Array-based detection of genetic alterations associated with disease

An in situ method of screening a chromosome sample containing human breast cancer tissue or breast cancer cells for the presence of breast cancer cells that have a change in copy number of a target polynucleotide sequence on chromosome 20, the method comprising:

• (a) contacting the chromosome sample with a fluorescently-labeled probe which binds selectively to a target polynucleotide sequence on a region in which copy number is altered in breast cancer cells, wherein the region is selected from the group consisting of Flpter 0.603, 0.646, 0.694, and 0.722 on chromosome 20, and wherein the probe is contacted with the sample under conditions in which the probe binds selectively with the target polynucleotide sequence to form a stable hybridization complex in situ;
• and
• (b) detecting the formation of a hybridization complex in situ at a region selected from the group consisting of Flpter 0.603, 0.646, 0.694, and 0.722 on chromosome 20, wherein the detection comprises fluorescence in situ hybridization (FISH) and the probe hybridizes to a region on chromosome 20 comprising the src gene, the D20S44 locus, the humsem1 gene, or the D20S178 locus.