Deep sequencing of melanoma for driver mutations
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ABSTRACT:
PROVIDER: EGAS00001000857 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Targeted DNA sequencing of uveal melanoma driver mutations
| PRJNA1258313 | ENA
Project description:Targeted DNA sequencing of uveal melanoma driver mutations
| PRJNA1258314 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE29996: Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Affymetrix SNP array data] GSE29998: Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Illumina mRNA expression array data] Refer to individual Series
2012-10-25 | E-GEOD-29999 | biostudies-arrayexpress
Project description:MicroRNAs are 18-23 nucleotide non-coding RNAs that regulate gene expression in a sequence specific manner. Little is known about the repertoire and function of miRNAs in melanoma or the melanocytic lineage. We therefore undertook a comprehensive analysis of the miRNAome in a diverse range of pigment cells including: melanoblasts, melanocytes, congenital nevocytes, acral, mucosal, cutaneous and uveal melanoma cells. We sequenced 12 small RNA libraries using Illumina's GAII platform. This massively parallel sequencing approach revealed a total of 539 known mature and mature-star sequences, along with the prediction of 389 novel miRNA candidates. Using the relative proportion of the total unique read counts against total number of reads, hierarchal clustering of all novel candidates plus known miRNAs gave good separation of the different histological subtypes. Some of the novel miRNAs may be specific to the melanocytic lineage and as such could be used as biomarkers to assist in the early detection of distant metastasises by measuring the circulating levels in blood. Follow up studies of the functional roles of these pigment cell miRNAs and the identification of their targets should shed further light on their role in the development and progression of melanoma. Illumina GAII deep sequencing of 12 melanoma and pigment cell lines
2010-03-22 | E-GEOD-18381 | biostudies-arrayexpress
Project description:Whole exome sequencing identified frequent driver mutations in a series of paediatric glioblastomas We used microarray-based profiling to investigate differences in gene expression according to mutational status of driver genes RNA from 27 primary tumor samples was subject to QC by Agilent BioAnalyser analysis and then hybridised to an Affymetrix U133 Plus2 gene expression array
2012-03-01 | E-GEOD-34824 | biostudies-arrayexpress
Project description:Here, we combine comparative regulatory genomics with machine learning to investigate enhancer logic in melanoma. Through epigenomics profiling of 26 melanoma cell lines across six species, we examine the conservation of the two main melanoma states and underlying master regulators. By training a deep neural network on topic models derived from the human lines, we were able to classify not only human melanoma enhancers, but also regulatory regions in the other species. The deep learning model revealed important genomic features (i.e. TF binding motifs) for the different melanoma states, how they co-occur within melanoma enhancers, and where they are placed with respect to the central enhancer nucleosome. This in-depth analysis of the melanoma enhancer code allowed us to propose a mechanistic model of TF binding in MEL melanoma enhancers. Finally, by exploiting the deep layers of our model, we are able to identify causal mutations for melanoma enhancer loss and gain through evolution, not only affecting enhancer accessibility but also activity.
2020-04-22 | GSE142238 | GEO
Project description:While common mutations in potent proto-oncogenes and tumor suppressors induce melanoma formation, no recurrent mutations associated with the late stages of melanomagenesis have been identified. Instead, non-mutational mechanisms such as the deregulation of transcriptiona or epigenetic programs typically promote the malignang progression and metastasis of melanoma. We have previously identified the small MAFG transcription factor MAFG as a critical target of the melanoma suppressor miRNA miRN-29, prompting an in-depth evaluation of the role of MAFG in melanoma. MAFG expression is elevated in melanoma compared to melanocytes and increases with tumor stage. Ectopic expression of MAFG in human melanocytes and melanoma cells enhances proliferation in virto and promotes melanoma growth in vivo. Moreover, MAFG overexpression in BRAFV600E; PTEN+/- mice accelerated melanomagenesis, significantly shortening overall survival. Despite being a critical NRF2 dimerization partner, NRF2 was dispensable for the effects of MAFG. Moreover, MAFG overexpression in melanoma had no effect on the activity of NRF2 transcriptional reporters, nor did it induce transcriptional programs associated with NRF2. RNA sequencing and pathway analysis revealed MAFG-mediated effects on melanoma-associated processes such as pigmentation. Indeed, MAFG downregulated MITF and its target genes in the pigmentation pathway in melanoma cells. We next analyzed the connection between MAFG and MITF and found that MAFG binds to MITF to impede its binding to melanocytic differentiation genes, thus promoting a less differentiated and more aggressive phenotype. Our study establishes MAFG as a potent driver of melanoma development through the relocation of MITF.
2026-02-19 | GSE274945 | GEO
Project description:While common mutations in potent proto-oncogenes and tumor suppressors induce melanoma formation, no recurrent mutations associated with the late stages of melanomagenesis have been identified. Instead, non-mutational mechanisms such as the deregulation of transcriptiona or epigenetic programs typically promote the malignant progression and metastasis of melanoma. We have previously identified the small MAFG transcription factor MAFG as a critical target of the melanoma suppressor miRNA miRN-29, prompting an in-depth evaluation of the role of MAFG in melanoma. MAFG expression is elevated in melanoma compared to melanocytes and increases with tumor stage. Ectopic expression of MAFG in human melanocytes and melanoma cells enhances proliferation in virto and promotes melanoma growth in vivo. Moreover, MAFG overexpression in BRAFV600E; PTEN+/- mice accelerated melanomagenesis, significantly shortening overall survival. Despite being a critical NRF2 dimerization partner, NRF2 was dispensable for the effects of MAFG. Moreover, MAFG overexpression in melanoma had no effect on the activity of NRF2 transcriptional reporters, nor did it induce transcriptional programs associated with NRF2. RNA sequencing and pathway analysis revealed MAFG-mediated effects on melanoma-associated processes such as pigmentation. Indeed, MAFG downregulated MITF and its target genes in the pigmentation pathway in melanoma cells. We next analyzed the connection between MAFG and MITF and found that MAFG binds to MITF to impede its binding to melanocytic differentiation genes, thus promoting a less differentiated and more aggressive phenotype. Our study establishes MAFG as a potent driver of melanoma development through the relocation of MITF.
2024-10-09 | GSE274810 | GEO
Project description:The purpose of the study is to detect somatic mutations in hepatocellular carcinoma using circulating free-DNA. We used deep-sequencing data of a panel of 60 commonly mutated genes in hepatocellular carcinoma.
2018-04-29 | E-MTAB-5123 | biostudies-arrayexpress
Project description:We profiled CRC organoids engineered with different combinations of driver mutations. All organoids were derived from one mouse and then mutations were sequentially introduced by CRISPR Cas9
2022-09-16 | GSE207668 | GEO