Affymetrix was supplied with 1,396 samples (the 1,350 COGA samples along with some blind duplicates) to analyze on the GeneChip® Mapping 10k Array [27]. Total genomic DNA was digested with the restriction enzyme XbaI, followed by ligation of adaptors. A single primer recognizing the adaptor sequence is used to amplify the ligated DNA fragments and PCR conditions were set to preferentially amplify fragments in the range of 250–1000 bp. The amplified DNA was labeled and hybridized to GeneChip® arrays containing 25-mer DNA probes designed to hybridize with target sequence corresponding to 11,560 SNPs which are known to be located within fragments which will be amplified by the assay.
