{"entity": "researcher", "timestamp": "2026-07-20T13:48:43.182Z", "family": "Engvall", "given": "Marie", "initials": "M", "orcid": "0000-0002-7394-9191", "affiliations": ["Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden. Marie.Engvall@igp.uu.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/0be7a9a5a518448ba7afb6f7a2cb3ca1.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/0be7a9a5a518448ba7afb6f7a2cb3ca1"}}, "publications": [{"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": "b79f5777524a411aaeeead5f8f3bc30f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b79f5777524a411aaeeead5f8f3bc30f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b79f5777524a411aaeeead5f8f3bc30f"}}, "title": "Familial platelet disorder due to germline exonic deletions in RUNX1: a diagnostic challenge with distinct alterations of the transcript isoform equilibrium.", "authors": [{"family": "Engvall", "given": "Marie", "initials": "M", "orcid": "0000-0002-7394-9191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be7a9a5a518448ba7afb6f7a2cb3ca1.json"}}, {"family": "Karlsson", "given": "Ylva", "initials": "Y"}, {"family": "Kuchinskaya", "given": "Ekaterina", "initials": "E"}, {"family": "J\u00f6rnegren", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Mathot", "given": "Lucy", "initials": "L"}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Palle", "given": "Josefine", "initials": "J"}, {"family": "Ljungstr\u00f6m", "given": "Viktor", "initials": "V"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Hellstr\u00f6m Lindberg", "given": "Eva", "initials": "E"}, {"family": "Cammenga", "given": "J\u00f6rg", "initials": "J"}, {"family": "Baliakas", "given": "Panagiotis", "initials": "P"}], "type": "journal article", "published": "2022-10-00", "journal": {"title": "Leuk. Lymphoma", "issn": "1029-2403", "volume": "63", "issue": "10", "pages": "2311-2320", "issn-l": "1026-8022"}, "abstract": "Germline pathogenic variants in RUNX1 are associated with familial platelet disorder with predisposition to myeloid malignancies (FPD/MM) with intragenic deletions in RUNX1 accounting for almost 7% of all reported variants. We present two new pedigrees with FPD/MM carrying two different germline RUNX1 intragenic deletions. The aforementioned deletions encompass exons 1-2 and 9-10 respectively, with the exon 9-10 deletion being previously unreported. RNA sequencing of patients carrying the exon 9-10 deletion revealed a fusion with LINC00160 resulting in a change in the 3' sequence of RUNX1. Expression analysis of the transcript isoform demonstrated altered RUNX1a/b/c ratios in carriers from both families compared to controls. Our data provide evidence on the impact of intragenic RUNX1 deletions on transcript isoform expression and highlight the importance of routinely performing copy number variant analysis in patients with suspected MM with germline predisposition.", "doi": "10.1080/10428194.2022.2067997", "pmid": "35533071", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2025-02-14T14:05:36.881Z", "modified": "2025-02-14T14:05:44.766Z"}, {"entity": "publication", "iuid": "d0290e65d9f045e798c9c885b9c72cbd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d0290e65d9f045e798c9c885b9c72cbd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d0290e65d9f045e798c9c885b9c72cbd"}}, "title": "Detection of leukemia gene fusions by targeted RNA-sequencing in routine diagnostics.", "authors": [{"family": "Engvall", "given": "Marie", "initials": "M", "orcid": "0000-0002-7394-9191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be7a9a5a518448ba7afb6f7a2cb3ca1.json"}}, {"family": "Cahill", "given": "Nicola", "initials": "N"}, {"family": "Jonsson", "given": "Britt-Inger", "initials": "BI"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M"}, {"family": "Hallb\u00f6\u00f6k", "given": "Helene", "initials": "H"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}], "type": "journal article", "published": "2020-07-29", "journal": {"title": "BMC Med Genomics", "issn": "1755-8794", "volume": "13", "issue": "1", "pages": "106", "issn-l": "1755-8794"}, "abstract": "We have evaluated an NGS-based method to detect recurrent gene fusions of diagnostic and prognostic importance in hematological malignancies. Our goal was to achieve a highly specific assay with a simple workflow, short turnaround time and low cost.\n\nThe assay uses a commercially available anchored multiplex PCR panel for target enrichment and library preparation, followed by sequencing using a MiSeq instrument. The panel includes all recurrent gene fusions in AML and ALL and is designed to detect gene-specific fusions without prior knowledge of the partner sequence or specific break points. Diagnostic RNA samples from 27 cases with hematological malignancies encompassing 23 different transcript variants were analyzed. In addition, 12 cases from a validation cohort were assessed.\n\nAll known fusion transcripts were identified with a high degree of confidence, with a large number of reads covering the breakpoints. Importantly, we could identify gene fusions where conventional methods had failed due to cryptic rearrangements or rare fusion partners. The newly-identified fusion partners were verified by RT-PCR and transcript-specific qPCR was designed for patient-specific follow-up. In addition, 12 cases were correctly assessed in a blind test, without prior knowledge of molecular cytogenetics or diagnosis.\n\nIn summary, our results demonstrate that targeted RNA sequencing using anchored multiplex PCR can be implemented in a clinical laboratory for the detection of recurrent and rare gene fusions in hematological diagnostic samples.", "doi": "10.1186/s12920-020-00739-4", "pmid": "32727569", "labels": {"Clinical Genomics Uppsala": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1186/s12920-020-00739-4"}, {"db": "pmc", "key": "PMC7388219"}], "notes": [], "created": "2020-11-06T13:03:04.566Z", "modified": "2021-11-10T12:48:54.750Z"}]}