Genetic analysis of desmoplastic melanoma
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA293389 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR2343650.fastq.gz | Fastqsanger.gz | |||
| SRR2343650_1.fastq.gz | Fastqsanger.gz | |||
| SRR2343650_2.fastq.gz | Fastqsanger.gz |
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Project description:High resolution aCGH was performed on 10 primary Desmoplastic Melanomas (DMs). DMs are a rare subtype of melanoma known for their pronounced desmoplastic stroma and spindled melanocytes. 10 samples were hybridized to Agilent 1 Million feature two color arrays as compared to a panel of normal male DNA. 6 samples were hybridized to Agilent 244K feature two color arrays as compared to a panel of normal male DNA. 34 samples were hybridized to Agilent 180K feature two color arrays as compared to a panel of normal male DNA. 50 unique primary tumors were hybridized compared to normal male DNA.
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Project description:High resolution aCGH was performed on 10 primary Desmoplastic Melanomas (DMs). DMs are a rare subtype of melanoma known for their pronounced desmoplastic stroma and spindled melanocytes. 10 samples were hybridized to Agilent 1 Million feature two color arrays as compared to a panel of normal male DNA. 6 samples were hybridized to Agilent 244K feature two color arrays as compared to a panel of normal male DNA. 34 samples were hybridized to Agilent 180K feature two color arrays as compared to a panel of normal male DNA.
2015-08-07 | GSE55150 | GEO
Project description:<p>Desmoplastic melanoma is an infrequent variant of melanoma with sarcomatous histology, distinct clinical behavior, and unknown pathogenesis. We performed low-coverage genome and high-coverage exome sequencing of 20 desmoplastic melanomas, followed by targeted sequencing of 293 genes to validate candidate genes. A high mutation burden (median 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers. Mutation patterns strongly implicate UV-radiation as the dominant mutagen, indicating a superficially located cell of origin. Novel alterations included recurrent promoter mutations of NF-kappa B inhibitor epsilon, NFKBIE (IkBε) in 14.5% of samples. Commonly mutated oncogenes in melanomas, in particular BRAF(V600E) and NRAS(Q61K/R), were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS, and PIK3CA, some of which being candidates for targeted therapies.</p> <p><i>Reprinted from:</i><br/> Shain, A. H. et al. Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway. <i>Nat. Genet. <br/> With permission from Nature Genetics</i> </p>
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Project description:Desmoplastic malignant mesothelioma is a rare tumor. Due to the rarity, genomic profile of desmoplastic malignant mesothelioma is not unveiled. To elucidate genomic profile of desmoplastic malignant mesothelioma, we used illumina infinium omini exomeexpress in an established patient-derived cell line of desmoplastic malignant mesothelioma.
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