Many oligonucleotide arrays comprise of spotted short oligonucleotides from throughout the genome under study. Hybridization of tumor DNA samples to these arrays will provide copy number estimates at each reference point with varying degrees of accuracy. In addition to copy number changes, however, tumors often undergo loss of heterozygosity for specific regions of the genome without copy number changes and these genetic changes can only be identified using arrays that identify polymorphic alleles at each reference point. In addition, because the hybridization intensity can be measured at each of the allelic variants, allelic ratios can be established which give indications of ploidy status in the tumor which is not generally possible using most other oligonucleotide array designs. The only arrays currently available that simultaneously report copy number, ploidy, and loss of heterozygosity are the Affymetrix SNP mapping arrays.