{"entity": "researcher", "timestamp": "2026-07-18T02:39:04.089Z", "family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "affiliations": ["Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.", "Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7"}}, "publications": [{"entity": "publication", "iuid": "b894c8f51e7b40e7b9e2c3472acdd17e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b894c8f51e7b40e7b9e2c3472acdd17e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b894c8f51e7b40e7b9e2c3472acdd17e"}}, "title": "A novel PML germline variant as a candidate predisposing genetic aberration in familial acute myeloid leukaemia.", "authors": [{"family": "Soussi", "given": "Thierry", "initials": "T", "orcid": "0000-0001-8184-3293", "researcher": {"href": "https://publications.scilifelab.se/researcher/fce7c1391f634a9684352a3c49401939.json"}}, {"family": "Kundu", "given": "Snehangshu", "initials": "S", "orcid": "0000-0003-3541-5583", "researcher": {"href": "https://publications.scilifelab.se/researcher/2fa7619cacd842b6a6151964710315d2.json"}}, {"family": "Gerbaud", "given": "Pauline", "initials": "P"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Baskin", "given": "Berivan", "initials": "B"}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Delhommeau", "given": "Fran\u00e7ois", "initials": "F", "orcid": "0000-0002-4915-0734", "researcher": {"href": "https://publications.scilifelab.se/researcher/c51994ab468649ffb31f061f2a6f8023.json"}}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T", "orcid": "0000-0001-6668-4140", "researcher": {"href": "https://publications.scilifelab.se/researcher/909f00a5bf6e465f9ff560b12bcd863a.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Br. J. Haematol.", "issn": "1365-2141", "volume": "207", "issue": "3", "pages": "1118-1121", "issn-l": "0007-1048"}, "abstract": null, "doi": "10.1111/bjh.20255", "pmid": "40954117", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12436221"}], "notes": [], "created": "2025-11-26T14:14:25.189Z", "modified": "2025-11-26T14:14:25.660Z"}, {"entity": "publication", "iuid": "4ed7da9adac244919a18efaef8b67a03", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ed7da9adac244919a18efaef8b67a03.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ed7da9adac244919a18efaef8b67a03"}}, "title": "MALNC: a new mutant NPM1/IDH2R140 and PML-RARA-associated lncRNA with impact on AML cell proliferation, maturation and drug response.", "authors": [{"family": "Cozzi", "given": "Elisabetta", "initials": "E", "orcid": "0009-0003-5311-7974", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb6657fdce5a4c8e99ad05f000ef8de3.json"}}, {"family": "Neddermeyer", "given": "Anne", "initials": "A"}, {"family": "Zhong", "given": "Xiangfu", "initials": "X", "orcid": "0000-0002-1872-1186", "researcher": {"href": "https://publications.scilifelab.se/researcher/b625a888935a42a89d7df3522e249413.json"}}, {"family": "Gamboa-Cede\u00f1o", "given": "Angelica Mar\u00eda", "initials": "AM"}, {"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications.scilifelab.se/researcher/0921ab7566514fb0a3cd0daf2baabe6e.json"}}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Bj\u00f6rklund", "given": "My", "initials": "M", "orcid": "0000-0002-2325-6012", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cc743cdb2604ffdbc78303d70985c48.json"}}, {"family": "Struyf", "given": "Nona", "initials": "N"}, {"family": "Karlsson", "given": "Kasper", "initials": "K"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "M\u00e5nsson", "given": "Alma", "initials": "A", "orcid": "0009-0006-1982-7712", "researcher": {"href": "https://publications.scilifelab.se/researcher/6ccda3e6f49f43f5bcf5576d7acc16e5.json"}}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Nilsson", "given": "Christer", "initials": "C", "orcid": "0000-0003-0695-0050", "researcher": {"href": "https://publications.scilifelab.se/researcher/7f78180b33fa48cd86474d5c3cdaa852.json"}}, {"family": "Fiskesund", "given": "Roland", "initials": "R"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "Bartek", "given": "Jiri", "initials": "J"}, {"family": "Kallioniemi", "given": "Olli-Pekka", "initials": "OP"}, {"family": "Qian", "given": "Hong", "initials": "H"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2025-08-23", "journal": {"title": "Cancer Gene Ther", "issn": "1476-5500", "issn-l": null}, "abstract": "As the non-coding genome remains poorly characterized in acute myeloid leukemia (AML), we aimed to identify and functionally characterize novel long non-coding RNAs (lncRNAs) relevant to AML biology and treatment. We first identified lncRNAs overexpressed in AML blasts and, among them, discovered a novel transcript, which we named myeloid and AML-associated intergenic long non-coding RNA (MALNC). MALNC is overexpressed in AML, particularly in cases with the PML-RARA fusion or IDH2R140/NPM1 co-mutations, and is associated with a distinct gene expression profile. Functional studies showed that MALNC knockout impairs AML cell proliferation and colony formation, enhances ATRA-induced differentiation, and sensitizes cells to arsenic trioxide. Transcriptomic analysis revealed that MALNC loss alters the expression of retinoic acid pathway genes, and chromatin binding studies showed that MALNC binds to genes related to the retinoic acid and Rho GTPase pathways. In conclusion, we have identified MALNC as a novel lncRNA that promotes leukemic cell proliferation, counteracts ATRA-induced differentiation, and modulates drug sensitivity in AML.", "doi": "10.1038/s41417-025-00954-0", "pmid": "40849353", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41417-025-00954-0"}], "notes": [], "created": "2025-09-08T07:03:20.085Z", "modified": "2025-11-14T11:06:29.062Z"}, {"entity": "publication", "iuid": "309e4cb30adc40c79c9ac77e220eece6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/309e4cb30adc40c79c9ac77e220eece6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/309e4cb30adc40c79c9ac77e220eece6"}}, "title": "Validation of Guidelines for Genetic Investigation of Myeloid Neoplasms with Germline Predisposition: Results from a Prospective Cohort Study.", "authors": [{"family": "Tesi", "given": "Bianca", "initials": "B", "orcid": "0000-0002-8253-2507", "researcher": {"href": "https://publications.scilifelab.se/researcher/96a994cd257c4833a4efe79e26b900ff.json"}}, {"family": "Robelius", "given": "Anna", "initials": "A", "orcid": "0000-0002-8853-1863", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cfc6bb334e455d9f64172ff43e3428.json"}}, {"family": "Baskin", "given": "Berivan", "initials": "B", "orcid": "0000-0001-5994-9868", "researcher": {"href": "https://publications.scilifelab.se/researcher/97aa30696594447c999c200bd11f996b.json"}}, {"family": "Lazarevic", "given": "Vladimir", "initials": "V", "orcid": "0000-0002-1782-4423", "researcher": {"href": "https://publications.scilifelab.se/researcher/7113f0d0569247d4ac94b73ddc6ca74e.json"}}, {"family": "Deneberg", "given": "Stefan", "initials": "S", "orcid": "0000-0003-1888-5567", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1eb998009ee4a468be8e7f8109ef088.json"}}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M", "orcid": "0000-0003-2468-0226", "researcher": {"href": "https://publications.scilifelab.se/researcher/8717164448ee4e2797fefd365103ddc8.json"}}, {"family": "Fogelstrand", "given": "Linda", "initials": "L", "orcid": "0000-0003-3698-8519", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39ff709aa0646b8ad5e520780a0ad49.json"}}, {"family": "Ungerstedt", "given": "Johanna", "initials": "J", "orcid": "0000-0002-0202-7296", "researcher": {"href": "https://publications.scilifelab.se/researcher/04b6b5dd2f4845e38f4ad133608fe022.json"}}, {"family": "Pandzic", "given": "Tatjana", "initials": "T", "orcid": "0009-0006-9032-4616", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b7ad159e7524989a3eacd65b251ca9f.json"}}, {"family": "Tobiasson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3633-5852", "researcher": {"href": "https://publications.scilifelab.se/researcher/37b88e8e02af4145b95cc379c68ebee9.json"}}, {"family": "Garelius", "given": "Hege Gravdahl", "initials": "HG", "orcid": "0000-0003-2553-7659", "researcher": {"href": "https://publications.scilifelab.se/researcher/25307333f50942bbb7db3f84e094f7f3.json"}}, {"family": "Kuchinskaya", "given": "Ekaterina", "initials": "E", "orcid": "0009-0009-3347-6658", "researcher": {"href": "https://publications.scilifelab.se/researcher/d229b0af7f884fcb9d2a2832f59888ff.json"}}, {"family": "Persson", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-5374-4770", "researcher": {"href": "https://publications.scilifelab.se/researcher/33f1e0d34d5844e5b9d042b4d68df22c.json"}}, {"family": "\u00c5gerstam", "given": "Helena", "initials": "H", "orcid": "0009-0002-8216-3876", "researcher": {"href": "https://publications.scilifelab.se/researcher/55f2c7f5067949dbbce9a4bf505807b6.json"}}, {"family": "Hallb\u00f6\u00f6k", "given": "Helene", "initials": "H", "orcid": "0000-0002-5764-3213", "researcher": {"href": "https://publications.scilifelab.se/researcher/2478793f7c5945ba9f00cde3f39b62c4.json"}}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}, {"family": "Nordin", "given": "Jessika", "initials": "J", "orcid": "0000-0002-8414-2190", "researcher": {"href": "https://publications.scilifelab.se/researcher/2603df7f3ff84e6980605b9e8eef4c2f.json"}}, {"family": "Norberg", "given": "Anna", "initials": "A", "orcid": "0000-0003-2947-8879", "researcher": {"href": "https://publications.scilifelab.se/researcher/32e3c81cf4da410db2feaac562e88846.json"}}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC", "orcid": "0000-0002-4018-5551", "researcher": {"href": "https://publications.scilifelab.se/researcher/829bcbc2bb734d848f7b370546aca35c.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S", "orcid": "0000-0001-8374-8978", "researcher": {"href": "https://publications.scilifelab.se/researcher/4be462a447404937857936f77677da2f.json"}}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Vennstr\u00f6m", "given": "Lovisa", "initials": "L", "orcid": "0009-0002-7300-5438", "researcher": {"href": "https://publications.scilifelab.se/researcher/e3b702bc59b147d3adb508358d4e1a18.json"}}, {"family": "Ejerblad", "given": "Elisabeth", "initials": "E", "orcid": "0009-0009-8190-1073", "researcher": {"href": "https://publications.scilifelab.se/researcher/6a6b1722a4b34be5a9f3f0780dd34261.json"}}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Cammenga", "given": "J\u00f6rg", "initials": "J", "orcid": "0009-0001-0668-607X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f6daacdf33e7443c94c98bec4dec5cf5.json"}}, {"family": "J\u00e4dersten", "given": "Martin", "initials": "M", "orcid": "0000-0001-5217-3235", "researcher": {"href": "https://publications.scilifelab.se/researcher/f5b56c006df74965adab16c28afeb453.json"}}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E", "orcid": "0000-0002-7839-3743", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bf8d52e24234fa8b348ad08f58d1d48.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "journal article", "published": "2025-07-15", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "volume": "31", "issue": "14", "pages": "3062-3071", "issn-l": "1078-0432"}, "abstract": "In a multicenter prospective cohort study, we assessed the diagnostic yield of the Nordic guidelines for germline investigation in myeloid neoplasms and mapped the spectrum of inherited and somatic variants.\n\nEighty-five patients (acute myeloid leukemia, n = 38; myelodysplastic syndromes, n = 26; thrombocytopenia, n = 14; and other, n = 7) fulfilling the Nordic criteria for germline investigation, based on (i) medical history or family history suggestive of a germline condition and (ii) relevant findings from the somatic diagnostic work-up (CytoMol), were recruited. The genetic analysis included enhanced whole-exome sequencing (n = 69) or sequencing of specific variants of interest (n = 16).\n\nPathogenic or likely pathogenic (P/LP) germline variants were identified in 35% of patients (30/85). The diagnostic yield varied from 6% (1/16) in the family history group to 52% (17/33) in the CytoMol group. Germline DDX41 P/LP variants were the most frequent finding (13/30, 43% of all positive cases) almost exclusively found within the CytoMol group (12/13). Seven variants of unknown significance were also detected (TERT n = 2 and DDX41, RTEL1, ETV6, PARN, and SAMD9 n = 1). Five patients carried a P/LP variant in genes associated with another hereditary cancer syndrome (BRCA1 n = 3; PALB2 n = 1; and CHEK2; n = 1). Survival analysis showed a trend for longer survival among patients with acute myeloid leukemia and confirmed or suspected germline predisposition that underwent allogeneic stem cell transplantation.\n\nThe implementation of the Nordic guidelines in a prospective Swedish cohort results in a high overall diagnostic yield (35%), proving the feasibility and utility of these or similar guidelines in a clinical setting.", "doi": "10.1158/1078-0432.CCR-24-4251", "pmid": "40388595", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12260513"}, {"db": "pii", "key": "762516"}], "notes": [], "created": "2025-11-06T06:30:44.017Z", "modified": "2025-11-26T14:14:22.824Z"}, {"entity": "publication", "iuid": "72f3950c5f524c7085d950d0a69ea825", "links": {"self": {"href": "https://publications.scilifelab.se/publication/72f3950c5f524c7085d950d0a69ea825.json"}, "display": {"href": "https://publications.scilifelab.se/publication/72f3950c5f524c7085d950d0a69ea825"}}, "title": "Single cell sequencing reveals shared clonal signatures in non-malignant B- and tumor cells in T-prolymphocytic leukemia", "authors": [{"family": "Hesselager", "given": "Caroline", "initials": "C"}, {"family": "Th\u00f6rn", "given": "Ingrid", "initials": "I"}, {"family": "Marincevic", "given": "Millaray", "initials": "M"}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Alml\u00f6f", "given": "Jonas", "initials": "J", "orcid": "0000-0002-1211-9821", "researcher": {"href": "https://publications.scilifelab.se/researcher/046904cd12eb4764bd2dcadc876f65d7.json"}}, {"family": "L\u00f6fgren", "given": "Sara", "initials": "S", "orcid": "0000-0002-1680-7349", "researcher": {"href": "https://publications.scilifelab.se/researcher/8fdb4e41eab84ead8f399965e24dfea5.json"}}, {"family": "Westr\u00f6m", "given": "Simone", "initials": "S"}, {"family": "Nord", "given": "Helena", "initials": "H", "orcid": "0000-0002-6098-0237", "researcher": {"href": "https://publications.scilifelab.se/researcher/22d8cc445c6b41b4a8488d620995d8c3.json"}}, {"family": "Sutton", "given": "Lesley Ann", "initials": "LA"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Amini", "given": "Rose Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}], "type": "journal-article", "published": "2025-02-00", "journal": {"title": "Blood Neoplasia", "issn": "2950-3280", "pages": "100076", "issn-l": null}, "abstract": null, "doi": "10.1016/j.bneo.2025.100076", "pmid": null, "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-03-19T05:00:30.506Z", "modified": "2025-04-03T08:27:33.854Z"}, {"entity": "publication", "iuid": "bb530dc3000448379fac83628a00a444", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb530dc3000448379fac83628a00a444.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb530dc3000448379fac83628a00a444"}}, "title": "A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Lenner", "given": "Felix", "initials": "F"}, {"family": "Ten Berk de Boer", "given": "Esmee", "initials": "E"}, {"family": "Ek", "given": "Marlene", "initials": "M"}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "Vaz", "given": "Raquel", "initials": "R"}, {"family": "Ottosson", "given": "Jesper", "initials": "J"}, {"family": "Jonson", "given": "Tord", "initials": "T"}, {"family": "Ivarsson", "given": "Sofie", "initials": "S"}, {"family": "Thunstr\u00f6m", "given": "Sofia", "initials": "S"}, {"family": "Topa", "given": "Alexandra", "initials": "A"}, {"family": "Stenberg", "given": "Simon", "initials": "S"}, {"family": "Rohlin", "given": "Anna", "initials": "A"}, {"family": "Sandestig", "given": "Anna", "initials": "A"}, {"family": "Nordling", "given": "Margareta", "initials": "M"}, {"family": "Palmeb\u00e4ck", "given": "Pia", "initials": "P"}, {"family": "Burstedt", "given": "Magnus", "initials": "M"}, {"family": "Nordin", "given": "Frida", "initials": "F"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Sobol", "given": "Maria", "initials": "M"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}, {"family": "H\u00f6ijer", "given": "Ida", "initials": "I"}, {"family": "Saether", "given": "Kristine Bilgrav", "initials": "KB"}, {"family": "Lovmar", "given": "Lovisa", "initials": "L"}, {"family": "Ehrencrona", "given": "Hans", "initials": "H"}, {"family": "Melin", "given": "Malin", "initials": "M"}, {"family": "Feuk", "given": "Lars", "initials": "L"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications.scilifelab.se/researcher/07f3e6152da043d38c7a81974fcf8c23.json"}}], "type": "journal article", "published": "2024-11-20", "journal": {"title": "Genome Res.", "issn": "1549-5469", "volume": "34", "issue": "11", "pages": "1774-1784", "issn-l": "1088-9051"}, "abstract": "Clinical genetic laboratories often require a comprehensive analysis of chromosomal rearrangements/structural variants (SVs), from large events like translocations and inversions to supernumerary ring/marker chromosomes and small deletions or duplications. Understanding the complexity of these events and their clinical consequences requires pinpointing breakpoint junctions and resolving the derivative chromosome structure. This task often surpasses the capabilities of short-read sequencing technologies. In contrast, long-read sequencing techniques present a compelling alternative for clinical diagnostics. Here, Genomic Medicine Sweden-Rare Diseases has explored the utility of HiFi Revio long-read genome sequencing (lrGS) for digital karyotyping of SVs nationwide. The 16 samples from 13 families were collected from all Swedish healthcare regions. Prior investigations had identified 16 SVs, ranging from simple to complex rearrangements, including inversions, translocations, and copy number variants. We have established a national pipeline and a shared variant database for variant calling and filtering. Using lrGS, 14 of the 16 known SVs are detected. Of these, 13 are mapped at nucleotide resolution, and one complex rearrangement is only visible by read depth. Two Chromosome 21 rearrangements, one mosaic, remain undetected. Average read lengths are 8.3-18.8 kb with coverage exceeding 20\u00d7 for all samples. De novo assembly results in a limited number of phased contigs per individual (N50 6-86 Mb), enabling direct characterization of the chromosomal rearrangements. In a national pilot study, we demonstrate the utility of HiFi Revio lrGS for analyzing chromosomal rearrangements. Based on our results, we propose a 5-year plan to expand lrGS use for rare disease diagnostics in Sweden.", "doi": "10.1101/gr.279510.124", "pmid": "39472022", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Technology development", "NGI Long read": "Technology development", "National Genomics Infrastructure": "Technology development", "Clinical Genomics Uppsala": "Collaborative", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics Ume\u00e5": "Collaborative", "Clinical Genomics": "Collaborative", "Clinical Genomics Stockholm": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11610602"}, {"db": "pii", "key": "gr.279510.124"}, {"db": "medline", "key": "9509184"}], "notes": [], "created": "2024-11-04T20:46:04.978Z", "modified": "2025-11-26T07:54:28.658Z"}, {"entity": "publication", "iuid": "f09756a4b05e4c2892feeb79a38f290e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f09756a4b05e4c2892feeb79a38f290e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f09756a4b05e4c2892feeb79a38f290e"}}, "title": "Pathogenic DDX41 variants, possible response predictors to low-dose melphalan in hypo- and normocellular MDS and AML.", "authors": [{"family": "Nyquist", "given": "Otto Emil", "initials": "OE", "orcid": "0009-0005-2776-3686", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1497b7d2e3048a0977c1569a430a7fa.json"}}, {"family": "Dalgaard", "given": "Jakob", "initials": "J"}, {"family": "Spetalen", "given": "Signe", "initials": "S"}, {"family": "Torkildsen", "given": "Synne", "initials": "S"}, {"family": "Fr\u00f8en", "given": "Hege", "initials": "H"}, {"family": "Galteland", "given": "Eivind", "initials": "E"}, {"family": "Klungs\u00f8yr", "given": "Ole", "initials": "O"}, {"family": "Bergrem", "given": "Astrid", "initials": "A"}, {"family": "Vo", "given": "Camilla", "initials": "C"}, {"family": "S\u00f8rb\u00f8", "given": "Hjalmar", "initials": "H"}, {"family": "Eiken", "given": "Birgitte", "initials": "B"}, {"family": "Lerdal", "given": "Hedda", "initials": "H"}, {"family": "Solvang", "given": "Ann-Karin", "initials": "AK"}, {"family": "Jensvoll", "given": "Hilde", "initials": "H"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Dybedal", "given": "Ingunn", "initials": "I", "orcid": "0000-0002-3229-3069", "researcher": {"href": "https://publications.scilifelab.se/researcher/05a8dc8dd4d542698516276a578cac50.json"}}], "type": "letter", "published": "2023-11-28", "journal": {"title": "Br. J. Haematol.", "issn": "1365-2141", "issn-l": "0007-1048"}, "abstract": null, "doi": "10.1111/bjh.19226", "pmid": "38016923", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-12-01T12:46:09.282Z", "modified": "2023-12-01T12:46:09.360Z"}, {"entity": "publication", "iuid": "6fac894c455046668ab3f18eed8a7f8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6fac894c455046668ab3f18eed8a7f8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6fac894c455046668ab3f18eed8a7f8d"}}, "title": "Somatic Exonic Deletions in RUNX1 Constitutes a Novel Recurrent Genomic Abnormality in Acute Myeloid Leukemia.", "authors": [{"family": "Eriksson", "given": "Anna", "initials": "A", "orcid": "0000-0002-8853-1863", "researcher": {"href": "https://publications.scilifelab.se/researcher/53cfc6bb334e455d9f64172ff43e3428.json"}}, {"family": "Engvall", "given": "Marie", "initials": "M", "orcid": "0000-0002-7394-9191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be7a9a5a518448ba7afb6f7a2cb3ca1.json"}}, {"family": "Mathot", "given": "Lucy", "initials": "L", "orcid": "0000-0002-2990-2038", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9f3bfe35ddf41e5beb4312d3408a7ea.json"}}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A", "orcid": "0000-0001-8749-7299", "researcher": {"href": "https://publications.scilifelab.se/researcher/47a3ea9e722b4c72a7f00a61b5c9fe0a.json"}}, {"family": "Rippin", "given": "Martin", "initials": "M", "orcid": "0000-0003-4362-0122", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b30009265224c56b99e1afd024b5240.json"}}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "research support, non-u.s. gov't", "published": "2023-08-01", "journal": {"title": "Clin. Cancer Res.", "issn": "1557-3265", "issn-l": "1078-0432", "volume": "29", "issue": "15", "pages": "2826-2834"}, "abstract": "In acute myeloid leukemia (AML), somatic mutations (commonly missense, nonsense, and frameshift indels) in RUNX1 are associated with a dismal clinical outcome. Inherited RUNX1 mutations cause familial platelet disorder. As approximately 5%-10% of germline RUNX1 mutations are large exonic deletions, we hypothesized that such exonic RUNX1 aberrations may also be acquired during the development of AML.\n\nSixty patients with well-characterized AML were analyzed with multiplex ligation-dependent probe amplification (n = 60), microarray (n = 11), and/or whole-genome sequencing (n = 8).\n\nIn total, 25 (42% of the cohort) RUNX1-aberrant patients (defined by the presence of classical mutations and/or exonic deletions) were identified. Sixteen patients (27%) carried only exonic deletions, 5 (8%) carried classical mutations, and 4 (7%) carried both exonic deletions and mutations. No significant difference was observed between patients with classical RUNX1 mutations and RUNX1 exonic deletions in median overall survival (OS, 53.1 vs. 38.8 months, respectively, P = 0.63). When applying the European Leukemia Net (ELN) classification including the RUNX1-aberrant group, 20% of the patients initially stratified as intermediate-risk (5% of the whole cohort) were reassigned to the high-risk group, which improved the performance of ELN classification regarding OS between intermediate- and high-risk groups (18.9 vs. 9.6 months, P = 0.09).\n\nSomatic RUNX1 exonic deletions constitute a novel recurrent aberration in AML. Our findings have important clinical implications regarding AML classification, risk stratification, and treatment decision. Moreover, they argue in favor of further investigating such genomic aberrations not only in RUNX1 but also in other genes implicated in cancer biology and management. See related commentary by Chakraborty and Stengel, p. 2742.", "doi": "10.1158/1078-0432.CCR-23-0122", "pmid": "37022349", "labels": {"Clinical Genomics Uppsala": "Collaborative", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "725154"}], "notes": [], "created": "2023-11-29T08:28:02.202Z", "modified": "2024-01-16T13:48:32.633Z"}, {"entity": "publication", "iuid": "9787b70004ea41a3aecd22371d76935d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9787b70004ea41a3aecd22371d76935d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9787b70004ea41a3aecd22371d76935d"}}, "title": "BTK and PLCG2 remain unmutated in one-third of patients with CLL relapsing on ibrutinib.", "authors": [{"family": "Bonfiglio", "given": "Silvia", "initials": "S", "orcid": "0000-0002-4422-1580", "researcher": {"href": "https://publications.scilifelab.se/researcher/893715fc9cc843669563d8a9791fa6d0.json"}}, {"family": "Sutton", "given": "Lesley-Ann", "initials": "LA"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Capasso", "given": "Antonella", "initials": "A"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Westr\u00f6m", "given": "Simone", "initials": "S"}, {"family": "Foroughi-Asl", "given": "Hassan", "initials": "H"}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Gellerbring", "given": "Anna", "initials": "A"}, {"family": "Lyander", "given": "Anna", "initials": "A"}, {"family": "Gandini", "given": "Francesca", "initials": "F", "orcid": "0000-0001-8930-8295", "researcher": {"href": "https://publications.scilifelab.se/researcher/41feea8a61914af89215acfc54ec1751.json"}}, {"family": "Gaidano", "given": "Gianluca", "initials": "G", "orcid": "0000-0002-4681-0151", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9af4cedf69e47a5a4ecf0da0ed88c8e.json"}}, {"family": "Trentin", "given": "Livio", "initials": "L", "orcid": "0000-0003-1222-6149", "researcher": {"href": "https://publications.scilifelab.se/researcher/005d6d4e9e294ab7a1d7448c9aae45da.json"}}, {"family": "Bonello", "given": "Lisa", "initials": "L"}, {"family": "Reda", "given": "Gianluigi", "initials": "G"}, {"family": "B\u00f6d\u00f6r", "given": "Csaba", "initials": "C"}, {"family": "Stavroyianni", "given": "Niki", "initials": "N"}, {"family": "Tam", "given": "Constantine S", "initials": "CS", "orcid": "0000-0002-9759-5017", "researcher": {"href": "https://publications.scilifelab.se/researcher/2861e5af1279456c804b7da8037ebad1.json"}}, {"family": "Marasca", "given": "Roberto", "initials": "R", "orcid": "0000-0002-6431-6878", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8c880bbd36f4b9bb48f13ffa060fc7e.json"}}, {"family": "Forconi", "given": "Francesco", "initials": "F", "orcid": "0000-0002-2211-1831", "researcher": {"href": "https://publications.scilifelab.se/researcher/ad6219eb25ad4023855b634fd584f6ee.json"}}, {"family": "Panayiotidis", "given": "Panayiotis", "initials": "P", "orcid": "0000-0003-0387-3993", "researcher": {"href": "https://publications.scilifelab.se/researcher/b584b3dee8c44a6f96cb1b46a20dc416.json"}}, {"family": "Ringshausen", "given": "Ingo", "initials": "I", "orcid": "0000-0002-7247-311X", "researcher": {"href": "https://publications.scilifelab.se/researcher/e786421082ac47afbf82c976026f6ca9.json"}}, {"family": "Jaksic", "given": "Ozren", "initials": "O"}, {"family": "Frustaci", "given": "Anna Maria", "initials": "AM", "orcid": "0000-0003-2587-7901", "researcher": {"href": "https://publications.scilifelab.se/researcher/20640340bc1f449c97f6ebe8142d2540.json"}}, {"family": "Iyengar", "given": "Sunil", "initials": "S", "orcid": "0000-0003-4863-4160", "researcher": {"href": "https://publications.scilifelab.se/researcher/322cce8738a74fc586545f9d196ec38b.json"}}, {"family": "Coscia", "given": "Marta", "initials": "M", "orcid": "0000-0003-2123-7675", "researcher": {"href": "https://publications.scilifelab.se/researcher/db2cb0d5220c44a6921a263a2117a83a.json"}}, {"family": "Mulligan", "given": "Stephen P", "initials": "SP"}, {"family": "Ysebaert", "given": "Lo\u00efc", "initials": "L"}, {"family": "Strugov", "given": "Vladimir", "initials": "V"}, {"family": "Pavlovsky", "given": "Carolina", "initials": "C"}, {"family": "Walewska", "given": "Renata", "initials": "R"}, {"family": "\u00d6sterborg", "given": "Anders", "initials": "A"}, {"family": "Cortese", "given": "Diego", "initials": "D"}, {"family": "Ranghetti", "given": "Pamela", "initials": "P"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K", "orcid": "0000-0001-8529-640X", "researcher": {"href": "https://publications.scilifelab.se/researcher/772756566c154559b2c70c8f0f44d1ad.json"}}, {"family": "Scarf\u00f2", "given": "Lydia", "initials": "L", "orcid": "0000-0002-0844-0989", "researcher": {"href": "https://publications.scilifelab.se/researcher/47c4c336efb24d86b41c872d03836c78.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-9067-9058", "researcher": {"href": "https://publications.scilifelab.se/researcher/6deac213de5346c2b7cb5328bbce8568.json"}}, {"family": "Ghia", "given": "Paolo", "initials": "P", "orcid": "0000-0003-3750-7342", "researcher": {"href": "https://publications.scilifelab.se/researcher/46f24783739d44c7b73a1be28c344a35.json"}}], "type": "observational study", "published": "2023-06-27", "journal": {"title": "Blood Adv", "issn": "2473-9537", "volume": "7", "issue": "12", "pages": "2794-2806", "issn-l": "2473-9529"}, "abstract": "Patients with chronic lymphocytic leukemia (CLL) progressing on ibrutinib constitute an unmet need. Though Bruton tyrosine kinase (BTK) and PLCG2 mutations are associated with ibrutinib resistance, their frequency and relevance to progression are not fully understood. In this multicenter retrospective observational study, we analyzed 98 patients with CLL on ibrutinib (49 relapsing after an initial response and 49 still responding after \u22651 year of continuous treatment) using a next-generation sequencing (NGS) panel (1% sensitivity) comprising 13 CLL-relevant genes including BTK and PLCG2. BTK hotspot mutations were validated by droplet digital polymerase chain reaction (ddPCR) (0.1% sensitivity). By integrating NGS and ddPCR results, 32 of 49 relapsing cases (65%) carried at least 1 hotspot BTK and/or PLCG2 mutation(s); in 6 of 32, BTK mutations were only detected by ddPCR (variant allele frequency [VAF] 0.1% to 1.2%). BTK/PLCG2 mutations were also identified in 6 of 49 responding patients (12%; 5/6 VAF <10%), of whom 2 progressed later. Among the relapsing patients, the BTK-mutated (BTKmut) group was enriched for EGR2 mutations, whereas BTK-wildtype (BTKwt) cases more frequently displayed BIRC3 and NFKBIE mutations. Using an extended capture-based panel, only BRAF and IKZF3 mutations showed a predominance in relapsing cases, who were enriched for del(8p) (n = 11; 3 BTKwt). Finally, no difference in TP53 mutation burden was observed between BTKmut and BTKwt relapsing cases, and ibrutinib treatment did not favor selection of TP53-aberrant clones. In conclusion, we show that BTK/PLCG2 mutations were absent in a substantial fraction (35%) of a real-world cohort failing ibrutinib, and propose additional mechanisms contributing to resistance.", "doi": "10.1182/bloodadvances.2022008821", "pmid": "36696464", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10279547"}, {"db": "pii", "key": "494230"}], "notes": [], "created": "2023-11-29T08:28:00.316Z", "modified": "2023-11-29T08:28:00.868Z"}, {"entity": "publication", "iuid": "477434a47b94448f836521f7892ec2be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/477434a47b94448f836521f7892ec2be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/477434a47b94448f836521f7892ec2be"}}, "title": "Early response evaluation by single cell signaling profiling in acute myeloid leukemia.", "authors": [{"family": "Tislevoll", "given": "Benedicte Sjo", "initials": "BS", "orcid": "0000-0003-4962-997X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6874ed44ded94d709e1d11fc62af6b43.json"}}, {"family": "Helles\u00f8y", "given": "Monica", "initials": "M", "orcid": "0000-0002-0115-7427", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2df980a59134a4e82c3ac5e0edfecc9.json"}}, {"family": "Fagerholt", "given": "Oda Helen Eck", "initials": "OHE", "orcid": "0000-0002-5712-8860", "researcher": {"href": "https://publications.scilifelab.se/researcher/38167da5fcd94d14856785c8dd3319e9.json"}}, {"family": "Gullaksen", "given": "Stein-Erik", "initials": "SE"}, {"family": "Srivastava", "given": "Aashish", "initials": "A", "orcid": "0000-0003-0532-3979", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69d8575b0dd4fc99fe8e6a601706a90.json"}}, {"family": "Birkeland", "given": "Even", "initials": "E"}, {"family": "Kleftogiannis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0003-1086-821X", "researcher": {"href": "https://publications.scilifelab.se/researcher/88b8cce357b54b3cb0d22e5dd995d8d0.json"}}, {"family": "Ayuda-Dur\u00e1n", "given": "Pilar", "initials": "P", "orcid": "0000-0002-9799-3680", "researcher": {"href": "https://publications.scilifelab.se/researcher/1c39b575f5e1485b98e6271d56da8751.json"}}, {"family": "Piechaczyk", "given": "Laure", "initials": "L"}, {"family": "Tadele", "given": "Dagim Shiferaw", "initials": "DS", "orcid": "0000-0001-8319-678X", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b2524c8c8754beda75c6118d372b56e.json"}}, {"family": "Skavland", "given": "J\u00f8rn", "initials": "J"}, {"family": "Baliakas", "given": "Panagotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Hovland", "given": "Randi", "initials": "R", "orcid": "0000-0001-8543-2213", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0ea76c7a8a349b9b4c367f294d455f5.json"}}, {"family": "Andresen", "given": "Vibeke", "initials": "V", "orcid": "0000-0002-2368-2978", "researcher": {"href": "https://publications.scilifelab.se/researcher/43af3d6b0a4a432796443809e2facaaf.json"}}, {"family": "Seternes", "given": "Ole Morten", "initials": "OM", "orcid": "0000-0001-8537-3612", "researcher": {"href": "https://publications.scilifelab.se/researcher/843d4ab66cf04591aa1ec42503ebd6bf.json"}}, {"family": "Tvedt", "given": "Tor Henrik Anderson", "initials": "THA"}, {"family": "Aghaeepour", "given": "Nima", "initials": "N", "orcid": "0000-0002-6117-8764", "researcher": {"href": "https://publications.scilifelab.se/researcher/a61941f98d9e43e289e94dc59ff9dfcc.json"}}, {"family": "Gavasso", "given": "Sonia", "initials": "S"}, {"family": "Porkka", "given": "Kimmo", "initials": "K", "orcid": "0000-0003-4112-5902", "researcher": {"href": "https://publications.scilifelab.se/researcher/6f4ebafb55b34613af79c4d16a3eb75c.json"}}, {"family": "Jonassen", "given": "Inge", "initials": "I", "orcid": "0000-0003-4110-0748", "researcher": {"href": "https://publications.scilifelab.se/researcher/c609d886fc37469196e4bb639a0a89bb.json"}}, {"family": "Fl\u00f8isand", "given": "Yngvar", "initials": "Y", "orcid": "0000-0001-7267-1944", "researcher": {"href": "https://publications.scilifelab.se/researcher/f221b95eed9649618358528c075e4da2.json"}}, {"family": "Enserink", "given": "Jorrit", "initials": "J", "orcid": "0000-0002-2394-5387", "researcher": {"href": "https://publications.scilifelab.se/researcher/b0f0fc1c8ab142d39502e5b3df86b1bc.json"}}, {"family": "Blaser", "given": "Nello", "initials": "N", "orcid": "0000-0001-9489-1657", "researcher": {"href": "https://publications.scilifelab.se/researcher/22c9faae544a4d188acd34946ead8647.json"}}, {"family": "Gjertsen", "given": "Bj\u00f8rn Tore", "initials": "BT", "orcid": "0000-0001-9358-9704", "researcher": {"href": "https://publications.scilifelab.se/researcher/96c4d4aadc5f4ffb85df2176935b77db.json"}}], "type": "journal article", "published": "2023-01-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "115", "issn-l": "2041-1723"}, "abstract": "Aberrant pro-survival signaling is a hallmark of cancer cells, but the response to chemotherapy is poorly understood. In this study, we investigate the initial signaling response to standard induction chemotherapy in a cohort of 32 acute myeloid leukemia (AML) patients, using 36-dimensional mass cytometry. Through supervised and unsupervised machine learning approaches, we find that reduction of extracellular-signal-regulated kinase (ERK) 1/2 and p38 mitogen-activated protein kinase (MAPK) phosphorylation in the myeloid cell compartment 24 h post-chemotherapy is a significant predictor of patient 5-year overall survival in this cohort. Validation by RNA sequencing shows induction of MAPK target gene expression in patients with high phospho-ERK1/2 24 h post-chemotherapy, while proteomics confirm an increase of the p38 prime target MAPK activated protein kinase 2 (MAPKAPK2). In this study, we demonstrate that mass cytometry can be a valuable tool for early response evaluation in AML and elucidate the potential of functional signaling analyses in precision oncology diagnostics.", "doi": "10.1038/s41467-022-35624-4", "pmid": "36611026", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9825407"}, {"db": "pii", "key": "10.1038/s41467-022-35624-4"}], "notes": [], "created": "2023-11-29T08:27:28.554Z", "modified": "2023-11-29T08:27:29.154Z"}, {"entity": "publication", "iuid": "7368f002684f458b8856e07c2d6c9408", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7368f002684f458b8856e07c2d6c9408.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7368f002684f458b8856e07c2d6c9408"}}, "title": "Clonal haematopoiesis as a risk factor for therapy-related myeloid neoplasms in patients with chronic lymphocytic leukaemia treated with chemo-(immuno)therapy.", "authors": [{"family": "Voso", "given": "Maria-Teresa", "initials": "MT", "orcid": "0000-0002-6164-4761", "researcher": {"href": "https://publications.scilifelab.se/researcher/54c19342a17e44249d7b4e4ae05d3e7a.json"}}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Falconi", "given": "Giulia", "initials": "G", "orcid": "0000-0001-7699-1427", "researcher": {"href": "https://publications.scilifelab.se/researcher/60c82def5f4b44b683081a00b2561795.json"}}, {"family": "Den\u010di\u0107-Fekete", "given": "Marija", "initials": "M"}, {"family": "De Bellis", "given": "Eleonora", "initials": "E"}, {"family": "Scarfo", "given": "Lydia", "initials": "L"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Iskas", "given": "Michail", "initials": "M"}, {"family": "Del Poeta", "given": "Giovanni", "initials": "G"}, {"family": "Ranghetti", "given": "Pamela", "initials": "P"}, {"family": "Laidou", "given": "Stamatia", "initials": "S"}, {"family": "Cristiano", "given": "Antonio", "initials": "A", "orcid": "0000-0001-7055-8577", "researcher": {"href": "https://publications.scilifelab.se/researcher/39724cb024bc454cb93672004976adf8.json"}}, {"family": "Plevova", "given": "Karla", "initials": "K"}, {"family": "Imbergamo", "given": "Silvia", "initials": "S"}, {"family": "Engvall", "given": "Marie", "initials": "M"}, {"family": "Zucchetto", "given": "Antonella", "initials": "A"}, {"family": "Salvetti", "given": "Chiara", "initials": "C"}, {"family": "Mauro", "given": "Francesca R", "initials": "FR", "orcid": "0000-0003-2425-9474", "researcher": {"href": "https://publications.scilifelab.se/researcher/caf70fdaaa53438c8e37018c3b3b9d2f.json"}}, {"family": "Stavroyianni", "given": "Niki", "initials": "N"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Ghia", "given": "Paolo", "initials": "P"}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K"}, {"family": "Fabiani", "given": "Emiliano", "initials": "E", "orcid": "0000-0002-6209-8934", "researcher": {"href": "https://publications.scilifelab.se/researcher/8be5f1e2d63c411dafcf2c2e839fb80d.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Br. J. Haematol.", "issn": "1365-2141", "volume": "198", "issue": "1", "pages": "103-113", "issn-l": "0007-1048"}, "abstract": "Clonal haematopoiesis of indeterminate potential (CHIP) may predispose for the development of therapy-related myeloid neoplasms (t-MN). Using target next-generation sequencing (t-NGS) panels and digital droplet polymerase chain reactions (ddPCR), we studied the myeloid gene mutation profiles of patients with chronic lymphocytic leukaemia (CLL) who developed a t-MN after treatment with chemo-(immuno)therapy. Using NGS, we detected a total of 30 pathogenic/likely pathogenic (P/LP) variants in 10 of 13 patients with a t-MN (77%, median number of variants for patient: 2, range 0-6). The prevalence of CHIP was then backtracked in paired samples taken at CLL diagnosis in eight of these patients. Six of them carried at least one CHIP-variant at the time of t-MN (median: 2, range: 1-5), and the same variants were present in the CLL sample in five cases. CHIP variants were present in 34 of 285 patients from a population-based CLL cohort, which translates into a significantly higher prevalence of CHIP in patients with a CLL who developed a t-MN, compared to the population-based cohort (5/8, 62.5% vs. 34/285, 12%, p = 0.0001). Our data show that CHIP may be considered as a novel parameter affecting treatment algorithms in patients with CLL, and highlight the potential of using chemo-free therapies in CHIP-positive cases.", "doi": "10.1111/bjh.18129", "pmid": "35277855", "labels": {"Clinical Genomics Uppsala": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-28T12:42:03.124Z", "modified": "2022-11-28T12:42:03.291Z"}, {"entity": "publication", "iuid": "c5707d7f269941cb9e6716038a773c9b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c5707d7f269941cb9e6716038a773c9b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c5707d7f269941cb9e6716038a773c9b"}}, "title": "Loss of Y and clonal hematopoiesis in blood-two sides of the same coin?", "authors": [{"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Davies", "given": "Hanna", "initials": "H"}, {"family": "Rychlicka-Buniowska", "given": "Edyta", "initials": "E"}, {"family": "Danielsson", "given": "Marcus", "initials": "M", "orcid": "0000-0003-4418-0165", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6b237ce613e4ef8a6d7ab2654c2c41e.json"}}, {"family": "Lacaze", "given": "Paul", "initials": "P"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP", "orcid": "0000-0002-1489-1452", "researcher": {"href": "https://publications.scilifelab.se/researcher/15b14282209342cfa9c82cdbf02999f6.json"}}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}, {"family": "Forsberg", "given": "Lars A", "initials": "LA", "orcid": "0000-0002-1701-755X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9ac2d8e983764a82982118b6db84029e.json"}}], "type": "letter", "published": "2022-03-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "issn-l": "0887-6924", "volume": "36", "issue": "3", "pages": "889-891"}, "abstract": null, "doi": "10.1038/s41375-021-01456-2", "pmid": "34725452", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Clinical Genomics Uppsala": "Service", "NGI SNP genotyping": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8885420"}, {"db": "pii", "key": "10.1038/s41375-021-01456-2"}], "notes": [], "created": "2021-11-26T16:27:55.997Z", "modified": "2024-01-16T13:48:37.346Z"}, {"entity": "publication", "iuid": "90da40e1f7324fa4a32dc842a59eb5aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90da40e1f7324fa4a32dc842a59eb5aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90da40e1f7324fa4a32dc842a59eb5aa"}}, "title": "Clonal hematopoiesis in patients with high-grade B-cell lymphoma is associated with inferior outcome.", "authors": [{"family": "Amini", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-0901-5252", "researcher": {"href": "https://publications.scilifelab.se/researcher/c157abcd61fa4900b5ad502b408d6d95.json"}}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Abdulla", "given": "Maysaa", "initials": "M", "orcid": "0000-0002-0766-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/7aa1427f158d44448862d0f1f28723b2.json"}}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Hollander", "given": "Peter", "initials": "P", "orcid": "0000-0002-0226-5681", "researcher": {"href": "https://publications.scilifelab.se/researcher/b1c6693d3ede463eb78e6da010db601f.json"}}, {"family": "Enblad", "given": "Gunilla", "initials": "G"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P", "orcid": "0000-0002-5634-7156", "researcher": {"href": "https://publications.scilifelab.se/researcher/17370bd509dc4b1081af5aed9e5117c7.json"}}], "type": "letter", "published": "2020-07-06", "journal": {"title": "Am. J. Hematol.", "issn": "1096-8652", "volume": "95", "issue": "10", "pages": null, "issn-l": "0361-8609"}, "abstract": null, "doi": "10.1002/ajh.25927", "pmid": "32628289", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2020-11-06T13:03:32.457Z", "modified": "2021-11-10T12:49:27.847Z"}]}