Method and compositions for detecting epidermal growth factor receptor variant forms in cancer cells

A method of diagnosing the therapeutic outcome for treating a patient having a cancer with an anti-EGFR therapeutic agent, the method comprising:

• a. obtaining a sample containing a plurality of cancer cells;
• b. hybridizing a set of chromosomal probes to the sample, wherein the set comprises an EGFR(v3)-probe and a probe to chromosome 7 different from an EGFR(v3)-probe;
• and
• c. visualizing the hybridization pattern of the set of chromosomal probes in the plurality of cancer cells in the sample,
• wherein the presence of at least one copy of chromosome 7 lacking a hybridization signal of the EGFR(v3)-probe in at least one cancer cell is indicative of the cancer having EGFR(v3) and
• wherein the cancer is predisposed to developing a resistance to treatment with the anti-EGFR therapeutic agent.

A method of screening a sample for a predisposition for forming an EGFR-associated cancer, the method comprising:

• a. obtaining a sample containing a plurality of cells;
• b. hybridizing a chromosomal probe to the sample, wherein the chromosomal probe is at least one member selected from the group consisting of a chromosome enumeration probe to chromosome 7, a chromosome arm probe to at least one arm of chromosome 7, and a locus specific probe to a gene or region of chromosome 7;
• and
• c. visualizing the hybridization pattern of the chromosomal probe in the plurality of cells of the sample,
• wherein the presence of three or more hybridization signals directed against chromosome 7 in at least one cell is indicative of amplification of chromosome 7 and of the sample being predisposed to forming an EGFR-associated cancer.