sequencing is introduced into clinical practice.", "doi": "10.3390/cancers16223816", "pmid": "39594770", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Clinical Genomics Stockholm": "Service", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11592761"}, {"db": "pii", "key": "cancers16223816"}], "notes": [], "created": "2024-11-14T08:02:41.749Z", "modified": "2025-11-18T20:44:32.464Z"}, {"entity": "publication", "iuid": "b789c181c1ab4a679ba3bd4e0df2e56f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b789c181c1ab4a679ba3bd4e0df2e56f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b789c181c1ab4a679ba3bd4e0df2e56f"}}, "title": "Comprehensive Genomic Profiling Alters Clinical Diagnoses in a Significant Fraction of Tumors Suspicious of Sarcoma.", "authors": [{"family": "\u00d6fverholm", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-6907-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba94eeea4d24e9c8c354fe1256fd0ce.json"}}, {"family": "Wallander", "given": "Karin", "initials": "K", "orcid": "0000-0001-8166-9678", "researcher": {"href": "https://publications.scilifelab.se/researcher/db174787efd74dc1b84f1bf56b74a22d.json"}}, {"family": "Haglund", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5484-8945", "researcher": {"href": "https://publications.scilifelab.se/researcher/7943ee4528064cafab37a2d91db8e480.json"}}, {"family": "Chellappa", "given": "Venkatesh", "initials": "V", "orcid": "0000-0003-1431-6949", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1af2e624b7d4783b0b61ff80ce8d8a1.json"}}, {"family": "Wejde", "given": "Johan", "initials": "J", "orcid": "0009-0009-1563-8158", "researcher": {"href": "https://publications.scilifelab.se/researcher/a974827370844ae0944a96892fb609da.json"}}, {"family": "Gellerbring", "given": "Anna", "initials": "A", "orcid": "0009-0002-4505-2173", "researcher": {"href": "https://publications.scilifelab.se/researcher/a267c2ecf411470a88bac75ab3ea58b2.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Renevey", "given": "Annick", "initials": "A", "orcid": "0000-0001-7411-6063", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0f6fb37ae984090b795b87229ffbd72.json"}}, {"family": "Caceres", "given": "Eva", "initials": "E", "orcid": "0000-0003-2890-2631", "researcher": {"href": "https://publications.scilifelab.se/researcher/df9019d6fdfc42c9b22d94c0af4bbd42.json"}}, {"family": "Tsagkozis", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-6631-2053", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae792176785f4fb3b5a1eb36478570f7.json"}}, {"family": "Mayrhofer", "given": "Markus", "initials": "M", "orcid": "0000-0003-3403-0083", "researcher": {"href": "https://publications.scilifelab.se/researcher/b08e9a0f0dc948dca3a3c40a1dd7c8cc.json"}}, {"family": "Papakonstantinou", "given": "Andri", "initials": "A", "orcid": "0000-0002-4232-4658", "researcher": {"href": "https://publications.scilifelab.se/researcher/92de2b7447a74c08ad49083ef803d4de.json"}}, {"family": "Linder-Stragliotto", "given": "Christina", "initials": "C", "orcid": "0009-0002-1247-7028", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ab128a5d5a2410ab055ae15e99374ed.json"}}, {"family": "Br\u00e4nstr\u00f6m", "given": "Robert", "initials": "R", "orcid": "0000-0001-6245-7223", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5818dd9c4e4b9eae136c135d411c66.json"}}, {"family": "Larsson", "given": "Olle", "initials": "O", "orcid": "0000-0001-8173-2956", "researcher": {"href": "https://publications.scilifelab.se/researcher/8cc0db662031464b8a5a56cc6ef3705e.json"}}, {"family": "Lindberg", "given": "Johan", "initials": "J", "orcid": "0000-0003-3610-6774", "researcher": {"href": "https://publications.scilifelab.se/researcher/1369ca149def47a8abb8abb90b23ca66.json"}}, {"family": "Lin", "given": "Yingbo", "initials": "Y", "orcid": "0000-0001-7190-2261", "researcher": {"href": "https://publications.scilifelab.se/researcher/3dfabc46c47741b9ace94b082d60184d.json"}}, {"family": "Haglund de Flon", "given": "Felix", "initials": "F", "orcid": "0000-0002-7015-3841", "researcher": {"href": "https://publications.scilifelab.se/researcher/891cbee146fa4e27bc8d26111283b854.json"}}], "type": "journal article", "published": "2024-06-14", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "issn-l": "1078-0432", "volume": "30", "issue": "12", "pages": "2647-2658"}, "abstract": "Tumor classification is a key component in personalized cancer care. For soft-tissue and bone tumors, this classification is currently based primarily on morphology assessment and IHC staining. However, these standard-of-care methods can pose challenges for pathologists. We therefore assessed how whole-genome and whole-transcriptome sequencing (WGTS) impacted tumor classification and clinical management when interpreted together with histomorphology.\n\nWe prospectively evaluated WGTS in routine diagnostics of 200 soft-tissue and bone tumors suspicious for malignancy, including DNA and RNA isolation from the tumor, and DNA isolation from a peripheral blood sample or any non-tumor tissue.\n\nOn the basis of specific genomic alterations or absence of presumed findings, WGTS resulted in reclassification of 7% (13/197) of the histopathologic diagnoses. Four cases were downgraded from low-grade sarcomas to benign lesions, and two cases were reclassified as metastatic malignant melanomas. Fusion genes associated with specific tumor entities were found in 30 samples. For malignant soft-tissue and bone tumors, we identified treatment relevant variants in 15% of cases. Germline pathogenic variants associated with a hereditary cancer syndrome were found in 22 participants (11%).\n\nWGTS provides an important dimension of data that aids in the classification of soft-tissue and bone tumors, correcting a significant fraction of clinical diagnoses, and identifies molecular targets relevant for precision medicine. However, genetic findings need to be evaluated in their morphopathologic context, just as germline findings need to be evaluated in the context of patient phenotype and family history.", "doi": "10.1158/1078-0432.CCR-24-0384", "pmid": "38573684", "labels": {"Clinical Genomics Stockholm": "Service", "Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "742915"}], "notes": [], "created": "2024-04-05T14:18:38.329Z", "modified": "2024-11-21T07:20:56.782Z"}, {"entity": "publication", "iuid": "804fe367d4ba45b59d3d3ed95177e766", "links": {"self": {"href": "https://publications.scilifelab.se/publication/804fe367d4ba45b59d3d3ed95177e766.json"}, "display": {"href": "https://publications.scilifelab.se/publication/804fe367d4ba45b59d3d3ed95177e766"}}, "title": "Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia.", "authors": [{"family": "Ivanov \u00d6fverholm", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-6907-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba94eeea4d24e9c8c354fe1256fd0ce.json"}}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V", "orcid": "0000-0001-9360-9859", "researcher": {"href": "https://publications.scilifelab.se/researcher/0607f2b65c12492cb30fb7a445d37937.json"}}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y", "orcid": "0000-0001-5576-2115", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb045b70f16140b6b6e69476d701012c.json"}}, {"family": "Tran", "given": "Anh Nhi", "initials": "AN"}, {"family": "Saft", "given": "Leonie", "initials": "L"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Harila-Saari", "given": "Arja", "initials": "A"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M", "orcid": "0000-0002-4974-425X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f9dec008f1b42868dd133e9a396c968.json"}}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G"}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Leuk. Lymphoma", "issn": "1029-2403", "issn-l": "1026-8022", "volume": "61", "issue": "3", "pages": "604-613"}, "abstract": "Intrachromosomal amplification of chromosome 21 (iAMP21) is a cytogenetic subtype associated with relapse and poor prognosis in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). The biology behind the high relapse risk is unknown and the aim of this study was to further characterize the genomic and transcriptional landscape of iAMP21. Using DNA arrays and sequencing, we could identify rearrangements and aberrations characteristic for iAMP21. RNA sequencing revealed that only half of the genes in the minimal region of amplification (20/45) were differentially expressed in iAMP21. Among them were the top overexpressed genes (p < 0.001) in iAMP21 vs. BCP ALL without iAMP21 and three candidate genes could be identified, the tyrosine kinase gene DYRK1A and chromatin remodeling genes CHAF1B and SON. While overexpression of DYRK1A and CHAF1B is associated with poor prognosis in malignant diseases including myeloid leukemia, this is the first study to show significant correlation with iAMP21-positive ALL.", "doi": "10.1080/10428194.2019.1678153", "pmid": "31640433", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-03T10:45:21.445Z", "modified": "2024-01-16T13:48:42.841Z"}]}