Supplemental Figure 6. DNA copy number alteration across chromosome 17 by array CGH. (a) DNA copy number profiles are illustrated for cell lines containing different numbers of X chromosomes, for breast cancer cell lines, and for breast tumors. Breast cancer cell lines and tumors are separately ordered by hierarchical clustering to highlight recurrent copy number changes. The 382 genes present on the microarrays and mapping to chromosome 17 are ordered by position along the chromosome. Fluorescence ratios are depicted by a log2 pseudocolor scale (indicated). Selected genes are indicated (as described in published Figure 2). An arrow denotes the location of a possible DNA copy number polymorphism (single-copy deletion in the single normal female genomic DNA reference sample), evidenced by a relative "amplification" of SCYA3L1 and SCYA4 in all samples, including non-tumor cell lines containing varying numbers of X chromosomes (but with presumably normal chromosomes 17). (b) Graphical display of DNA copy number profiles for breast cancer cell lines and tumors exhibiting 17q12-21.1 amplification. Fluorescence ratios (tumor/normal) are plotted on a log2 scale for genes ordered within this region of the chromosome. The smallest region amplified among all samples is highlighted in gray.