General principles of CGH-A and SNP-A arrays. (A) In CGH-A, control DNA is used as reference for the test DNA obtained from putative tumor DNA. Analysis of spectra generated through hybridization of differentially labeled DNA to oligo or BAC probes on array is shown below. Decreased copy number in the tumor DNA results in decreased intensity of the signal for the test and increased signal for reference DNA. (B) In SNP-A, hybridization of amplified and labeled DNA to probes corresponding to alleles for each locus results in a genotyping pattern allowing for determination of the heterozygosity or homozygosity for each allele. At the same time, intensity of the hybridization signals allows for determination of copy number changes.