IntegraChip genome-wide BAC arrays of 4,898 BAC clones (600-kb median spacing) were hybridized by the manufacturer, IntegraGen (Evry, France). The genomic positions of all clones on the array have been determined by BAC end sequencing. A genomic DNA labeling kit (Enzo, Farmingdale, NY) was used to label the sample DNA with Cy5 or with Cy3. The labeled products were purified with QiaQuick polymerase chain reaction (PCR) purification kits (Qiagen, Valencia, CA). After addition of tRNA (48 mg) plus a quantity of human Cot DNA (Invitrogen, Carlsbad, CA) equal to 50 times the mass of the labeled DNAs, the resulting products were concentrated by vacuum centrifugation, resuspended in 43 mL of hybridization solution (Ambion, Austin, TX) and deposited on the array under a coverslip. Hybridization in a sealed chamber (Corning Life Sciences, Acton, MA) was for 66 hours at 55_C, and then washed. Slides were scanned (Agilent Technologies, Santa Clara, CA), data were extracted with GenePix 6 (Axon InstrumentseMolecular Devices, Sunnyvale, CA), and copy number analysis was performed with GenoCensus (IntegraGen), which includes block Loess normalization.
