Tumor classification based on DNA copy number aberrations determined using SNP arrays

High-density single nucleotide polymorphism (SNP) array is a recently introduced technology that genotypes more than 10,000 human SNPs on a single array. It has been shown that SNP arrays can be used to determine not only SNP genotype calls, but also DNA copy number (DCN) aberrations, which are common in solid tumors. In the past, effective cancer classification has been demonstrated using microarray gene expression data, or DCN data derived from comparative genomic hybridization (CGH) arrays. However, the feasibility of cancer classification based on DCN aberrations determined by SNP arrays has not been previously investigated. In this study, we address this issue by applying state-of-the-art classification algorithms and feature selection algorithms to the DCN aberration data derived from a public SNP array dataset. Performance was measured via leave-one-out cross-validation (LOOCV) classification accuracy. Experimental results showed that the maximum accuracy was 73.33%, which is comparable to the maximum accuracy of 76.5% based on CGH-derived DCN data reported previously in the literature. These results suggest that DCN aberration data derived from SNP arrays is useful for etiology-based tumor classification.