{"entity": "researcher", "timestamp": "2026-05-20T23:04:34.009Z", "family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y", "orcid": "0000-0001-5576-2115", "affiliations": ["Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/eb045b70f16140b6b6e69476d701012c.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/eb045b70f16140b6b6e69476d701012c"}}, "publications": [{"entity": "publication", "iuid": "92996e534bd244ad802a06aba40392a9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/92996e534bd244ad802a06aba40392a9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/92996e534bd244ad802a06aba40392a9"}}, "title": "A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.", "authors": [{"family": "Lysenkova Wiklander", "given": "Mariya", "initials": "M", "orcid": "0000-0002-0012-2310", "researcher": {"href": "https://publications.scilifelab.se/researcher/48850e5606b9470caa6b130286055388.json"}}, {"family": "Arvidsson", "given": "Gustav", "initials": "G", "orcid": "0000-0001-7396-1820", "researcher": {"href": "https://publications.scilifelab.se/researcher/29beb4f9dd8b460382eab4f916fc1072.json"}}, {"family": "Bunikis", "given": "Ignas", "initials": "I", "orcid": "0009-0008-8375-0451", "researcher": {"href": "https://publications.scilifelab.se/researcher/d2a9c139b7d64681a5712250d3cf63ff.json"}}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y", "orcid": "0000-0001-5576-2115", "researcher": {"href": "https://publications.scilifelab.se/researcher/eb045b70f16140b6b6e69476d701012c.json"}}, {"family": "Gezelius", "given": "Henrik", "initials": "H", "orcid": "0000-0002-6242-6344", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ad329767af94f9f9ad2c96771ff01d9.json"}}, {"family": "Bremer", "given": "Anna", "initials": "A"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.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": "2024-08-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "issn-l": "2575-1077", "volume": "7", "issue": "8", "pages": null}, "abstract": "The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) ETV6::RUNX1 translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including CDKN2A, PAX5, BTG1, VPREB1, and TBL1XR1, as well as the glucocorticoid receptor NR3C1 Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.", "doi": "10.26508/lsa.202302481", "pmid": "38777370", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Collaborative", "NGI Long read": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "NGI Short read": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11111970"}, {"db": "pii", "key": "7/8/e202302481"}], "notes": [], "created": "2024-08-02T11:59:07.510Z", "modified": "2025-02-28T14:23:51.125Z"}, {"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"}]}