Primary_Melanoma_Genomic_Alterations
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Szilvia Ecsedi
PROVIDER: E-MTAB-947 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Comparison of gene expression patterns between primary melanomas with distinct biological parameters: our study applied different experimental factor types for comparisons, namely tumor surface ulceration, metastasis formation, and disease stage by Clark level and Breslow thickness. Our aim was to describe molecular signalling of primary melanomas based on differently expressed genes and to identify experimental factors that influenced by differently expressed genes. This assessment led us to map the most prevalent alterations associated with this clinical parameter.Out further aim was to conduct an integrated gene expression and copy number analysis combining our results from Affymetrix and NimbleGen microarrays. The main purpose of this part of the study was to give functional relevance to the copy number events by providing a statistically powerful integrated interpretation of gene expression changes and copy number alterations.
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Project description:An improved understanding of the molecular pathogenesis of brain metastases, one of the most common and devastating complications of advanced melanoma, may identify and prioritize rational therapeutic approaches for this disease. In particular, the identification of molecular differences between brain and extracranial metastases would support the need for the development of organ-specific therapeutic approaches. Hotspot mutations, copy number variations (CNV), global mRNA expression patterns, and protein expression and activation, quantitatively analyzed by mass-array genotyping, molecular inversion probe arrays, microarrays and reverse phase protein array (RPPA) were evaluated in pairs of melanoma brain metastases and extracranial metastases from patients who had undergone surgical resection for both types of tumors. Somatic copy number variation (CNV) in 47 melanoma brain metastases (BM, except for patient 01, who had a spinal cord metastasis) and extracranial metastases (EM) were analyzed by molecular inversion probe (MIP) array (Affymetrix OncoScan FFPE Express 2.0). DNA were extracted from regions with >70% viable tumor cells from formalin-fixed and paraffin-embedded (FFPE) tissues. Of the 47 tumor samples, 22 were matched BM and EM from the same patients. In addition, 24 DNA samples from normal tissues were included as diploid controls.
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