{"entity": "researcher", "timestamp": "2026-07-14T03:37:12.571Z", "family": "Oksa", "given": "Laura", "initials": "L", "orcid": "0000-0003-4468-9877", "affiliations": ["Tampere Center for Child, Adolescent and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.", "Tampere University Hospital, Tays Cancer Center, Tampere, Finland."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/5526f0f44427441bb2a49f27f00b5683.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/5526f0f44427441bb2a49f27f00b5683"}}, "publications": [{"entity": "publication", "iuid": "2cac753de106445cbf229064ef982197", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2cac753de106445cbf229064ef982197.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2cac753de106445cbf229064ef982197"}}, "title": "Genomic determinants of therapy response in ETV6::RUNX1 leukemia.", "authors": [{"family": "Oksa", "given": "Laura", "initials": "L", "orcid": "0000-0003-4468-9877", "researcher": {"href": "https://publications.scilifelab.se/researcher/5526f0f44427441bb2a49f27f00b5683.json"}}, {"family": "Moisio", "given": "Sanni", "initials": "S", "orcid": "0009-0009-4446-015X", "researcher": {"href": "https://publications.scilifelab.se/researcher/de1112350e9042bfa9a8707d2c255bf5.json"}}, {"family": "Maqbool", "given": "Khurram", "initials": "K", "orcid": "0000-0003-2981-2582", "researcher": {"href": "https://publications.scilifelab.se/researcher/7ea06b85057744018f754c373fef3ca5.json"}}, {"family": "Kramer", "given": "Roger", "initials": "R"}, {"family": "Nikkil\u00e4", "given": "Atte", "initials": "A"}, {"family": "Jayasingha", "given": "Buddika", "initials": "B"}, {"family": "M\u00e4kinen", "given": "Artturi", "initials": "A", "orcid": "0000-0002-5521-9216", "researcher": {"href": "https://publications.scilifelab.se/researcher/74542e2da6d542d8a40b93b692c7b760.json"}}, {"family": "Foroughi-Asl", "given": "Hassan", "initials": "H"}, {"family": "Rounioja", "given": "Samuli", "initials": "S"}, {"family": "Suhonen", "given": "Janne", "initials": "J"}, {"family": "Krali", "given": "Olga", "initials": "O", "orcid": "0000-0002-6436-9531", "researcher": {"href": "https://publications.scilifelab.se/researcher/14a6e2f99d3b4758a10af78b93777779.json"}}, {"family": "Voutilainen", "given": "Miikka", "initials": "M", "orcid": "0000-0001-9367-3471", "researcher": {"href": "https://publications.scilifelab.se/researcher/390e63751ebb46e3873d801ce0c620d1.json"}}, {"family": "Lahnalampi", "given": "Mari", "initials": "M", "orcid": "0000-0003-4050-4935", "researcher": {"href": "https://publications.scilifelab.se/researcher/31d154912d9f4b9ca680f9d019035d46.json"}}, {"family": "Veps\u00e4l\u00e4inen", "given": "Kaisa", "initials": "K"}, {"family": "Huang", "given": "Sui", "initials": "S"}, {"family": "Duque-Afonso", "given": "Jesus", "initials": "J", "orcid": "0000-0002-8287-5673", "researcher": {"href": "https://publications.scilifelab.se/researcher/cc78f208850b4a999859f110a3850bfa.json"}}, {"family": "Hauer", "given": "Julia", "initials": "J", "orcid": "0000-0002-4058-3058", "researcher": {"href": "https://publications.scilifelab.se/researcher/9387a9c586f74172a9d251fff4d71637.json"}}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.json"}}, {"family": "Lohi", "given": "Olli", "initials": "O", "orcid": "0000-0001-9195-0797", "researcher": {"href": "https://publications.scilifelab.se/researcher/e11a59310dfc40e6a111367914fdba9e.json"}}, {"family": "Hein\u00e4niemi", "given": "Merja", "initials": "M", "orcid": "0000-0001-6190-3439", "researcher": {"href": "https://publications.scilifelab.se/researcher/be7efa5a7c9a4da18b397a07ebd8d9ec.json"}}], "type": "journal article", "published": "2025-09-00", "journal": {"title": "Leukemia", "issn": "1476-5551", "issn-l": "0887-6924", "volume": "39", "issue": "9", "pages": "2125-2139"}, "abstract": "ETV6::RUNX1 leukemia is the second most common subtype of childhood B cell acute lymphoblastic leukemia (B-ALL). Although it generally has a low relapse risk, a significant proportion of B-ALL relapses occur within this subtype due to its relatively high incidence. Measurable residual disease at the end of induction therapy is a well-established biomarker predicting treatment outcomes, while no genomic biomarkers are routinely applied in clinics. In this study, we used multiomic data from ETV6::RUNX1 leukemias to identify genomic features predictive of therapy response at disease presentation. In the deeply characterized sub-cohort we discovered that fast-responding cases frequently exhibited the APOBEC mutational signature and the gene expression signature of high cell cycle activity. In contrast, rearrangements of IGK genes were more frequent in slow responders. Additionally, response-related mutations were identified in transcriptional regulators and tumor suppressor genes (INTS1, NF1, TP53). Copy number analysis revealed that fast responders harbored more frequent deletions of chr12 p-arm, leading to transcriptomic changes affecting genes associated with induction therapy response (KRAS, FKBP4), while a shorter gain in chr12 was more common in slow responders. The identified genetic and transcriptomic markers of treatment sensitivity pave the way for improved disease classification at presentation, potentially improving clinical outcomes.", "doi": "10.1038/s41375-025-02683-7", "pmid": "40634509", "labels": {"NGI SNP genotyping": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service", "Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12380598"}, {"db": "pii", "key": "10.1038/s41375-025-02683-7"}], "notes": [], "created": "2025-09-08T11:39:55.025Z", "modified": "2025-11-18T20:46:15.313Z"}, {"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"}]}