{"entity": "researcher", "timestamp": "2026-09-23T21:54:42.240Z", "family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "affiliations": ["Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.", "Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e5a7c4ae89f441ca0fa14238aa9511b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e5a7c4ae89f441ca0fa14238aa9511b"}}, "publications": [{"entity": "publication", "iuid": "fabb8cc4033742df8dba5f2c6b5f8a32", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fabb8cc4033742df8dba5f2c6b5f8a32.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fabb8cc4033742df8dba5f2c6b5f8a32"}}, "title": "The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma.", "authors": [{"family": "Krynina", "given": "Olha", "initials": "O", "orcid": "0009-0006-6911-557X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/517b17142f0a4e2692f81a14ab9958b2.json"}}, {"family": "de St\u00e5hl", "given": "Teresita D\u00edaz", "initials": "TD"}, {"family": "Jylh\u00e4", "given": "Cecilia", "initials": "C"}, {"family": "Arthur", "given": "Cecilia", "initials": "C"}, {"family": "Giraud", "given": "Geraldine", "initials": "G"}, {"family": "Nyman", "given": "Per", "initials": "P"}, {"family": "Fritzberg", "given": "Anders", "initials": "A"}, {"family": "Sandgren", "given": "Johanna", "initials": "J"}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e5a7c4ae89f441ca0fa14238aa9511b.json"}}, {"family": "Sandvik", "given": "Ulrika", "initials": "U"}], "type": "journal article", "published": "2024-01-24", "journal": {"title": "Neurooncol Adv", "issn": "2632-2498", "volume": "6", "issue": "1", "pages": "vdae008", "issn-l": null}, "abstract": "Low-grade gliomas (LGGs) represent children's most prevalent central nervous system tumor, necessitating molecular profiling to diagnose and determine the most suitable treatment. Developing highly sensitive screening techniques for liquid biopsy samples is particularly beneficial, as it enables the early detection and molecular characterization of tumors with minimally invasive samples.\n\nWe examined CSF and plasma samples from patients with pilocytic astrocytoma (PA) using custom multiplexed droplet digital polymerase chain reaction (ddPCR) assays based on whole genome sequencing data. These assays included a screening test to analyze BRAF duplication and a targeted assay for the detection of patient-specific KIAA1549::BRAF fusion junction sequences or single nucleotide variants.\n\nOur findings revealed that 5 out of 13 individual cerebrospinal fluid (CSF) samples tested positive for circulating tumor DNA (ctDNA). Among these cases, 3 exhibited the KIAA1549::BRAF fusion, which was detected through copy number variation (CNV) analysis (n = 1) or a fusion-specific probe (n = 2), while 1 case each displayed the BRAF V600E mutation and the FGFR1 N577K mutation. Additionally, a quantitative analysis of cell-free DNA (cfDNA) concentrations in PA CSF samples showed that most cases had low cfDNA levels, below the limit of detection of our assay (<1.9 ng).\n\nWhile CNV analysis of CSF samples from LGGs still has some limitations, it has the potential to serve as a valuable complementary tool. Furthermore, it can also be multiplexed with other aberrations, for example, to the BRAF V600 test, to provide important insights into the molecular characteristics of LGGs.", "doi": "10.1093/noajnl/vdae008", "pmid": "38371226", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10874216"}, {"db": "pii", "key": "vdae008"}], "notes": [], "created": "2026-09-23T11:25:50.187Z", "modified": "2026-09-23T11:25:50.324Z"}, {"entity": "publication", "iuid": "c49d024a51654ae79653a603c99a7379", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c49d024a51654ae79653a603c99a7379.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c49d024a51654ae79653a603c99a7379"}}, "title": "Sensitive Detection of Cell-Free Tumour DNA Using Optimised Targeted Sequencing Can Predict Prognosis in Gastro-Oesophageal Cancer.", "authors": [{"family": "Wallander", "given": "Karin", "initials": "K", "orcid": "0000-0001-8166-9678", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2d3f581341864b9696eb87f2eb139335.json"}}, {"family": "Haider", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-0759-3932", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef882ad3a8d74e1787677446c20045ae.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b323a794f5054c77b32cc4452f45df32.json"}}, {"family": "Foroughi-Asl", "given": "Hassan", "initials": "H"}, {"family": "Gellerbring", "given": "Anna", "initials": "A"}, {"family": "Lyander", "given": "Anna", "initials": "A"}, {"family": "Chozhan", "given": "Athithyan", "initials": "A"}, {"family": "Cuba Gyllensten", "given": "Ollanta", "initials": "O"}, {"family": "H\u00e4gglund", "given": "Moa", "initials": "M", "orcid": "0000-0003-3765-4342", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c2a00a2a4fb94d278b2c71e1c5160469.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a4f538e838c483eb968174f2df89165.json"}}, {"family": "Nordenskj\u00f6ld", "given": "Magnus", "initials": "M"}, {"family": "Lindblad", "given": "Mats", "initials": "M"}, {"family": "Tham", "given": "Emma", "initials": "E", "orcid": "0000-0001-6079-164X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e5a7c4ae89f441ca0fa14238aa9511b.json"}}], "type": "journal article", "published": "2023-02-11", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "volume": "15", "issue": "4", "issn-l": "2072-6694"}, "abstract": "In this longitudinal study, cell-free tumour DNA (a liquid biopsy) from plasma was explored as a prognostic biomarker for gastro-oesophageal cancer. Both tumour-informed and tumour-agnostic approaches for plasma variant filtering were evaluated in 47 participants. This was possible through sequencing of DNA from tissue biopsies from all participants and cell-free DNA from plasma sampled before and after surgery (n = 42), as well as DNA from white blood cells (n = 21) using a custom gene panel with and without unique molecular identifiers (UMIs). A subset of the plasma samples (n = 12) was also assayed with targeted droplet digital PCR (ddPCR). In 17/31 (55%) diagnostic plasma samples, tissue-verified cancer-associated variants could be detected by the gene panel. In the tumour-agnostic approach, 26 participants (59%) had cancer-associated variants, and UMIs were necessary to filter the true variants from the technical artefacts. Additionally, clonal haematopoietic variants could be excluded using the matched white blood cells or follow-up plasma samples. ddPCR detected its targets in 10/12 (83%) and provided an ultra-sensitive method for follow-up. Detectable cancer-associated variants in plasma correlated to a shorter overall survival and shorter time to progression, with a significant correlation for the tumour-informed approaches. In summary, liquid biopsy gene panel sequencing using a tumour-agnostic approach can be applied to all patients regardless of the presence of a tissue biopsy, although this requires UMIs and the exclusion of clonal haematopoietic variants. However, if sequencing data from tumour biopsies are available, a tumour-informed approach improves the value of cell-free tumour DNA as a negative prognostic biomarker in gastro-oesophageal cancer patients.", "doi": "10.3390/cancers15041160", "pmid": "36831507", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9954085"}, {"db": "pii", "key": "cancers15041160"}], "notes": [], "created": "2026-09-23T12:15:49.447Z", "modified": "2026-09-23T12:15:49.595Z"}]}