{"entity": "researcher", "timestamp": "2026-08-09T07:53:15.314Z", "family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "affiliations": ["Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.", "Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817"}}, "publications": [{"entity": "publication", "iuid": "0b48959ee84c4ee890a0e427e268d9c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0b48959ee84c4ee890a0e427e268d9c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0b48959ee84c4ee890a0e427e268d9c6"}}, "title": "Novel activating SNRNP70-ALK fusion in congenital infant-type hemispheric glioma displays clinical response to lorlatinib: a case-report", "authors": [{"family": "Arthur", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0645-6530", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b07104d934d413a9c9546e7e9933051.json"}}, {"family": "Georgantzi", "given": "Kleopatra", "initials": "K"}, {"family": "de St\u00e5hl", "given": "Teresita D\u00edaz", "initials": "TD"}, {"family": "Guan", "given": "Jikui", "initials": "J", "orcid": "0000-0003-1723-0307", "researcher": {"href": "https://publications.scilifelab.se/researcher/a39044157aa7475485fb489a003b63d1.json"}}, {"family": "Oder", "given": "Blaz", "initials": "B", "orcid": "0000-0001-7984-3104", "researcher": {"href": "https://publications.scilifelab.se/researcher/9851f9fc65fc44aea55d0c1567be7887.json"}}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "Illies", "given": "Christopher", "initials": "C"}, {"family": "Sandgren", "given": "Johanna", "initials": "J", "orcid": "0000-0001-6776-2649", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d5b6b16fdbe470f83de8748227f8987.json"}}, {"family": "Svoboda", "given": "Jan", "initials": "J"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Sandvik", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-9273-2158", "researcher": {"href": "https://publications.scilifelab.se/researcher/72b8c0bf76054dc8ba15fa80fa78918e.json"}}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a683cea1874ac290d91c325a648be8.json"}}, {"family": "Hallberg", "given": "Bengt", "initials": "B"}, {"family": "Palmer", "given": "Ruth", "initials": "R", "orcid": "0000-0002-2735-8470", "researcher": {"href": "https://publications.scilifelab.se/researcher/808281ecc2634b66a274895e58a122bd.json"}}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6689dd9aff584082a57398141a538111.json"}}], "type": "journal-article", "published": "2026-02-26", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "10", "issue": "1", "issn-l": null}, "abstract": "We report a child with an antenatally detected brain tumor that progressed over three years' time despite surgery, chemo- and proton therapy. Retrospective whole-genome and transcriptome sequencing with methylation analysis of primary tumor tissue led to the molecular diagnosis infant-type hemispheric glioma, and identified a novel SNRNP70::ALK fusion, providing a therapeutic target for compassionate-use precision treatment with the ALK tyrosine kinase inhibitor lorlatinib. Functional studies confirmed the fusion protein to be expressed and active in the patient's tumor. After two years of therapy, the child has sustained partial tumor regression on MRI and no new neurological symptoms. We conclude that comprehensive multi-omics analyses are required for correct molecular diagnosis in childhood CNS tumors and can radically impact patient outcome by identifying molecular targets for precision treatment.", "doi": "10.1038/s41698-026-01336-x", "pmid": "41748687", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service", "NGI Short read": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12996540"}, {"db": "pii", "key": "10.1038/s41698-026-01336-x"}], "notes": [], "created": "2026-03-23T15:20:36.846Z", "modified": "2026-03-24T09:13:14.286Z"}, {"entity": "publication", "iuid": "6d6faf7279134df68f3e4160a4981f61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6d6faf7279134df68f3e4160a4981f61"}}, "title": "The genomic landscape of relapsed infant and childhood KMT2A-rearranged acute leukemia.", "authors": [{"family": "Ahlgren", "given": "Louise", "initials": "L"}, {"family": "Pilheden", "given": "Mattias", "initials": "M"}, {"family": "Sturesson", "given": "Helena", "initials": "H"}, {"family": "Song", "given": "Guangchun", "initials": "G", "orcid": "0000-0002-0190-8315", "researcher": {"href": "https://publications.scilifelab.se/researcher/f133bb6165494dfaba8173b0e8191765.json"}}, {"family": "Walsh", "given": "Michael P", "initials": "MP"}, {"family": "Yang", "given": "Minjun", "initials": "M", "orcid": "0000-0002-3324-1498", "researcher": {"href": "https://publications.scilifelab.se/researcher/62822d0b9c6c4a01a53829b9b05443ba.json"}}, {"family": "Maillard", "given": "Maud", "initials": "M"}, {"family": "Zhao", "given": "Huanbin", "initials": "H", "orcid": "0009-0001-4418-6770", "researcher": {"href": "https://publications.scilifelab.se/researcher/02a78b74f32d4670b628a8e3fb78ea0a.json"}}, {"family": "Cheng", "given": "Zhongshan", "initials": "Z"}, {"family": "Singh", "given": "Varsha", "initials": "V"}, {"family": "Castor", "given": "Anders", "initials": "A", "orcid": "0009-0007-4634-0704", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed2d2dab933049f5b69cdf0ff1e1d8a1.json"}}, {"family": "Pronk", "given": "Cornelis Jan", "initials": "CJ", "orcid": "0000-0002-0073-9660", "researcher": {"href": "https://publications.scilifelab.se/researcher/76e42ba48d824aa0b42e871e9f11b00a.json"}}, {"family": "Marquart", "given": "Hanne Vibeke", "initials": "HV", "orcid": "0000-0001-9740-6522", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9476b7116154ea9990d7c61c675c794.json"}}, {"family": "Lausen", "given": "Birgitte", "initials": "B", "orcid": "0000-0002-5306-0774", "researcher": {"href": "https://publications.scilifelab.se/researcher/dc5eadc48e354c4cb70d68d420bfa6fe.json"}}, {"family": "Schneider", "given": "Pauline", "initials": "P", "orcid": "0000-0003-0162-9436", "researcher": {"href": "https://publications.scilifelab.se/researcher/39a9fea74e284217b80716966bca995b.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Pokrovskaja Tamm", "given": "Katja", "initials": "K", "orcid": "0000-0001-6359-1256", "researcher": {"href": "https://publications.scilifelab.se/researcher/09ec3ee706764024bd748c7a77443845.json"}}, {"family": "Abrahamsson", "given": "Jonas", "initials": "J", "orcid": "0000-0002-9240-3522", "researcher": {"href": "https://publications.scilifelab.se/researcher/0f3199957bd147ec91bbdc04413f1dba.json"}}, {"family": "Lohi", "given": "Olli", "initials": "O", "orcid": "0000-0001-9195-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11a59310dfc40e6a111367914fdba9e.json"}}, {"family": "Fogelstrand", "given": "Linda", "initials": "L", "orcid": "0000-0003-3698-8519", "researcher": {"href": "https://publications.scilifelab.se/researcher/f39ff709aa0646b8ad5e520780a0ad49.json"}}, {"family": "Menendez", "given": "Pablo", "initials": "P"}, {"family": "Pieters", "given": "Rob", "initials": "R", "orcid": "0000-0003-2997-3570", "researcher": {"href": "https://publications.scilifelab.se/researcher/bb567d1e17e0428c843c07682decb31c.json"}}, {"family": "Zhang", "given": "Jinghui", "initials": "J", "orcid": "0000-0003-3350-9682", "researcher": {"href": "https://publications.scilifelab.se/researcher/38fe8464634149a39bc8accf6077bac4.json"}}, {"family": "Lindkvist-Petersson", "given": "Karin", "initials": "K", "orcid": "0000-0002-5209-3160", "researcher": {"href": "https://publications.scilifelab.se/researcher/efe1ac8c58f640ba98b97c6a5e52b9d5.json"}}, {"family": "Yang", "given": "Jun J", "initials": "JJ", "orcid": "0000-0002-0770-9659", "researcher": {"href": "https://publications.scilifelab.se/researcher/023457113ddc4e3a8309d0b4936c097e.json"}}, {"family": "Gruber", "given": "Tanja A", "initials": "TA", "orcid": "0000-0003-1072-7257", "researcher": {"href": "https://publications.scilifelab.se/researcher/c16c5b66f56f40fd93a9f398b0487a64.json"}}, {"family": "Stam", "given": "Ronald W", "initials": "RW", "orcid": "0000-0003-4986-1656", "researcher": {"href": "https://publications.scilifelab.se/researcher/f528aaa6b3ba479f85619e1496e3f395.json"}}, {"family": "Ma", "given": "Jing", "initials": "J"}, {"family": "Hagstr\u00f6m-Andersson", "given": "Anna K", "initials": "AK", "orcid": "0000-0002-2904-1311", "researcher": {"href": "https://publications.scilifelab.se/researcher/bc93a87c663d471ba64fc3be63212a89.json"}}], "type": "journal article", "published": "2025-10-08", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "8964", "issn-l": "2041-1723"}, "abstract": "To study the mechanisms of relapse in KMT2A-rearranged (KMT2A-r) acute lymphoblastic (ALL) and acute myeloid leukemia (AML), we performed whole-genome and exome sequencing of infants and children with relapsed ALL/AML (n = 36), and longitudinal deep-sequencing of 257 samples in 30 patients. Somatic alterations in drug-response genes, most commonly in TP53 and IKZF1 (64%), were highly enriched in early relapse ALL (79%, 9-36 months after diagnosis), but rare in very early relapse ALL (<9 months, 9%). A marked chemotherapy-exposure signature was detected for mutations in early relapse ALL but not in very early ALL or AML relapse, in line with different mechanisms of relapse. Longitudinal analyses could track residual leukemia cells, clonal drug responses, and the upcoming relapse. These results highlight that KMT2A-r ALL and AML evade therapy differently and provide insights into the mechanisms of relapse in this highly lethal form of pediatric acute leukemia.", "doi": "10.1038/s41467-025-64190-8", "pmid": "41062506", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12508131"}, {"db": "pii", "key": "10.1038/s41467-025-64190-8"}], "notes": [], "created": "2025-10-28T09:43:15.594Z", "modified": "2025-11-07T07:22:38.375Z"}, {"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": "cd6a9939959448618e775f67f2d1f3bd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cd6a9939959448618e775f67f2d1f3bd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cd6a9939959448618e775f67f2d1f3bd"}}, "title": "Precision Diagnostics in Myeloid Malignancies: Development and Validation of a National Capture-Based Gene Panel.", "authors": [{"family": "Orsmark-Pietras", "given": "Christina", "initials": "C", "orcid": "0000-0002-6533-0305", "researcher": {"href": "https://publications.scilifelab.se/researcher/66a38c96c9854fb18eb2420689d620e2.json"}}, {"family": "Lyander", "given": "Anna", "initials": "A"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Staffas", "given": "Anna", "initials": "A"}, {"family": "Awier", "given": "Hero", "initials": "H"}, {"family": "Krstic", "given": "Aleksandra", "initials": "A"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P"}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "H\u00e5kansson", "given": "Cecilia Brunhoff", "initials": "CB"}, {"family": "Gellerbring", "given": "Anna", "initials": "A"}, {"family": "Hagstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Juliusson", "given": "Gunnar", "initials": "G"}, {"family": "Lazarevic", "given": "Vladimir", "initials": "V", "orcid": "0000-0002-1782-4423", "researcher": {"href": "https://publications.scilifelab.se/researcher/7113f0d0569247d4ac94b73ddc6ca74e.json"}}, {"family": "Munters", "given": "Arielle", "initials": "A"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Wadelius", "given": "Mia", "initials": "M"}, {"family": "\u00c5s", "given": "Joel", "initials": "J"}, {"family": "Fogelstrand", "given": "Linda", "initials": "L"}, {"family": "Wirta", "given": "Valtteri", "initials": "V"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "SciLifeLab Clinical Genomics Platform and Genomic Medicine Sweden", "given": "", "initials": ""}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Genes Chromosomes Cancer", "issn": "1098-2264", "volume": "63", "issue": "7", "pages": "e23257", "issn-l": "1045-2257"}, "abstract": "Gene panel sequencing has become a common diagnostic tool for detecting somatically acquired mutations in myeloid neoplasms. However, many panels have restricted content, provide insufficient sensitivity levels, or lack clinically validated workflows. We here describe the development and validation of the Genomic Medicine Sweden myeloid gene panel (GMS-MGP), a capture-based 191 gene panel including mandatory genes in contemporary guidelines as well as emerging candidates. The GMS-MGP displayed uniform coverage across all targets, including recognized difficult GC-rich areas. The validation of 117 previously described somatic variants showed a 100% concordance with a limit-of-detection of a 0.5% variant allele frequency (VAF), achieved by utilizing error correction and filtering against a panel-of-normals. A national interlaboratory comparison investigating 56 somatic variants demonstrated highly concordant results in both detection rate and reported VAFs. In addition, prospective analysis of 323 patients analyzed with the GMS-MGP as part of standard-of-care identified clinically significant genes as well as recurrent mutations in less well-studied genes. In conclusion, the GMS-MGP workflow supports sensitive detection of all clinically relevant genes, facilitates novel findings, and is, based on the capture-based design, easy to update once new guidelines become available. The GMS-MGP provides an important step toward nationally harmonized precision diagnostics of myeloid malignancies.", "doi": "10.1002/gcc.23257", "pmid": "39031442", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics Uppsala": "Technology development", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2024-11-14T09:34:09.763Z", "modified": "2024-11-22T09:46:55.839Z"}, {"entity": "publication", "iuid": "c7fce16085b242e4a0c1e4d445e7cc5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7fce16085b242e4a0c1e4d445e7cc5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7fce16085b242e4a0c1e4d445e7cc5f"}}, "title": "Multimodal classification of molecular subtypes in pediatric acute lymphoblastic leukemia.", "authors": [{"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "Arvidsson", "given": "Gustav", "initials": "G"}, {"family": "Enblad", "given": "Anna Pia", "initials": "AP"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Sayyab", "given": "Shumaila", "initials": "S"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M"}, {"family": "Suhonen", "given": "Janne", "initials": "J"}, {"family": "Oksa", "given": "Laura", "initials": "L", "orcid": "0000-0003-4468-9877", "researcher": {"href": "https://publications.scilifelab.se/researcher/5526f0f44427441bb2a49f27f00b5683.json"}}, {"family": "Veps\u00e4l\u00e4inen", "given": "Kaisa", "initials": "K"}, {"family": "\u00d6fverholm", "given": "Ingegerd", "initials": "I"}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H"}, {"family": "Fioretos", "given": "Thoas", "initials": "T"}, {"family": "Madsen", "given": "Hans O", "initials": "HO"}, {"family": "Marquart", "given": "Hanne Vibeke", "initials": "HV"}, {"family": "Flaegstad", "given": "Trond", "initials": "T"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "J\u00f3nsson", "given": "\u00d3lafur G", "initials": "\u00d3G"}, {"family": "Kanerva", "given": "Jukka", "initials": "J"}, {"family": "Lohi", "given": "Olli", "initials": "O"}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}], "type": "journal article", "published": "2023-12-08", "journal": {"title": "NPJ Precis Oncol", "issn": "2397-768X", "volume": "7", "issue": "1", "pages": "131", "issn-l": null}, "abstract": "Genomic analyses have redefined the molecular subgrouping of pediatric acute lymphoblastic leukemia (ALL). Molecular subgroups guide risk-stratification and targeted therapies, but outcomes of recently identified subtypes are often unclear, owing to limited cases with comprehensive profiling and cross-protocol studies. We developed a machine learning tool (ALLIUM) for the molecular subclassification of ALL in retrospective cohorts as well as for up-front diagnostics. ALLIUM uses DNA methylation and gene expression data from 1131 Nordic ALL patients to predict 17 ALL subtypes with high accuracy. ALLIUM was used to revise and verify the molecular subtype of 281 B-cell precursor ALL (BCP-ALL) cases with previously undefined molecular phenotype, resulting in a single revised subtype for 81.5% of these cases. Our study shows the power of combining DNA methylation and gene expression data for resolving ALL subtypes and provides a comprehensive population-based retrospective cohort study of molecular subtype frequencies in the Nordic countries.", "doi": "10.1038/s41698-023-00479-5", "pmid": "38066241", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI SNP genotyping": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10709574"}, {"db": "pii", "key": "10.1038/s41698-023-00479-5"}], "notes": [], "created": "2024-11-05T18:15:42.686Z", "modified": "2024-11-21T08:31:51.959Z"}, {"entity": "publication", "iuid": "852e50de0ff44bb69e3ae276fde5166a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/852e50de0ff44bb69e3ae276fde5166a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/852e50de0ff44bb69e3ae276fde5166a"}}, "title": "The clinical picture of ERCC6L2 disease: from bone marrow failure to acute leukemia.", "authors": [{"family": "Hakkarainen", "given": "Marja", "initials": "M", "orcid": "0000-0003-3793-4803", "researcher": {"href": "https://publications.scilifelab.se/researcher/1becf84cc9234d38ad9e742c9a5c7c78.json"}}, {"family": "Kaaja", "given": "Ilse", "initials": "I", "orcid": "0009-0001-0415-8679", "researcher": {"href": "https://publications.scilifelab.se/researcher/49f3cdb42300418db11c5f539cd06ddf.json"}}, {"family": "Douglas", "given": "Suvi P M", "initials": "SPM", "orcid": "0000-0003-4412-688X", "researcher": {"href": "https://publications.scilifelab.se/researcher/0207afd92f6b4fab92c62bd60fe38f35.json"}}, {"family": "Vulliamy", "given": "Tom", "initials": "T"}, {"family": "Dokal", "given": "Inderjeet", "initials": "I"}, {"family": "Soulier", "given": "Jean", "initials": "J"}, {"family": "Larcher", "given": "Lise", "initials": "L", "orcid": "0000-0002-9461-0728", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c34e3e607594c2db0295b1a53b76598.json"}}, {"family": "Peffault de Latour", "given": "R\u00e9gis", "initials": "R"}, {"family": "Leblanc", "given": "Thierry", "initials": "T"}, {"family": "Sicre de Fontbrune", "given": "Flore", "initials": "F", "orcid": "0000-0003-2000-1556", "researcher": {"href": "https://publications.scilifelab.se/researcher/b75df183570948138e4136d27825bcb7.json"}}, {"family": "Siitonen", "given": "Timo", "initials": "T"}, {"family": "Lohi", "given": "Olli", "initials": "O"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Shimamura", "given": "Akiko", "initials": "A", "orcid": "0000-0002-4683-9958", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c755fa5ea30491f9e51986f7d46ce3f.json"}}, {"family": "Beier", "given": "Fabian", "initials": "F"}, {"family": "Jackson", "given": "Sharon", "initials": "S", "orcid": "0000-0003-3584-8872", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a5812de566c48c0a53b999d54da34c6.json"}}, {"family": "Kuperman", "given": "Amir Asher", "initials": "AA", "orcid": "0000-0003-1873-7660", "researcher": {"href": "https://publications.scilifelab.se/researcher/90057c462dac454b845aef84a71079ff.json"}}, {"family": "Falik Zaccai", "given": "Tzipora", "initials": "T"}, {"family": "Tamary", "given": "Hannah", "initials": "H"}, {"family": "Mecucci", "given": "Cristina", "initials": "C", "orcid": "0000-0002-1623-0148", "researcher": {"href": "https://publications.scilifelab.se/researcher/011fe0cc467d49568a01fe9442b1a55c.json"}}, {"family": "Capolsini", "given": "Ilaria", "initials": "I"}, {"family": "Jahnukainen", "given": "Kirsi", "initials": "K", "orcid": "0000-0001-9296-2028", "researcher": {"href": "https://publications.scilifelab.se/researcher/ec8cc2ae60a245e4807ce50c05273ded.json"}}, {"family": "Salmenniemi", "given": "Urpu", "initials": "U"}, {"family": "Niinim\u00e4ki", "given": "Riitta", "initials": "R", "orcid": "0000-0003-0190-5664", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a0915065497402397a3df623b539fa3.json"}}, {"family": "Varilo", "given": "Teppo", "initials": "T"}, {"family": "Kilpivaara", "given": "Outi", "initials": "O"}, {"family": "Wartiovaara-Kautto", "given": "Ulla", "initials": "U"}], "type": "journal article", "published": "2023-06-08", "journal": {"title": "Blood", "issn": "1528-0020", "volume": "141", "issue": "23", "pages": "2853-2866", "issn-l": "0006-4971"}, "abstract": "Biallelic germ line excision repair cross-complementing 6 like 2 (ERCC6L2) variants strongly predispose to bone marrow failure (BMF) and myeloid malignancies, characterized by somatic TP53-mutated clones and erythroid predominance. We present a series of 52 subjects (35 families) with ERCC6L2 biallelic germ line variants collected retrospectively from 11 centers globally, with a follow-up of 1165 person-years. At initial investigations, 32 individuals were diagnosed with BMF and 15 with a hematological malignancy (HM). The subjects presented with 19 different variants of ERCC6L2, and we identified a founder mutation, c.1424delT, in Finnish patients. The median age of the subjects at baseline was 18 years (range, 2-65 years). Changes in the complete blood count were mild despite severe bone marrow (BM) hypoplasia and somatic TP53 mutations, with no significant difference between subjects with or without HMs. Signs of progressive disease included increasing TP53 variant allele frequency, dysplasia in megakaryocytes and/or erythroid lineage, and erythroid predominance in the BM morphology. The median age at the onset of HM was 37.0 years (95% CI, 31.5-42.5; range, 12-65 years). The overall survival (OS) at 3 years was 95% (95% CI, 85-100) and 19% (95% CI, 0-39) for patients with BMF and HM, respectively. Patients with myelodysplastic syndrome or acute myeloid leukemia with mutated TP53 undergoing hematopoietic stem cell transplantation had a poor outcome with a 3-year OS of 28% (95% CI, 0-61). Our results demonstrated the importance of early recognition and active surveillance in patients with biallelic germ line ERCC6L2 variants.", "doi": "10.1182/blood.2022019425", "pmid": "36952636", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "495066"}], "notes": [], "created": "2023-11-22T21:43:41.499Z", "modified": "2023-11-22T21:43:41.899Z"}, {"entity": "publication", "iuid": "14f4d2b869aa4a2dabad06efa432aa96", "links": {"self": {"href": "https://publications.scilifelab.se/publication/14f4d2b869aa4a2dabad06efa432aa96.json"}, "display": {"href": "https://publications.scilifelab.se/publication/14f4d2b869aa4a2dabad06efa432aa96"}}, "title": "Simultaneous Ultra-Sensitive Detection of Structural and Single Nucleotide Variants Using Multiplex Droplet Digital PCR in Liquid Biopsies from Children with Medulloblastoma.", "authors": [{"family": "Arthur", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-0645-6530", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b07104d934d413a9c9546e7e9933051.json"}}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "de St\u00e5hl", "given": "Teresita D\u00edaz", "initials": "TD", "orcid": "0000-0001-5933-6623", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f51158ce6e14f3b96bf16a214689d1d.json"}}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Harila", "given": "Arja", "initials": "A"}, {"family": "Barbany", "given": "Gisela", "initials": "G", "orcid": "0000-0003-3185-2962", "researcher": {"href": "https://publications.scilifelab.se/researcher/13fda0d702d543f981898ebd53849817.json"}}, {"family": "Sandvik", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-9273-2158", "researcher": {"href": "https://publications.scilifelab.se/researcher/72b8c0bf76054dc8ba15fa80fa78918e.json"}}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications.scilifelab.se/researcher/6689dd9aff584082a57398141a538111.json"}}], "type": "journal article", "published": "2023-03-25", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "15", "issue": "7", "issn-l": "2072-6694"}, "abstract": "Medulloblastoma is a malignant embryonal tumor of the central nervous system (CNS) that mainly affects infants and children. Prognosis is highly variable, and molecular biomarkers for measurable residual disease (MRD) detection are lacking. Analysis of cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) using broad genomic approaches, such as low-coverage whole-genome sequencing, has shown promising prognostic value. However, more sensitive methods are needed for MRD analysis. Here, we show the technical feasibility of capturing medulloblastoma-associated structural variants and point mutations simultaneously in cfDNA using multiplexed droplet digital PCR (ddPCR). Assay sensitivity was assessed with a dilution series of tumor in normal genomic DNA, and the limit of detection was below 100 pg of input DNA for all assays. False positive rates were zero for structural variant assays. Liquid biopsies (CSF and plasma, n = 47) were analyzed from 12 children with medulloblastoma, all with negative CSF cytology. MRD was detected in 75% (9/12) of patients overall. In CSF samples taken before or within 21 days of surgery, MRD was detected in 88% (7/8) of patients with localized disease and in one patient with the metastasized disease. Our results suggest that this approach could expand the utility of ddPCR and complement broader analyses of cfDNA for MRD detection.", "doi": "10.3390/cancers15071972", "pmid": "37046633", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10092983"}, {"db": "pii", "key": "cancers15071972"}], "notes": [], "created": "2023-11-29T11:43:56.624Z", "modified": "2024-01-16T13:48:33.819Z"}]}