Perlegen performed genotyping using custom high-density oligonucleotide arrays as previously described15. Initially, a pilot phase was carried out on chromosome 2p to optimize experimental workflow and data handling. Details of amplicons used in the experiment and PCR primers can be found at http://genome.perlegen.com/pcr/ and also on the HapMap website. The arrays were tiled with sets of 25-bp probes for each SNP, with either 40 or 24 probes per SNP. These consisted of four sets of features, corresponding to forward and reverse strand tilings of sequences complementary to each of the two SNP alleles. Within a feature set, the position of the SNP within the oligonucleotide varied from position 11 to position 15. Mismatch probes were used to measure background, and by comparison with the perfect match probes, to detect the presence or absence of a specific PCR product. The 40-feature and 24-feature tilings both provided 10 perfect-match features for each SNP allele and differed only in the number of mismatch probes.
