Genomic profiling of chondrosarcoma: chromosomal patterns in central and peripheral tumors (Illumina)

Gene expression profiling of 17 fresh frozen chondrosarcoma biopsies using the Human-6 v2 Expression BeadChip (Illumina Inc., San Diego, CA, USA). DNA copy number analyses was also performed in these tumors. Keywords: chondrosarcoma, gene expression profiling, Illumina Samples displaying a tumor content of >70%, as determined from haematoxylin and eosin-stained frozen sections, were analyzed using the Homo sapiens-6 v2 Expression BeadChips (Illumina Inc., San Diego, CA, USA), containing more than 48,000 transcript probes. In samples demonstrating a lower amount of tumor versus normal tissue, macrodissection of tumor material was performed. For each hybridization, 200 ng of total RNA were processed according to the Illumina® TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX, USA), to produce double-stranded cDNA and subsequently to generate biotin-labelled cRNA. Following the manufacturer’s specifications (Illumina), 1.5 µg of the biotin labeled cRNA were hybridized onto the Homo sapiens-6 v2 Expression BeadChips overnight, and subsequently detected with streptavidin-Cy3 using an Illumina® BeadArray Reader. Image analysis was performed using the Illumina® BeadStudio Application Software.