T/R ratio plots for comparative genome hybridization. A) Custom BAC Array CGH of chromosome 15 shows trisomy up to BP4. FISH probes used are circled in red. Notably, FISH probe pDJ204m06 was not used on the array thus is not shown. Clones used for BLAST search for homology against chromsome 9 BP are circled in green. B) Schematic of chromosome 15q11.1-13.3 showing the position of genes based on the UCSC genome browser. Highlighted in red are maternally expressed transcripts, and paternally expressed transcripts in black. (Below) The relative positions of the 5 BP clusters are shown with sequence homology indicated by color, blue indicating regions of homology to HERC2, green indicating regions of homology to GOLGA8E, yellow indicating regions of homology between CHRNA7. The black and white hatching indicates the heteromorphic region near the centromere that includes a number of pseudogenes and can expand in the normal population. Above the breakpoint schematic is the Affymetrix 6.0 whole genome array that shows the density of SNP coverage for this region with notable gaps at the positions of the common BPs, although not all probes for detecting copy number variations are shown in the UCSC browser. C) Nimble CGH Array of chromosome 9 shows trisomy distal to position 132,510,300 (Build 36.1) in 9q34.1. D) Duplicated genes in chromosome 9 based on the UCSC genome browser.