Array–CGH of cancer cell line BT474. (A) DNA equivalent to 300,000 cells from breast cancer cell line BT474 was cohybridized with a similar amount of normal human female DNA from peripheral blood lymphocytes to a cDNA microarray containing replicate probes for 4600 genes. BT474 to female fluorescence log₂ ratio profiles were ordered by chromosomes, and into each chromosome, according to the position as assessed by SOURCE (http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceSearch). Ratio values were connected by lines. A log₂ ratio near 0 indicates an equal copy-number representation of that gene in both genomes. Dashed lines at −0.642 and 0.642 represent nonparametric bounds for log₂ ratios as described in Methods. (B) DNA from 1000 cells, obtained from the BT474 cell line, or DNA from peripheral lymphocytes of a normal human female was amplified using large fragment Bst DNA polymerase and cohybridized to the microarray in the same conditions as before. Nonparametric bounds for this experiment are denoted with dashed lines at −0.546 and 0.546. Arrows indicate gene-dosage alterations observed in both the unamplified and the whole genome-amplified experiments except for shaded areas in Chromosomes 17 and 20 in both figures. These chromosomes are very rich in altered genes, and can be observed in more detail in Figure 6.