Affymetrix CytoScan HD and OncoScan array data for malignant melanoma samples

Malignant melanoma is a highly metastatic disease disseminating to several distant sites. This potential is also of great clinical impact for patient survival and therapeutic success. Knowledge about melanoma genomics is mainly based on lymphatic or skin metastases derived data, whereas data from distant sites is rather limited. Therefore, an autopsy-based visceral metastasis biobank was established and an array-based CNV analysis was performed focusing primarily on major organs (brain, lung and liver) on a total of 38 samples (10 primary and 28 organ metastasse). A unique picture emerged about organ specific CNV type distributions or gene alterations including the frequent loss of DNA damage error genes in brain metastases, the presence of HGF/MET autocrine loop in brain and lung metastases, the traces of immunogenic mimicry exclusive for lung metastases or the correlation of BRAF copy number and mutant allele frequency especially in lung metastases. All these above phenomena have a great influence on therapy efficacy or resistance. Affymetrix CytoScan HD or OncoScan arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved or FFPE archived diagnostic and/or autopsy cutaneous melanoma samples. Copy number analysis of Affymetrix CytoScan and OncoScan arrays was performed for 38 malignant melanoma of the skin.