Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of novel copy number alterations by high-resolution aCGH from FFPE cutaneous melanoma samples

ABSTRACT: We investigated a cohort of 34 archival cutaneous melanoma samples by Agilent 40 kb-resolution CGH array. We found a non-random distribution of precise CNAs predictive for clinical outcome. Although most of the alterations defined in this study have been already reported, we mapped novel melanoma-specific CNAs at highest accuracy. Moreover, our data revealed distinct amplifications hotspots, some of which were validated by quantitative real-time PCR, enabling the identification of novel melanoma oncogenic candidates. Keywords: Cutaneous melanoma, Copy number alterations, Biomarkers, FFPE

ORGANISM(S): Homo sapiens

PROVIDER: GSE45354 | GEO | 2013/07/01

SECONDARY ACCESSION(S): PRJNA193525

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identification of novel copy number alterations by high-resolution aCGH from FFPE cutaneous melanoma samples

Project description:We investigated a cohort of 34 archival cutaneous melanoma samples by Agilent 40 kb-resolution CGH array. We found a non-random distribution of precise CNAs predictive for clinical outcome. Although most of the alterations defined in this study have been already reported, we mapped novel melanoma-specific CNAs at highest accuracy. Moreover, our data revealed distinct amplifications hotspots, some of which were validated by quantitative real-time PCR, enabling the identification of novel melanoma oncogenic candidates. Keywords: Cutaneous melanoma, Copy number alterations, Biomarkers, FFPE We examined 34 primary melanoma formalin-fixed and paraffin-embedded (FFPE) samples by using array comparative genomic hybridization (aCGH) for DNA copy number alterations (CNAs). Genomic DNA was extracted, referred to a sex-matched diploid commercial control DNA (Promega Corporation, Madison, WI, cat. G1417 and G1521), and hybridized on the Agilent SurePrint G3 Human CGH Microarray 8x60k, cat. G4827A.

2013-07-01 | E-GEOD-45354 | biostudies-arrayexpress

Analysis of whole-genome chromosomal alterations in primary cutaneous melanoma

Project description:In this experiment, FFPE samples of 41 primary cutaneous melanoma, 2 metastatic melanoma and 6 normal skin were used for DNA extraction and genotyping by Affymetrix OncoScan FFPE Assay, in order to define chromosomal alterations in copy number and loss of heterozygosity. Genomic damage was then correlated with clinical features of melanoma.

2015-11-01 | E-MTAB-3481 | biostudies-arrayexpress

hnRNP M and HSP 90α as Potential Biomarkers in Early Stage Cutaneous Head and Neck Melanoma Tissue

Project description:Background: Timely diagnosis is important for successful treatment of cutaneous melanoma. Currently, Breslow tumor thickness and mitotic rate are used for malignant melanoma classification and prognosis, but these parameters can assess disease progression risk only to a certain degree. Therefore, there is a need for new melanoma protein biomarkers that would aid early and accurate diagnosis and prediction of their metastatic potential. Methodology and Findings: This retrospective case control study is based on proteomic profiling of formalin-fixed archival tissues of 31 early-stage head and neck cutaneous malignant melanoma samples using liquid chromatography / mass spectrometry. A melanoma proteomic profile was identified and protein expression levels were compared to the proteome profile of melanocytic naevi and correlated to established prognostic factors and disease-specific survival. In accordance with the American Joint Committee on Cancer guidelines, recursive partitioning multivariate analysis was used to identify potential biomarkers associated with metastatic potential of early-melanoma. Heterogeneous nuclear ribonucleoprotein M and heat shock protein 90 alpha were profiled as independent prognostic factors. Their elevated expression was clinically relevant for predicting an exceedingly high metastatic hazard ratio. These proteins were superior in estimating disease progression risk when compared to Breslow thickness and mitotic rate. Conclusions and Significance: Identification of biomarkers in early stage cutaneous head and neck melanoma is an important step towards predicting metastatic potential and prognosis of the disease. Clinical confirmation and further validation of the proteins identified in this study would provide a novel tool for identifying patients at risk for developing metastatic disease.

2019-11-27 | PXD015137 | Pride

Genome-wide promoter methylation analysis identifies epigenetic silencing of MAPK13 in primary cutaneous melanoma

Project description:The implication of epigenetic alterations in the pathogenesis of melanoma is increasingly recognized. Here we performed genome-wide DNA methylation analysis of primary cutaneous melanoma and benign melanocytic naevus interrogating 14,495 genes using beadchip technology. This first genome-wide view of promoter methylation in primary cutaneous melanoma revealed an array of recurrent DNA methylation alterations with potential diagnostic applications. Among 106 frequently hypermethylated genes there were many novel methylation targets and tumor suppressor genes. Highly recurrent methylation of the HOXA9, MAPK13, CDH11, PLEKHG6, PPP1R3C and CLDN11genes was established. Promoter methylation of MAPK13, encoding p38?, was present in 67% of primary and 85% of metastatic melanomas. Restoration of MAPK13 expression in melanoma cells exhibiting epigenetic silencing of this gene reduced proliferation, indicative of tumor suppressive functions. This study demonstrates that DNA methylation alterations are widespread in melanoma and suggests that epigenetic silencing of MAPK13 contributes to melanoma progression. Bisulphite converted genomic DNA from 5 fresh-frozen benign naevus and 24 fresh-frozen primary melanoma biopsy samples were hybridised to Illumina's Infinium HumanMethylation27 Beadchips

2013-04-24 | E-GEOD-45266 | biostudies-arrayexpress

Genome-wide promoter methylation analysis identifies epigenetic silencing of MAPK13 in primary cutaneous melanoma

2013-04-24 | GSE45266 | GEO

mRNA expression in ulcerated primary cutaneous melanoma

Project description:mRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma

2022-08-13 | GSE211091 | GEO

microRNA expression in ulcerated primary cutaneous melanoma

Project description:microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma

2022-08-13 | GSE211090 | GEO

Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure

Project description:Ultraviolet radiation (UV) is causally linked to cutaneous melanoma, yet the underlying epigenetic mechanisms, known as molecular sensors of exposure, have never been characterized in clinical biospecimen. DNA methylome, genome and transcriptome analyses of cutaneous melanoma in two cohorts identified UV-related alterations in regulatory regions and immunological pathways and revealed novel cancer driver genes affecting patient survival. TAPBP, the top gene and a member of the immunoglobulin superfamily, encompassed several CpG methylation sites altered by UV and independently validated by bisulfite pyrosequencing, providing cost-effective opportunities for clinical application. The DNA methylome also highlighted non UV-related aberrations underlying pathological differences between cutaneous and acral melanomas. Unsupervised epigenomic mapping demonstrated that non UV-mutant cutaneous melanoma more closely resembles acral rather than UV-exposed cutaneous melanoma, with the latter showing better patient prognosis than the other two forms. These gene-environment interactions in multi-ethnic backgrounds reveal translationally impactful mechanisms in melanomagenesis.

2022-05-12 | GSE202750 | GEO

mRNA expression in ulcerated primary cutaneous melanoma (validation cohort)

Project description:mRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma

2022-08-13 | GSE211093 | GEO

microRNA expression in ulcerated primary cutaneous melanoma (validation cohort)

Project description:microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma (n=6) compared to non-ulcerated primary cutaneous melanoma (n=6)

2022-08-13 | GSE211092 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data