{"entity": "journal", "iuid": "2ab4d1a2402e43e69a9b0e28d33ecc86", "timestamp": "2026-06-09T03:08:52.917Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Leuk.%20Lymphoma.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Leuk.%20Lymphoma"}}, "title": "Leuk. Lymphoma", "issn": "1029-2403", "issn-l": "1026-8022", "publications_count": 8, "publications": [{"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": "9f724da96e0345b6919d263fb50f54d0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9f724da96e0345b6919d263fb50f54d0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9f724da96e0345b6919d263fb50f54d0"}}, "title": "Limited benefit in patients with MDS receiving venetoclax and azacitidine as a bridge to allogeneic stem cell transplantation.", "authors": [{"family": "J\u00e4dersten", "given": "Martin", "initials": "M"}, {"family": "Boriskina", "given": "Ksenia", "initials": "K"}, {"family": "Lindholm", "given": "Carolin", "initials": "C"}, {"family": "Westr\u00f6m", "given": "Simone", "initials": "S"}, {"family": "Cavelier", "given": "Lucia", "initials": "L"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "Eva", "initials": "E"}, {"family": "Mielke", "given": "Stephan", "initials": "S"}, {"family": "Tobiasson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3633-5852", "researcher": {"href": "https://publications.scilifelab.se/researcher/37b88e8e02af4145b95cc379c68ebee9.json"}}], "type": "letter", "published": "2021-11-15", "journal": {"title": "Leuk. Lymphoma", "issn": "1029-2403", "pages": "1-4", "issn-l": "1026-8022"}, "abstract": null, "doi": "10.1080/10428194.2021.2002319", "pmid": "34775885", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2021-12-06T08:29:19.584Z", "modified": "2021-12-06T08:29:19.616Z"}, {"entity": "publication", "iuid": "9fc2be432daf49e191b7c3507411a025", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9fc2be432daf49e191b7c3507411a025.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9fc2be432daf49e191b7c3507411a025"}}, "title": "Targeted genomic investigations in a population-based cohort of mantle cell lymphoma reveal novel clinically relevant targets.", "authors": [{"family": "Rodrigues", "given": "Joana M", "initials": "JM", "orcid": "0000-0003-1806-331X", "researcher": {"href": "https://publications.scilifelab.se/researcher/4d0327df136c44f8849534033826393b.json"}}, {"family": "Porwit", "given": "Anna", "initials": "A"}, {"family": "Hassan", "given": "May", "initials": "M"}, {"family": "Ek", "given": "Sara", "initials": "S", "orcid": "0000-0002-1388-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/56861b5f5cac4b23ab86b19b4650aa3d.json"}}, {"family": "Jerkeman", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2021-11-00", "journal": {"title": "Leuk. Lymphoma", "issn": "1029-2403", "volume": "62", "issue": "11", "pages": "2637-2647", "issn-l": "1026-8022"}, "abstract": "Mantle cell lymphoma (MCL) is an aggressive B-cell neoplasm that follows a heterogeneous clinical course. Recurrent mutations have been described, but their applicability in the clinical setting is currently limited. The main reasons are challenges in the sequencing of DNA retrieved from formalin-fixed tissue commonly used for tissue collection in clinical biobanks. In this study, we sequenced 77 samples from a population-based de novo MCL cohort to investigate the utility of targeted sequencing in guiding personalized treatment approaches. Tumors were genetically variable, and a similar genetic landscape as previous studies using non-formalin fixed samples was identified, with recurrent mutations including ATM, KMT2D, and TP53. Novel alterations that can be considered actionable and/or indicative of treatment response were also identified. Our approach shows the potential benefits of using target sequencing of formalin fixed samples to facilitate treatment selection and individualized clinical decisions in MCL.", "doi": "10.1080/10428194.2021.1933480", "pmid": "34080947", "labels": {"Clinical Genomics Lund": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2022-11-14T12:22:35.901Z", "modified": "2022-11-14T12:23:20.446Z"}, {"entity": "publication", "iuid": "a312d31ab7164798812e6b118c157b4e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a312d31ab7164798812e6b118c157b4e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a312d31ab7164798812e6b118c157b4e"}}, "title": "Proteomic analysis in diffuse large B-cell lymphoma identifies dysregulated tumor microenvironment proteins in non-GCB/ABC subtype patients.", "authors": [{"family": "Bram Ednersson", "given": "Susanne", "initials": "S"}, {"family": "Stern", "given": "Mimmie", "initials": "M"}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "Nilsson-Ehle", "given": "Herman", "initials": "H"}, {"family": "Hasselblom", "given": "Sverker", "initials": "S"}, {"family": "Thorsell", "given": "Annika", "initials": "A"}, {"family": "Andersson", "given": "Per-Ola", "initials": "PO"}], "type": "journal article", "published": "2021-10-00", "journal": {"title": "Leuk. Lymphoma", "issn": "1029-2403", "volume": "62", "issue": "10", "pages": "2360-2373", "issn-l": "1026-8022"}, "abstract": "The complexity of the activated B-cell like (ABC) diffuse large B-cell lymphoma (DLBCL) subtype is probably not only explained by genetic alterations and methods to measure global protein expression could bring new knowledge regarding the pathophysiology. We used quantitative proteomics to analyze the global protein expression of formalin-fixed paraffin-embedded (FFPE) tumor tissues from 202 DLBCL patients. We identified 6430 proteins and 498 were significantly regulated between the germinal center B-cell like (GCB) and non-GCB groups. A number of proteins previously not described to be upregulated in non-GCB or ABC DLBCL was found, e.g. CD64, CD85A, guanylate-binding protein 1 (GBP1), interferon-induced proteins with tetratricopeptide repeat (IFIT)2, and mixed lineage kinase domain-like protein (MLKL) and immunohistochemical staining showed higher expression of GBP1 and MLKL. A cluster analysis revealed that the most prominent cluster contained proteins involved in the tumor microenvironment and regulation of the immune system. Our data suggest that the therapeutic focus should be expanded toward the tumor microenvironment in non-GCB/ABC subtype patients.", "doi": "10.1080/10428194.2021.1913147", "pmid": "34114929", "labels": {"Glycoproteomics and MS Proteomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2023-03-07T14:31:56.735Z", "modified": "2024-01-16T13:46:30.052Z"}, {"entity": "publication", "iuid": "804fe367d4ba45b59d3d3ed95177e766", "links": {"self": {"href": "https://publications.scilifelab.se/publication/804fe367d4ba45b59d3d3ed95177e766.json"}, "display": {"href": "https://publications.scilifelab.se/publication/804fe367d4ba45b59d3d3ed95177e766"}}, "title": "Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia.", "authors": [{"family": "Ivanov \u00d6fverholm", "given": "Ingegerd", "initials": "I", "orcid": "0000-0002-6907-8004", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ba94eeea4d24e9c8c354fe1256fd0ce.json"}}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V", "orcid": "0000-0001-9360-9859", "researcher": {"href": "https://publications.scilifelab.se/researcher/0607f2b65c12492cb30fb7a445d37937.json"}}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications.scilifelab.se/researcher/c250909cc40f42ff9d6e2f640d12451b.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y", "orcid": "0000-0001-5576-2115", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb045b70f16140b6b6e69476d701012c.json"}}, {"family": "Tran", "given": "Anh Nhi", "initials": "AN"}, {"family": "Saft", "given": "Leonie", "initials": "L"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b3f854e51704270831e155518265ea6.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Harila-Saari", "given": "Arja", "initials": "A"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M", "orcid": "0000-0002-4974-425X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f9dec008f1b42868dd133e9a396c968.json"}}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications.scilifelab.se/researcher/08e74c6ddc27493696beca0883027cdd.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Barbany", "given": "Gisela", "initials": "G"}], "type": "journal article", "published": "2020-03-00", "journal": {"title": "Leuk. Lymphoma", "issn": "1029-2403", "issn-l": "1026-8022", "volume": "61", "issue": "3", "pages": "604-613"}, "abstract": "Intrachromosomal amplification of chromosome 21 (iAMP21) is a cytogenetic subtype associated with relapse and poor prognosis in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). The biology behind the high relapse risk is unknown and the aim of this study was to further characterize the genomic and transcriptional landscape of iAMP21. Using DNA arrays and sequencing, we could identify rearrangements and aberrations characteristic for iAMP21. RNA sequencing revealed that only half of the genes in the minimal region of amplification (20/45) were differentially expressed in iAMP21. Among them were the top overexpressed genes (p < 0.001) in iAMP21 vs. BCP ALL without iAMP21 and three candidate genes could be identified, the tyrosine kinase gene DYRK1A and chromatin remodeling genes CHAF1B and SON. While overexpression of DYRK1A and CHAF1B is associated with poor prognosis in malignant diseases including myeloid leukemia, this is the first study to show significant correlation with iAMP21-positive ALL.", "doi": "10.1080/10428194.2019.1678153", "pmid": "31640433", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2019-12-03T10:45:21.445Z", "modified": "2024-01-16T13:48:42.841Z"}, {"entity": "publication", "iuid": "594a00afe45c46328b7df7fca7382dac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/594a00afe45c46328b7df7fca7382dac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/594a00afe45c46328b7df7fca7382dac"}}, "title": "Angioimmunoblastic T-cell lymphoma and myelodysplastic syndrome with mutations in TET2, DNMT3 and CUX1 - azacitidine induces only lymphoma remission.", "authors": [{"family": "Tobiasson", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3633-5852", "researcher": {"href": "https://publications.scilifelab.se/researcher/37b88e8e02af4145b95cc379c68ebee9.json"}}, {"family": "Pandzic", "given": "Tatjana", "initials": "T"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Sander", "given": "Birgitta", "initials": "B"}, {"family": "Wahlin", "given": "Bj\u00f6rn Engelbrekt", "initials": "BE"}], "type": "case reports", "published": "2019-12-00", "journal": {"title": "Leuk. Lymphoma", "issn": "1029-2403", "volume": "60", "issue": "13", "pages": "3316-3319", "issn-l": "1026-8022"}, "abstract": null, "doi": "10.1080/10428194.2019.1627541", "pmid": "31204875", "labels": {"Clinical Genomics Uppsala": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [], "notes": [], "created": "2019-12-20T07:54:03.422Z", "modified": "2021-07-08T12:52:24.367Z"}, {"entity": "publication", "iuid": "47cee6993e1f4c3ab51716fc8d4921f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/47cee6993e1f4c3ab51716fc8d4921f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/47cee6993e1f4c3ab51716fc8d4921f6"}}, "title": "Detailed gene dose analysis reveals recurrent focal gene deletions in pediatric B-cell precursor acute lymphoblastic leukemia.", "authors": [{"family": "Ivanov \u00d6fverholm", "given": "Ingegerd", "initials": "I"}, {"family": "Tran", "given": "Anh Nhi", "initials": "AN"}, {"family": "Olsson", "given": "Linda", "initials": "L"}, {"family": "Zachariadis", "given": "Vasilios", "initials": "V"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Rudd", "given": "Eva", "initials": "E"}, {"family": "Syk Lundberg", "given": "Elisabeth", "initials": "E"}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Johansson", "given": "Bertil", "initials": "B"}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Barbany", "given": "Gisela", "initials": "G"}], "type": "journal article", "published": "2016-09-00", "journal": {"volume": "57", "issn": "1029-2403", "issue": "9", "pages": "2161-2170", "title": "Leuk. Lymphoma", "issn-l": "1026-8022"}, "abstract": "To identify copy number alterations (CNAs) in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL), array comparative genomic hybridization was performed on 50 cases; detected CNAs were validated in a cohort of 191 cases analyzed by single nucleotide polymorphism arrays. Apart from CNAs involving leukemia-associated genes, recurrent deletions targeting genes not previously implicated in BCP ALL, e.g. INIP, IRF1 and PDE4B, were identified. Deletions of the DNA repair gene INIP were exclusively found in cases with t(12;21), and deletions of SH2B3 were associated with intrachromosomal amplification of chromosome 21 (p\u2009<\u20090.001). A majority of BTLA deletions (7/11; 64%) affected samples with gain of 21q chromosome material, suggesting that BTLA deletions are associated with both germline and somatic gain of chromosome 21. In cases without known risk-associated cytogenetic markers, CNAs associated with adverse prognosis were identified in 50% (10/20), indicating that a majority of these cases could be assigned to distinct genetic subtypes.", "doi": "10.3109/10428194.2015.1136740", "pmid": "27090575", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:02:22.352Z", "modified": "2017-09-06T11:51:11.854Z"}, {"entity": "publication", "iuid": "57b77b874057458eaa21f9cb61d8bfe7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/57b77b874057458eaa21f9cb61d8bfe7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/57b77b874057458eaa21f9cb61d8bfe7"}}, "title": "Serum nuclear magnetic resonance-based metabolomics and outcome in diffuse large B-cell lymphoma patients - a pilot study.", "authors": [{"family": "Stenson", "given": "Martin", "initials": "M"}, {"family": "Pedersen", "given": "Anders", "initials": "A"}, {"family": "Hasselblom", "given": "Sverker", "initials": "S"}, {"family": "Nilsson-Ehle", "given": "Herman", "initials": "H"}, {"family": "Karlsson", "given": "Bengt G\u00f6ran", "initials": "BG"}, {"family": "Pinto", "given": "Rui", "initials": "R"}, {"family": "Andersson", "given": "Per-Ola", "initials": "PO"}], "type": "journal article", "published": "2016-08-00", "journal": {"volume": "57", "issn": "1029-2403", "issue": "8", "pages": "1814-1822", "title": "Leuk. Lymphoma", "issn-l": "1026-8022"}, "abstract": "The prognosis for diffuse large B-cell lymphoma (DLBCL) patients with early relapse or refractory disease is dismal. To determine if clinical outcome correlated to diverse serum metabolomic profiles, we used (1)H nuclear magnetic resonance (NMR) spectroscopy and compared two groups of DLBCL patients treated with immunochemotherapy: i) refractory/early relapse (REF/REL; n=27) and ii) long-term progression-free (CURED; n\u2009=\u200960). A supervised multivariate analysis showed a separation between the groups. Among discriminating metabolites higher in the REF/REL group were the amino acids lysine and arginine, the degradation product cadaverine and a compound in oxidative stress (2-hydroxybutyrate). In contrast, the amino acids aspartate, valine and ornithine, and a metabolite in the glutathione cycle, pyroglutamate, were higher in CURED patients. Together, our data indicate that NMR-based serum metabolomics can identify a signature for DLBCL patients with high-risk of failing immunochemotherapy, prompting for larger validating studies which could lead to more individualized treatment of this disease.", "doi": "10.3109/10428194.2016.1140164", "pmid": "26887805", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Support and Infrastructure": "Collaborative", "Bioinformatics (NBIS)": "Collaborative", "Swedish NMR Centre": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:51.012Z", "modified": "2025-10-17T13:04:00.417Z"}], "created": "2017-05-09T09:12:52.333Z", "modified": "2020-11-27T13:14:00.694Z"}