A single nucleotide polymorphism (SNP) is the most common type of genetic variation, and millions of SNPs have been documented so far. Because of dense distribution of SNPs across the genome, SNPs are viewed as ideal markers for research use in the post-genomic era. The application of the high-density whole genome-wide SNP array not only leads to more rapid, economical, and high throughput genotyping but also makes the investigation of the genetic variety or change in global patterns possible. The SNP array will be widely used in various research fields, such as large-scale genome-wide linkage and association studies to discover susceptibility genes in cancer, and loss of heterozygosity analysis to discover tumor suppressor genes and tumor molecular markers, and so on.