{"entity": "researcher", "timestamp": "2026-08-20T20:52:54.763Z", "family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "affiliations": ["Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ff9fe255d640c0a2bbed0913fe208d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ff9fe255d640c0a2bbed0913fe208d"}}, "publications": [{"entity": "publication", "iuid": "afa87c9d58584b1caa68e7eac3b20e44", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/afa87c9d58584b1caa68e7eac3b20e44.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/afa87c9d58584b1caa68e7eac3b20e44"}}, "title": "Diagnostic Yield From a Nationwide Implementation of Precision Medicine for all Children With Cancer.", "authors": [{"family": "Wadensten", "given": "Elisabeth", "initials": "E"}, {"family": "Wessman", "given": "Sandra", "initials": "S", "orcid": "0000-0002-2035-2092", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d95567cab7404bdda2b61558c00ec446.json"}}, {"family": "Abel", "given": "Frida", "initials": "F", "orcid": "0000-0001-6958-4487", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/daddf59b269246e7aa22b214f4d8ddcd.json"}}, {"family": "Diaz De St\u00e5hl", "given": "Teresita", "initials": "T", "orcid": "0000-0001-5933-6623", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f642682a7cb4d648ecc3fa016e7569d.json"}}, {"family": "Tesi", "given": "Bianca", "initials": "B"}, {"family": "Orsmark Pietras", "given": "Christina", "initials": "C"}, {"family": "Arvidsson", "given": "Linda", "initials": "L"}, {"family": "Taylan", "given": "Fulya", "initials": "F", "orcid": "0000-0002-2907-0235", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc9bc4b87d0f43b9a0528e936921e5ae.json"}}, {"family": "Fransson", "given": "Susanne", "initials": "S", "orcid": "0000-0002-9713-3074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bd0dd92b148e4ec5aa0577e5c72cf912.json"}}, {"family": "Vogt", "given": "Hartmut", "initials": "H", "orcid": "0000-0001-6009-7789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/06785b3196a54727ba196337e3c30e95.json"}}, {"family": "Poluha", "given": "Anna", "initials": "A", "orcid": "0000-0002-4716-9423", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/39d693db32f545588e14bc02d3a8549e.json"}}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S"}, {"family": "Hellberg", "given": "Maria", "initials": "M"}, {"family": "Lagerstedt-Robinson", "given": "Kristina", "initials": "K"}, {"family": "Raj Somarajan", "given": "Praveen", "initials": "P", "orcid": "0009-0005-5981-2286", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/828d59fa698842e5a15445ea305ff31b.json"}}, {"family": "Samuelsson", "given": "Sofie", "initials": "S"}, {"family": "Orrsj\u00f6", "given": "Sara", "initials": "S", "orcid": "0009-0008-9223-3923", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0601b0c65ba4f24877ef146d0ceeffe.json"}}, {"family": "Maqbool", "given": "Khurram", "initials": "K", "orcid": "0000-0003-2981-2582", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ae3c7cd13b74462da918d013a96c7e3f.json"}}, {"family": "Henning", "given": "Karin", "initials": "K"}, {"family": "Strid", "given": "Tobias", "initials": "T"}, {"family": "Ek", "given": "Torben", "initials": "T", "orcid": "0000-0002-0518-983X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/850c29cc84154b34a326b6c6d8972441.json"}}, {"family": "Fagman", "given": "Henrik", "initials": "H"}, {"family": "Olsson Bontell", "given": "Thomas", "initials": "T"}, {"family": "Martinsson", "given": "Tommy", "initials": "T", "orcid": "0000-0002-9403-3123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b0a7ec78cfc1491d854e69db043391e0.json"}}, {"family": "Puls", "given": "Florian", "initials": "F", "orcid": "0000-0002-9841-4230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0290b39bf8df4d799729504d5ab0ae8a.json"}}, {"family": "Kogner", "given": "Per", "initials": "P", "orcid": "0000-0002-2202-9694", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aaa43812c53f4506be50ad29266dd237.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a4f538e838c483eb968174f2df89165.json"}}, {"family": "Pronk", "given": "Cornelis Jan", "initials": "CJ", "orcid": "0000-0002-0073-9660", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6f007476115a4a29b4859fbe84fad34d.json"}}, {"family": "Wille", "given": "Joakim", "initials": "J", "orcid": "0009-0008-6426-9830", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c13112bf82844897891fc8de8dacb6a2.json"}}, {"family": "Rosenquist", "given": "Richard", "initials": "R", "orcid": "0000-0002-0211-8788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dc038c13a8cb44bd93f3552ed250a179.json"}}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ff9fe255d640c0a2bbed0913fe208d.json"}}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}, {"family": "Sabel", "given": "Magnus", "initials": "M", "orcid": "0000-0002-3072-657X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb21eb962ff640199034b2dfa827d793.json"}}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U", "orcid": "0000-0001-5606-5442", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4e358be0b4243ffaf8526ff84dc31ed.json"}}, {"family": "Grillner", "given": "Pernilla", "initials": "P"}, {"family": "Nordgren", "given": "Ann", "initials": "A", "orcid": "0000-0003-3285-4281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02de5158a75e4fa9a5c7b8bf417a8fea.json"}}, {"family": "Ljungman", "given": "Gustaf", "initials": "G"}, {"family": "Sandgren", "given": "Johanna", "initials": "J", "orcid": "0000-0001-6776-2649", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14214db9a98248228cf8825461ad73fd.json"}}, {"family": "Gisselsson", "given": "David", "initials": "D", "orcid": "0000-0002-0301-426X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/43d7ebbd276e40eaae0dc9ea6d905d99.json"}}, {"family": "Genomic Medicine Sweden Childhood Cancer Working Group", "given": "", "initials": ""}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "JCO Precis Oncol", "issn": "2473-4284", "volume": "7", "pages": "e2300039", "issn-l": null}, "abstract": "Several studies have indicated that broad genomic characterization of childhood cancer provides diagnostically and/or therapeutically relevant information in selected high-risk cases. However, the extent to which such characterization offers clinically actionable data in a prospective broadly inclusive setting remains largely unexplored.\n\nWe implemented prospective whole-genome sequencing (WGS) of tumor and germline, complemented by whole-transcriptome sequencing (RNA-Seq) for all children diagnosed with a primary or relapsed solid malignancy in Sweden. Multidisciplinary molecular tumor boards were set up to integrate genomic data in the clinical decision process along with a medicolegal framework enabling secondary use of sequencing data for research purposes.\n\nDuring the study's first 14 months, 118 solid tumors from 117 patients were subjected to WGS, with complementary RNA-Seq for fusion gene detection in 52 tumors. There was no significant geographic bias in patient enrollment, and the included tumor types reflected the annual national incidence of pediatric solid tumor types. Of the 112 tumors with somatic mutations, 106 (95%) exhibited alterations with a clear clinical correlation. In 46 of 118 tumors (39%), sequencing only corroborated histopathological diagnoses, while in 59 cases (50%), it contributed to additional subclassification or detection of prognostic markers. Potential treatment targets were found in 31 patients (26%), most commonly ALK mutations/fusions (n = 4), RAS/RAF/MEK/ERK pathway mutations (n = 14), FGFR1 mutations/fusions (n = 5), IDH1 mutations (n = 2), and NTRK2 gene fusions (n = 2). In one patient, the tumor diagnosis was revised based on sequencing. Clinically relevant germline variants were detected in 8 of 94 patients (8.5%).\n\nUp-front, large-scale genomic characterization of pediatric solid malignancies provides diagnostically valuable data in the majority of patients also in a largely unselected cohort.", "doi": "10.1200/PO.23.00039", "pmid": "37384868", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10581599"}], "notes": [], "created": "2026-08-20T12:37:55.415Z", "modified": "2026-08-20T12:37:56.263Z"}, {"entity": "publication", "iuid": "3adaf7e2d1d14eb7bb027bb18463c836", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3adaf7e2d1d14eb7bb027bb18463c836.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3adaf7e2d1d14eb7bb027bb18463c836"}}, "title": "Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples.", "authors": [{"family": "Mirzazadeh", "given": "Reza", "initials": "R"}, {"family": "Andrusivova", "given": "Zaneta", "initials": "Z"}, {"family": "Larsson", "given": "Ludvig", "initials": "L", "orcid": "0000-0003-4209-2911", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/36ad34c94b64432ab74d61fbc6d16905.json"}}, {"family": "Newton", "given": "Phillip T", "initials": "PT", "orcid": "0000-0003-2142-1798", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e490d4b3da4741b490395399f1b8c1.json"}}, {"family": "Galicia", "given": "Leire Alonso", "initials": "LA"}, {"family": "Abalo", "given": "Xes\u00fas M", "initials": "XM", "orcid": "0000-0002-1643-0705", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccb96c37f02b45d290b89f5b615052df.json"}}, {"family": "Avijgan", "given": "Mahtab", "initials": "M"}, {"family": "Kvastad", "given": "Linda", "initials": "L", "orcid": "0000-0001-5869-3485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/384e05b0be164cabb26bc3ce544742db.json"}}, {"family": "Denadai-Souza", "given": "Alexandre", "initials": "A", "orcid": "0000-0003-0385-1321", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e4f2a0f8d4d6470d8cf48d3a27b19b78.json"}}, {"family": "Stakenborg", "given": "Nathalie", "initials": "N", "orcid": "0000-0002-6229-0045", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d107940932374682934e1ee3860c20f2.json"}}, {"family": "Firsova", "given": "Alexandra B", "initials": "AB"}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Jurek", "given": "Aleksandra", "initials": "A"}, {"family": "Schultz", "given": "Niklas", "initials": "N"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ff9fe255d640c0a2bbed0913fe208d.json"}}, {"family": "Samakovlis", "given": "Christos", "initials": "C"}, {"family": "Boeckxstaens", "given": "Guy", "initials": "G", "orcid": "0000-0001-8267-5797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9a5224f2c1014dab80a2e50af25d7a18.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}], "type": "journal article", "published": "2023-01-31", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "509", "issn-l": "2041-1723"}, "abstract": "Spatially resolved transcriptomics has enabled precise genome-wide mRNA expression profiling within tissue sections. The performance of methods targeting the polyA tails of mRNA relies on the availability of specimens with high RNA quality. Moreover, the high cost of currently available spatial resolved transcriptomics assays requires a careful sample screening process to increase the chance of obtaining high-quality data. Indeed, the upfront analysis of RNA quality can show considerable variability due to sample handling, storage, and/or intrinsic factors. We present RNA-Rescue Spatial Transcriptomics (RRST), a workflow designed to improve mRNA recovery from fresh frozen specimens with moderate to low RNA quality. First, we provide a benchmark of RRST against the standard Visium spatial gene expression protocol on high RNA quality samples represented by mouse brain and prostate cancer samples. Then, we test the RRST protocol on tissue sections collected from five challenging tissue types, including human lung, colon, small intestine, pediatric brain tumor, and mouse bone/cartilage. In total, we analyze 52 tissue sections and demonstrate that RRST is a versatile, powerful, and reproducible protocol for fresh frozen specimens of different qualities and origins.", "doi": "10.1038/s41467-023-36071-5", "pmid": "36720873", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9889806"}, {"db": "pii", "key": "10.1038/s41467-023-36071-5"}], "notes": [], "created": "2026-08-20T08:52:29.319Z", "modified": "2026-08-20T08:52:29.623Z"}, {"entity": "publication", "iuid": "c9632adfafb44638a2e85c43a95b2e3f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c9632adfafb44638a2e85c43a95b2e3f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c9632adfafb44638a2e85c43a95b2e3f"}}, "title": "Correction to: SFRP2 induces a mesenchymal subtype transition by suppression of SOX2 in glioblastoma.", "authors": [{"family": "Guo", "given": "Min", "initials": "M", "orcid": "0000-0002-2291-1230", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/241d481edfb641f3ac83b9f3a7396381.json"}}, {"family": "Goudarzi", "given": "Kaveh M", "initials": "KM"}, {"family": "Abedi", "given": "Shiva", "initials": "S"}, {"family": "Pieber", "given": "Melanie", "initials": "M"}, {"family": "Sj\u00f6berg", "given": "Elin", "initials": "E", "orcid": "0000-0002-8799-4874", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/08c2f55f252d484c938584d3a03b3dde.json"}}, {"family": "Behnan", "given": "Jinan", "initials": "J", "orcid": "0000-0001-5780-0971", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c246b5b7bf5e4099a2d8b268fcc5e44b.json"}}, {"family": "Zhang", "given": "Xing-Mei", "initials": "XM"}, {"family": "Harris", "given": "Robert A", "initials": "RA"}, {"family": "Bartek", "given": "Jiri", "initials": "J"}, {"family": "Lindstr\u00f6m", "given": "Mikael S", "initials": "MS", "orcid": "0000-0003-1148-8497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/069306b8ab85484db417a144c0a7d325.json"}}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ff9fe255d640c0a2bbed0913fe208d.json"}}, {"family": "H\u00e4gerstrand", "given": "Daniel", "initials": "D", "orcid": "0000-0001-7270-0776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3221dc6f79b4d77bea303ab5e2b6fd2.json"}}], "type": "published erratum", "published": "2021-08-00", "journal": {"title": "Oncogene", "issn": "1476-5594", "volume": "40", "issue": "32", "pages": "5153", "issn-l": "0950-9232"}, "abstract": null, "doi": "10.1038/s41388-021-01929-9", "pmid": "34257430", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8363096"}, {"db": "pii", "key": "10.1038/s41388-021-01929-9"}], "notes": [], "created": "2026-08-20T08:48:31.302Z", "modified": "2026-08-20T08:48:31.517Z"}, {"entity": "publication", "iuid": "853fe45e2b8946ae9102a32e2959eb18", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/853fe45e2b8946ae9102a32e2959eb18.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/853fe45e2b8946ae9102a32e2959eb18"}}, "title": "The spatial RNA integrity number assay for in situ evaluation of transcriptome quality.", "authors": [{"family": "Kvastad", "given": "Linda", "initials": "L", "orcid": "0000-0001-5869-3485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/384e05b0be164cabb26bc3ce544742db.json"}}, {"family": "Carlberg", "given": "Konstantin", "initials": "K"}, {"family": "Larsson", "given": "Ludvig", "initials": "L"}, {"family": "Villacampa", "given": "Eva Gracia", "initials": "EG", "orcid": "0000-0003-0353-2101", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35a5dafa84024d5e82eb8f14632a3cf6.json"}}, {"family": "Stuckey", "given": "Alexander", "initials": "A"}, {"family": "Stenbeck", "given": "Linnea", "initials": "L", "orcid": "0000-0002-0210-7886", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b2de0dae49f4ab39d45281316703ca9.json"}}, {"family": "Mollbrink", "given": "Annelie", "initials": "A"}, {"family": "Zamboni", "given": "Margherita", "initials": "M", "orcid": "0000-0003-0664-4707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7dd167b1cb344898bccd0d60315db61c.json"}}, {"family": "Magnusson", "given": "Jens Peter", "initials": "JP", "orcid": "0000-0002-3928-8959", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc0f61d71be8461c8ad475e14311e7ba.json"}}, {"family": "Basmaci", "given": "Elisa", "initials": "E"}, {"family": "Shamikh", "given": "Alia", "initials": "A"}, {"family": "Prochazka", "given": "Gabriela", "initials": "G"}, {"family": "Schaupp", "given": "Anna-Lena", "initials": "AL"}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42b9688e2b634ae5b40b28b2ff23f9ee.json"}}, {"family": "Fugger", "given": "Lars", "initials": "L"}, {"family": "Nist\u00e9r", "given": "Monica", "initials": "M", "orcid": "0000-0002-1261-3790", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1ff9fe255d640c0a2bbed0913fe208d.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d9fa47767cd14ef2b9528c8b998cf095.json"}}], "type": "evaluation study", "published": "2021-01-08", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "4", "issue": "1", "pages": "57", "issn-l": "2399-3642"}, "abstract": "The RNA integrity number (RIN) is a frequently used quality metric to assess the completeness of rRNA, as a proxy for the corresponding mRNA in a tissue. Current methods operate at bulk resolution and provide a single average estimate for the whole sample. Spatial transcriptomics technologies have emerged and shown their value by placing gene expression into a tissue context, resulting in transcriptional information from all tissue regions. Thus, the ability to estimate RNA quality in situ has become of utmost importance to overcome the limitation with a bulk rRNA measurement. Here we show a new tool, the spatial RNA integrity number (sRIN) assay, to assess the rRNA completeness in a tissue wide manner at cellular resolution. We demonstrate the use of sRIN to identify spatial variation in tissue quality prior to more comprehensive spatial transcriptomics workflows.", "doi": "10.1038/s42003-020-01573-1", "pmid": "33420318", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7794352"}, {"db": "pii", "key": "10.1038/s42003-020-01573-1"}], "notes": [], "created": "2026-08-20T09:24:57.181Z", "modified": "2026-08-20T09:24:57.385Z"}]}