Renal
tumors with complex or unusual morphology require extensive workup for accurate classification.
Chromosomal aberrations that define subtypes of renal
epithelial neoplasms have been reported. We explored if whole-genome chromosome copy number and loss-of-heterozygosity analysis with single nucleotide polymorphism (SNP) arrays can be used to identify these aberrations and classify renal epithelial
tumors. We analyzed 20
paraffin-embedded tissues representing clear cell, papillary renal and
chromophobe renal cell carcinoma, as well as
oncocytoma with Affymetrix GeneChip 10K 2.0 Mapping arrays. SNP array results were in concordance with known genetic aberrations for each renal
tumor subtype. Additional
chromosomal aberrations were detected in all renal cell
tumor types. The unique patterns allowed 19 out of 20
tumors to be readily categorized by their chromosomal copy number aberrations. One
papillary renal cell carcinoma type 2 did not show the characteristic 7/17
trisomies. Clustering using the median copy number of each chromosomal arm correlated with histological class when using a restricted set of chromosomes. In addition, three morphologically challenging
tumors were analyzed to explore the potential clinical utility of this method. In these cases, the SNP array-based copy number evaluation yielded information with potential clinical value. These results show that SNP arrays can detect characteristic
chromosomal aberrations in
paraffin-embedded renal
tumors, and thus offer a high-resolution, genome-wide method that can be used as an ancillary study for classification and potentially for prognostic stratification of these
tumors.