Each SNP is represented by 40 unique 25-mer DNA probes scattered throughout the array: 20 probes designed against the A allele and 20 against the B allele. Each set of 20 allele-specific probes interrogate the DNA composition at and immediately surrounding the polymorphic site. Relative allele signals are computed from the probe intensities and are used as the input to a classification scheme [28] that produces high-confidence genotype calls for each SNP.
