Use of Single-Nucleotide Polymorphism Array for Tumor Aberrations in Gene Copy Numbers

Abstract

The single nucleotide polymorphism (SNP) array was originally developed to determine the genotypes of a study population for linkage analysis or individual genetic variation analysis. Over the last few years, the number of SNP loci that can be evaluated in a single assay has increased from approximately 1500 to more than 500,000, covering all 22 autosomes and the X chromosome. Because the hybridization signal of each oligonucleotide on the SNP array depends on the amount of target DNA, various statistic algorithms have been developed to estimate the copy number of each SNP locus. Several studies have demonstrated the utility of the SNP array analysis in the detection of gene copy number aberrations in tumor DNA. In this review, we discuss the use of the SNP array analysis in determining tumor aberrations in gene copy numbers, the challenge of using tumor samples in the analysis, and improvements in software for copy number measurement using SNP arrays. The unique ability of the SNP array to determine both the genotype and copy number has uncovered novel DNA amplification events that involve only a single allele.