Dataset features


Application: SNP array data analysis
Number of samples: 2
Release date: Oct 1 2008
Last update date: Dec 6 2012
Access: Public
Diseases: Carcinoma, Carcinosarcoma, Neoplasms, Salivary Gland Diseases, Sarcoma, Mixed Tumor, Malignant, Meningeal Carcinomatosis
Dataset link CGH analysis of two components of carcinosarcoma

Experimental Protocol

We investigated 1 FFPE salivary gland carcinosarcoma, of which we macrodissected the two components separately before DNA extraction. To explore the genomic profiles of the two distinct cellular components of the carcinosarcoma, we employed a 4x44k array CGH platform including 45.214 60-mer oligonucleotides. This allowed us a genome-wide survey and molecular karyotyping of genomic aberrations with an average resolution of 75 kb.18 Labeling of tumor and reference DNA was performed using the ENZO BioArray™ CGH Labeling System (Farmingdale, NY, USA). 500 ng genomic DNA of tumor was labeled in Cy3 and mixed with a normal human reference pool of ten healthy individuals (labeled with Cy5) prior to hybridization on a 4x44K Agilent slide (Amstelveen, The Netherlands) using the Agilent hybridization oven (G2545A) overnight at 20 rpm. The oligo CGH-microarray slide was scanned using a DNA microarray scanner G2565AB (Agilent Technologies Netherlands B.V., Amstelveen, The Netherlands).Washing, scanning and feature selection (Feature extraction software v.9.1) were furthermore performed using standard Agilent procedures. In order to determine exact breakpoints in the generated array CGH profiles, we segmented the obtained log2 ratios by DNAcopy. Sex chromosomes were discarded from the analysis, since all tumor samples were hybridized to a pool of reference DNA of the opposite gender. In the downstream analysis, only clones with no missing values were included. Segmented log2 ratios were converted to four levels of categorized data (i.e. losses, normals, gains, and amplifications) by CGHCall,20 implemented using the statistical software environment R [R Development Core Team (2006)].








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