3641bbb4-991f-45f9-a762-c57838a4f08c - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005305 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Patients with CYLD cutaneous syndrome (CCS; syn. Brooke-Spiegler syndrome) carry germline mutations in the tumor suppressor CYLD and develop multiple skin tumors with diverse histophenotypes. We comprehensively profiled the genomic landscape of 42 benign and malignant tumors across 13 individuals from four multigenerational families. Novel recurrent mutations were found in epigenetic modifiers DNMT3A and BCOR in 29% of benign tumors. Multi-level and microdissected sampling strikingly reveal that many clones with different DNMT3A mutations exist in these benign tumors, suggesting that intra-tumor heterogeneity is common. Integrated genomic, methylation and transcriptomic profiling in selected tumours suggest that isoform specific DNMT3A2 mutations are associated with dysregulated Wnt/ß-catenin pathway signaling. Phylogenetic and mutational signature analyses confirm cylindroma pulmonary metastases from primary skin tumours. These findings add novel dimensions to existing paradigms of cutaneous tumorigenesis and metastasis.
| EGAS00001003800 | EGA
Project description:Patients with CYLD cutaneous syndrome (CCS; syn. Brooke-Spiegler syndrome) carry germline mutations in the tumor suppressor CYLD and develop multiple skin tumors with diverse histophenotypes. We comprehensively profiled the genomic landscape of 42 benign and malignant tumors across 13 individuals from four multigenerational families. Novel recurrent mutations were found in epigenetic modifiers DNMT3A and BCOR in 29% of benign tumors. Multi-level and microdissected sampling strikingly reveal that many clones with different DNMT3A mutations exist in these benign tumors, suggesting that intra-tumor heterogeneity is common. Integrated genomic, methylation and transcriptomic profiling in selected tumours suggest that isoform specific DNMT3A2 mutations are associated with dysregulated Wnt/ß-catenin pathway signaling. Phylogenetic and mutational signature analyses confirm cylindroma pulmonary metastases from primary skin tumours. These findings add novel dimensions to existing paradigms of cutaneous tumorigenesis and metastasis.
| EGAS00001003841 | EGA
Project description:Patients with CYLD cutaneous syndrome (CCS; syn. Brooke-Spiegler syndrome) carry germline mutations in the tumor suppressor CYLD and develop multiple skin tumors with diverse histophenotypes. We comprehensively profiled the genomic landscape of 42 benign and malignant tumors across 13 individuals from four multigenerational families. Novel recurrent mutations were found in epigenetic modifiers DNMT3A and BCOR in 29% of benign tumors. Multi-level and microdissected sampling strikingly reveal that many clones with different DNMT3A mutations exist in these benign tumors, suggesting that intra-tumor heterogeneity is common. Integrated genomic, methylation and transcriptomic profiling in selected tumours suggest that isoform specific DNMT3A2 mutations are associated with dysregulated Wnt/ß-catenin pathway signaling. Phylogenetic and mutational signature analyses confirm cylindroma pulmonary metastases from primary skin tumours. These findings add novel dimensions to existing paradigms of cutaneous tumorigenesis and metastasis.
| EGAS00001003839 | EGA
Project description:Patients with CYLD cutaneous syndrome (CCS; syn. Brooke-Spiegler syndrome) carry germline mutations in the tumor suppressor CYLD and develop multiple skin tumors with diverse histophenotypes. We comprehensively profiled the genomic landscape of 42 benign and malignant tumors across 13 individuals from four multigenerational families. Novel recurrent mutations were found in epigenetic modifiers DNMT3A and BCOR in 29% of benign tumors. Multi-level and microdissected sampling strikingly reveal that many clones with different DNMT3A mutations exist in these benign tumors, suggesting that intra-tumor heterogeneity is common. Integrated genomic, methylation and transcriptomic profiling in selected tumours suggest that isoform specific DNMT3A2 mutations are associated with dysregulated Wnt/ß-catenin pathway signaling. Phylogenetic and mutational signature analyses confirm cylindroma pulmonary metastases from primary skin tumours. These findings add novel dimensions to existing paradigms of cutaneous tumorigenesis and metastasis.
| EGAS00001003840 | EGA
Project description:Analysis of the combined dataset of normal skin, actinic keratosis and cutaneous squamous cell carcinoma (cSCC) previously submitted in (GSE45216) at genomic/transciptomic level. We identified potential cSCC driver genes significantly mutated and upregulated in cSCC relative to normal skin.
2018-06-14 | GSE98774 | GEO
Project description:Solar urticaria (SU) is clinically characterised by rapid onset sunlight-induced urticaria, but its cutaneous pathophysiology is not well understood. The aim of this study was to investigate cutaneous cellular and molecular events in the evolution of SU responses following solar simulated ultraviolet radiation (SSR) exposure, and compare with responses in healthy controls (HC). Cutaneous biopsies were taken from unexposed skin and from skin exposed to a single low (physiological) dose of SSR, at 30 minutes, 3 hours and 24 hours post-exposure, in n=6 SU patients and n=6 HC. Biopsies were assessed by immunohistochemistry (n=6 SU, n=6 HC) and RNA-sequencing analysis (n=4 SU, n=4 HC). This dataset contains RNAseq data from the SU patients.
2024-03-18 | E-MTAB-12219 | biostudies-arrayexpress
Project description:The dataset includes samples of 19 patients with cutaneous melanoma, 11 samples from donors with benign nevi as well as 11 control skin samples. All DNAs were derived from FFPE material. The cutaneous melanoma and benign nevi samples were macrodissected prior to DNA isolation. For methylation profiling the MethylationEPIC array from Illumina was used.
2024-05-15 | E-MTAB-14045 | biostudies-arrayexpress
Project description:The project aims to look at mutational signatures in a rare inherited skin tumour syndrome called CYLD cutaneous syndrome. These patients develop multiple skin tumours that are seen at sun exposed and sun protected sites. We plan to carry out WGS on carefully curated tumours from such patients. We then plan to analyse this data for mutational signatures, comparing this between sun exposed and sun protected sites.
| EGAS00001002521 | EGA
Project description:Comparison of transcriptomes between CYLD defective skin tumours and perilesional skin
2011-08-16 | E-MTAB-352 | biostudies-arrayexpress
Project description:This dataset contains fibroblasts from different genital and extragenital regions, mostly from 46,XY individuals. Due to proven androgen receptor gene mutations, several individuals have varying degrees of undervirilization of the external genitalia ranging from complete androgen insensitivity syndrome (CAIS) to partial androgen insensitivity syndrome (PAIS). CAIS is a completely female person despite a 46,XY karyotype. AIS-3 individuals have ambigous external genitalia. AIS-4 means predominantly female (clitoral enlargement), AIS-2 means predominantly male (hypospadias). It is important for this experiment set, that it contains data from 3 differet independent datasets that are not directly cmparable with each other. This is because of different reference RNAs and different glass slides. The particular normalization procedure is described in the paper accompanying this dataset. Only then, all arrays are allowed to be clustered together. Dataset 2 and 3 have "DS-2" and "DS-3" in their experiment names. All other experiments belong to dataset 1. A cell type comparison design experiment design type compares cells of different type for example different cell lines. Disease State: normal male, normal female or ambiguous external genitalia according to grading scheme by Sinnecker et al. Cell Line: fibroblast cell lines from different regions of the genital skin, some from extragenital skin Sex/Mating type: 46,XY or 46,XX karyotype Computed
2010-06-25 | E-GEOD-6796 | biostudies-arrayexpress