Genomic DNA was prepared from blood [21,53,54], carefully quantitated and combined into pools representing 13 – 20 individuals of the same ethnicity and phenotype. Hybridization probes were prepared from the genomic DNA pools as described (Affymetrix Genechip Mapping Assay Manual) with precautions to avoid contamination that included use of dedicated preparation rooms and hoods. 50 ng of each pooled genomic DNA was digested by StyI or by NspI, ligated to appropriate adaptors and amplified using a GeneAmp PCR System 9700 (Applied Biosystems, Foster City, CA) with a 3 min 94°C hot start, 30 cycles of 30 sec 94°C, 45 sec 60°C, 15 sec at 68°C and a final 7 min 68°C extension. PCR products were purified (MinElute™ 96 UF kits, Qiagen, Valencia, CA). PCR products were quantitated and 40 μg were digested for 35 min at 37°C with 0.04 unit/μl DNase I. The 30–100 bp fragments resulting from DNAse treatments were end-labeled using terminal deoxynucleotidyl transferase and biotinylated dideoxynucleotides and hybridized to the appropriate Sty I or Nsp I early access Mendel® microarrays (Affymetrix, Santa Clara, CA). Arrays were stained,
