Genomic profiling of chRCC

Tumor areas displaying >80% cancer cells without hemorrhage or necrosis were marked on the hematoxylin and eosin slides. DNA from FFPE tumor tissue samples was obtained by punching 4 to 6 tissue cylinders (diameter 0.6 mm) from each sample. DNA extraction from FFPE tissue was done as described [32 (link)]. The double-strand DNA concentration (dsDNA) was determined using the fluorescence-based Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA). Tumors with poor DNA quality were excluded from the study. Genome-wide DNA copy-number alterations and allelic imbalances of 33 chRCC were determined using the Affymetrix OncoScan^® CNV Assay (Affymetrix/Thermo Fisher Scientific, Waltham, MA, USA) as previously described [33 (link)]. The demographic and clinicopathological characteristics for 33 Swiss chRCCs with clinical data are summarized in Table 1. Samples were further processed by IMGM Laboratories GmbH (Martinsried, Germany) for CNV (copy number variation) determination according to the Affymetrix OncoScan CNV Assay recommended protocol. The data were analyzed by the Nexus Copy Number 10.0 (Biodiscovery, Inc., El Segundo, CA, USA) software using Affymetrix TuScan algorithm. All array data were also manually reviewed for subtle alterations not automatically called by the software.