X chromosome and AR locus copy number analysis in CTCs from 9 metastatic CRPC patients. Each plot shows log2 hybridization ratio values (y-axis) at BAC clones (blue dots) distributed from the p terminus to the q terminus (x-axis). The black horizontal lines represent log2 ratio equal to 0. Red vertical lines demarcate the centromere. Broken black lines superimposed on BAC clones are the output of segmentation analysis providing high confidence copy number calls. Transparent blue bars identify the locus containing the androgen receptor gene (AR). At the bottom of each panel is an ideogram of chromosome X with cytoband regions showing gains (green) and losses (red). Bars on top of the ideogram (long arm) show results of copy number analysis at the AR locus (double green bar- high-level copy number gain; single green bar- low level copy number gain, grey bar- no copy number change). Paired samples are enclosed in black boxes: CTCs vs. CD45-positive (leukocytes) from patient #9 and CTCs vs. archival primary tumor (PT) from patients #17 and #20.