{"entity": "journal", "iuid": "3cae9b4d1bef493c943b8ff9f07da1d4", "timestamp": "2026-07-11T23:34:14.015Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Cancer%20Genet.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Cancer%20Genet"}}, "title": "Cancer Genet", "issn": "2210-7770", "issn-l": "2210-7762", "publications_count": 2, "publications": [{"entity": "publication", "iuid": "8aeb03e392624ccd8794e0fcc8e0eaf3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8aeb03e392624ccd8794e0fcc8e0eaf3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8aeb03e392624ccd8794e0fcc8e0eaf3"}}, "title": "Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development.", "authors": [{"family": "K\u00f6ster", "given": "Jan", "initials": "J"}, {"family": "Arbajian", "given": "Elsa", "initials": "E"}, {"family": "Viklund", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Hofvander", "given": "Jakob", "initials": "J"}, {"family": "Haglund", "given": "Felix", "initials": "F"}, {"family": "Bauer", "given": "Henrik", "initials": "H"}, {"family": "Magnusson", "given": "Linda", "initials": "L"}, {"family": "Mandahl", "given": "Nils", "initials": "N"}, {"family": "Mertens", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2020-02-00", "journal": {"title": "Cancer Genet", "issn": "2210-7762", "volume": "241", "issue": null, "pages": "34-41", "issn-l": null}, "abstract": "The dermatofibrosarcoma protuberans family of tumors (DPFT) comprises cutaneous soft tissue neoplasms associated with aberrant PDGFBR signaling, typically through a COL1A1-PDGFB fusion. The aim of the present study was to obtain a better understanding of the chromosomal origin of this fusion and to assess the spectrum of secondary mutations at the chromosome and nucleotide levels. We thus investigated 42 tumor samples from 35 patients using chromosome banding, fluorescence in situ hybridization, single nucleotide polymorphism arrays, and/or massively parallel sequencing (gene panel, whole exome and transcriptome sequencing) methods. We confirmed the age-associated differences in the origin of the COL1A1-PDGFB fusion and could show that it in most cases must arise after DNA synthesis, i.e., in the S or G2 phase of the cell cycle. Whereas there was a non-random pattern of secondary chromosomal rearrangements, single nucleotide variants seem to have little impact on tumor progression. No clear genomic differences between low-grade and high-grade DPFT were found, but the number of chromosomes and chromosomal imbalances as well as the frequency of 9p deletions all tended to be greater among the latter. Gene expression profiling of tumors with COL1A1-PDGFB fusions associated with unbalanced translocations or ring chromosomes identified several transcriptionally up-regulated genes in the amplified regions of chromosomes 17 and 22, including TBX2, PRKCA, MSI2, SOX9, SOX10, and PRAME.", "doi": "10.1016/j.cancergen.2019.12.001", "pmid": "31870844", "labels": {"Clinical Genomics Lund": null, "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": null}, "xrefs": [{"db": "pii", "key": "S2210-7762(19)30319-9"}], "notes": [], "created": "2020-12-02T03:51:59.521Z", "modified": "2024-01-16T13:48:42.988Z"}, {"entity": "publication", "iuid": "3fbc0fe2d60b4395bfbd219d0da586df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3fbc0fe2d60b4395bfbd219d0da586df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3fbc0fe2d60b4395bfbd219d0da586df"}}, "title": "Investigation of a putative melanoma susceptibility locus at chromosome 3q29.", "authors": [{"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "J\u00f6nsson", "given": "G\u00f6ran", "initials": "G"}, {"family": "Enerb\u00e4ck", "given": "Charlotta", "initials": "C"}, {"family": "Appelqvist", "given": "Frida", "initials": "F"}, {"family": "Olsson", "given": "H\u00e5kan", "initials": "H"}, {"family": "Ingvar", "given": "Christian", "initials": "C"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "H\u00f6iom", "given": "Veronica", "initials": "V"}], "type": "journal article", "published": "2014-03-00", "journal": {"volume": "207", "issn": "2210-7762", "issue": "3", "pages": "70-74", "title": "Cancer Genet", "issn-l": null}, "abstract": "Malignant melanoma, the most fatal form of skin cancer, is currently increasing in incidence in many populations. Approximately 10% of all cases occur in families with an inherited predisposition for melanoma. In Sweden, only a minor portion of such melanoma families carry a mutation in the known melanoma gene CDKN2A, and there is a need to identify additional melanoma susceptibility genes. In a recently performed genome-wide linkage screen, novel loci with suggestive evidence of linkage to melanoma were detected. In this study, we have further analyzed one region on chromosome 3q29. In all, 89 affected and 15 nonaffected family members from 42 melanoma-prone families were genotyped for 34 genetic markers. In a pooled linkage analysis of all 42 families, we detected significant evidence of linkage, with a maximum heterogeneity logarithm of odds (HLOD) score of 3.1 with 83% of the families contributing to the linkage score. The minimum critical region of linkage (defined by a 1LOD score support interval) maps to chromosome 3q29, spans 3.5 Mb of genomic sequence, and harbors 44 identified genes. Sequence variants within this region have previously been associated with cancer susceptibility. This study reports the presence of a putative novel melanoma susceptibility locus in the Swedish population, a finding that needs to be replicated in an independent study on other individuals with familial melanoma. Sequencing of genes in the region may identify novel melanoma-associated mutations.", "doi": "10.1016/j.cancergen.2014.02.007", "pmid": "24721441", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S2210-7762(14)00040-4"}], "notes": [], "created": "2017-05-04T14:58:27.073Z", "modified": "2020-01-21T13:56:01.841Z"}], "created": "2017-05-09T09:12:03.693Z", "modified": "2020-11-27T13:14:09.562Z"}