{"entity": "researcher", "timestamp": "2026-07-20T23:05:15.237Z", "family": "Haider", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-0759-3932", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/4084e066170543e699dd116c8e7c05df.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/4084e066170543e699dd116c8e7c05df"}}, "publications": [{"entity": "publication", "iuid": "8f4af9fc1bd845f8bc456a6a13cd3e34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f4af9fc1bd845f8bc456a6a13cd3e34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f4af9fc1bd845f8bc456a6a13cd3e34"}}, "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.scilifelab.se/researcher/db174787efd74dc1b84f1bf56b74a22d.json"}}, {"family": "Haider", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-0759-3932", "researcher": {"href": "https://publications.scilifelab.se/researcher/4084e066170543e699dd116c8e7c05df.json"}}, {"family": "Jeggari", "given": "Ashwini", "initials": "A", "orcid": "0000-0002-7155-9050", "researcher": {"href": "https://publications.scilifelab.se/researcher/083131be9eab46df9c789fb018316dff.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.scilifelab.se/researcher/b3de7b5aa952454e81d0ff55056c33a0.json"}}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications.scilifelab.se/researcher/cba024b2e3c347f6b981922d984ad2d6.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.scilifelab.se/researcher/6689dd9aff584082a57398141a538111.json"}}], "type": "journal article", "published": "2023-02-11", "journal": {"title": "Cancers (Basel)", "issn": "2072-6694", "issn-l": "2072-6694", "volume": "15", "issue": "4", "pages": null}, "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": {"Clinical Genomics Stockholm": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9954085"}, {"db": "pii", "key": "cancers15041160"}], "notes": [], "created": "2023-11-22T21:52:05.588Z", "modified": "2023-11-22T21:52:13.584Z"}, {"entity": "publication", "iuid": "363b739d24b643d29fe3d400f87f1af9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/363b739d24b643d29fe3d400f87f1af9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/363b739d24b643d29fe3d400f87f1af9"}}, "title": "DNA methylation and copy number variation profiling of T-cell lymphoblastic leukemia and lymphoma.", "authors": [{"family": "Haider", "given": "Zahra", "initials": "Z", "orcid": "0000-0002-0759-3932", "researcher": {"href": "https://publications.scilifelab.se/researcher/4084e066170543e699dd116c8e7c05df.json"}}, {"family": "Landfors", "given": "Mattias", "initials": "M"}, {"family": "Golovleva", "given": "Irina", "initials": "I", "orcid": "0000-0001-8741-0616", "researcher": {"href": "https://publications.scilifelab.se/researcher/b12b365ee27e430c9d17c5c07c762e28.json"}}, {"family": "Erlanson", "given": "Martin", "initials": "M"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "Fl\u00e6gstad", "given": "Trond", "initials": "T"}, {"family": "Kanerva", "given": "Jukka", "initials": "J"}, {"family": "Nor\u00e9n-Nystr\u00f6m", "given": "Ulrika", "initials": "U"}, {"family": "Hultdin", "given": "Magnus", "initials": "M"}, {"family": "Degerman", "given": "Sofie", "initials": "S", "orcid": "0000-0002-2783-0712", "researcher": {"href": "https://publications.scilifelab.se/researcher/8611162e883645f59195c4221199967f.json"}}], "type": "journal article", "published": "2020-04-28", "journal": {"title": "Blood Cancer J", "issn": "2044-5385", "issn-l": "2044-5385", "volume": "10", "issue": "4", "pages": "45"}, "abstract": "Despite having common overlapping immunophenotypic and morphological features, T-cell lymphoblastic leukemia (T-ALL) and lymphoma (T-LBL) have distinct clinical manifestations, which may represent separate diseases. We investigated and compared the epigenetic and genetic landscape of adult and pediatric T-ALL (n = 77) and T-LBL (n = 15) patient samples by high-resolution genome-wide DNA methylation and Copy Number Variation (CNV) BeadChip arrays. DNA methylation profiling identified the presence of CpG island methylator phenotype (CIMP) subgroups within both pediatric and adult T-LBL and T-ALL. An epigenetic signature of 128 differentially methylated CpG sites was identified, that clustered T-LBL and T-ALL separately. The most significant differentially methylated gene loci included the SGCE/PEG10 shared promoter region, previously implicated in lymphoid malignancies. CNV analysis confirmed overlapping recurrent aberrations between T-ALL and T-LBL, including 9p21.3 (CDKN2A/CDKN2B) deletions. A significantly higher frequency of chromosome 13q14.2 deletions was identified in T-LBL samples (36% in T-LBL vs. 0% in T-ALL). This deletion, encompassing the RB1, MIR15A and MIR16-1 gene loci, has been reported as a recurrent deletion in B-cell malignancies. Our study reveals epigenetic and genetic markers that can distinguish between T-LBL and T-ALL, and deepen the understanding of the biology underlying the diverse disease localization.", "doi": "10.1038/s41408-020-0310-9", "pmid": "32345961", "labels": {"Clinical Genomics Ume\u00e5": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41408-020-0310-9"}, {"db": "pmc", "key": "PMC7188684"}], "notes": [], "created": "2021-06-18T12:10:04.144Z", "modified": "2021-12-08T14:16:53.085Z"}]}