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This invention relates to methods of analyzing a tissue sample from a subject. In particular, the invention combines morphological staining and/or immunohistochemistry (IHC) with fluorescence in situ hybridization (FISH) within the same section of a tissue sample. The analysis can be automated or ma

This invention relates to methods of analyzing a tissue sample from a subject. In particular, the invention combines morphological staining and/or immunohistochemistry (IHC) with fluorescence in situ hybridization (FISH) within the same section of a tissue sample. The analysis can be automated or manual. The invention also relates to kits for use in the above methods.

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What is claimed is: 1. A method of correlating cellular morphology with the presence of a cellular target nucleic acid sequence in a section of a tissue sample comprising the following steps: (a) staining the section of tissue sample with a morphological stain; (b) determining cellular morphology i

What is claimed is: 1. A method of correlating cellular morphology with the presence of a cellular target nucleic acid sequence in a section of a tissue sample comprising the following steps: (a) staining the section of tissue sample with a morphological stain; (b) determining cellular morphology in the section of tissue sample; (c) hybridizing a first labeled nucleic acid probe to the target nucleic acid sequence in the same section of tissue sample, wherein said label is selected from the group of labels consisting of radioisotopes, colloidal gold particles, fluorescent labels, and enzyme-substrate labels; (d) detecting the presence of the first nucleic acid probe in the section of tissue sample; and (e) correlating step (b) with step (d). 2. The method of claim 1, wherein the first nucleic acid probe is constructed to hybridize to the target nucleic acid sequence indicating a genetic abnormality selected from the group consisting of amplification, addition, substitution, translocation and deletion. 3. The method of claim 1, wherein amplification of the target nucleic acid sequence is determined in step (d). 4. The method of claim 3, wherein the target nucleic acid sequence is HER2/neu gene. 5. The method of claim 1, wherein the morphological stain used in step (a) does not significantly autofluoresce at the same wavelength as a fluorescent label of the first nucleic acid probe. 6. The method of claim 1, further comprising hybridizing a second labeled nucleic acid probe to a nucleic acid sequence in the section of tissue sample, wherein the second nucleic acid probe comprises a label distinguishable from a label of the first nucleic acid probe. 7. The method of claim 6, wherein the second nucleic acid probe determines chromosome copy number. 8. The method of claim 1, wherein the morphological stain used in step (a) comprises xanthine dye and thiazine dye. 9. The method of claim 1, wherein the morphological stain comprises methylene blue, a xanthine dye, or a thiazine dye. 10. The method of claim 1, wherein the tissue sample is selected from the group consisting of breast, prostate, ovary, colon, lung, endometrium, stomach, salivary gland and pancreas tissue sample. 11. The method of claim 1, wherein the target nucleic acid sequence is selected from the group consisting of HER2/neu gene and the centromere of chromosome 17. 12. The method of claim 1, wherein the first nucleic acid probe is labeled with a fluorescent label selected from the group consisting of derivatives of Texas Red, fluorescein, phycocrytherin, rhodamine, phycocyanin, dansyl, umbelliferone, a green fluorophore, and an orange fluorophore. 13. The method of claim 1, wherein the section of tissue sample is not destained prior to step (c). 14. The method of claim 1, wherein the section of tissue sample is obtained from fixed, paraffin-embedded tissue sample. 15. A method of correlating cellular morphology and the presence of a cellular target protein with the presence of a cellular target nucleic acid sequence in a section of a tissue sample comprising the following steps: (a) staining the section of tissue sample with a morphological stain; (b) determining cellular morphology in the section of tissue sample; (c) contacting the section of sample tissue with an antibody which specifically binds to the target protein; (d) determining binding of the antibody to the section of tissue sample; (e) hybridizing a labeled nucleic acid probe to the target nucleic acid sequence in the same section of tissue sample, wherein said label is selected from the group of labels consisting of radioisotopes, colloidal gold particles, fluorescent labels, and enzyme-substrate labels; (f) detecting the presence of the labeled nucleic acid probe in the section of tissue sample; and (g) correlating step (b) and (d) with step (f), wherein the morphological stain used in step (a) does not significantly interfere with detection of the labeled nucleic acid probe used in step (e). 16. A kit comprising: (a) a morphological stain; (b) a labeled probe complementary to a genetic abnormality in a cellular target nucleic acid sequence, where a genetic abnormality comprises a deletion, substitution, addition, translocation, or amplification of a nucleic acid sequence relative to the normal native cellular target nucleic acid sequence, and wherein said label is selected from the group of labels consisting of radioisotopes, colloidal gold particles, fluorescent labels, and enzyme-substrate labels; (c) a primary antibody which specifically binds a cellular target protein; (d) a labeled secondary antibody which specifically binds to the primary antibody; and (e) instructions for applying the stain (a) and probes (b), (c) and (d) to the same section of tissue sample wherein autofluorescence of the morphological stain does not significantly interfere with detection of the labeled nucleic acid probe. 17. The kit of claim 16, wherein the nucleic acid probe hybridizes to HER2/neu nucleic acid. 18. The kit of claim 16, wherein the morphological stain comprises methylene blue, a xanthine dye, or a thiazine dye. 19. The kit of claim 16, wherein the secondary antibody is labeled with an enzymatic label which catalyzes chemical alteration of a substrate compound. 20. The kit of claim 16, wherein the nucleic acid probe hybridizes to HER2/neu nucleic acid and the primary antibody specifically binds to HER2 protein. 21. The kit of claim 20, further comprising instructions describing methods for applying the probe to a section of tissue sample having a score of 1+ or 2+ for HER2 Protein Staining Intensity and for analyzing the results of said application. 22. The method of claim 1, wherein the first nucleic acid probe is labeled with a radioisotope label selected from the group consisting of 35S, 14C, 125I, 3H, and 131I. 23. The method of claim 1, wherein the first nucleic acid probe is labeled with colloidal gold particles. 24. The method of claim 1, wherein the first nucleic acid probe is labeled with an enzyme substrate label selected from the group of enzyme substrate labels consisting of horseradish peroxidase (HRPO), alkaline phosphatase (AP), and β-D-galactosidase (β-D-Gal). 25. The method of claim 15, wherein the first nucleic acid probe is labeled with a radioisotope label selected from the group consisting of 35S, 14C, 125I, 3H, and 131I. 26. The method of claim 15, wherein the first nucleic acid probe is labeled with colloidal gold particles. 27. The method of claim 15, wherein the first nucleic acid probe is labeled with an enzyme substrate label selected from the group of enzyme substrate labels consisting of HRPO, AP, and β-D-Gal. 28. The method of claim 15, wherein the first nucleic acid probe is labeled with a fluorescent label selected from the group consisting of derivatives of Texas Red, fluorescein, phycocrytherin, rhodamine, phycocyanin, dansyl, umbelliferone, a green fluorophore, and an orange fluorophore. 29. The kit of claim 16, wherein the first nucleic acid probe is labeled with a radioisotope label selected from the group consisting of 35S, 14C, 125I, 3H, and 131I. 30. The kit of claim 16, wherein the first nucleic acid probe is labeled with colloidal gold particles. 31. The kit of claim 16, wherein the first nucleic acid probe is labeled with an enzyme substrate label selected from the group of enzyme substrate labels consisting of HRPO, AP, and β-D-Gal. 32. The kit of claim 16, wherein the first nucleic acid probe is labeled with a fluorescent label selected from the group consisting of derivatives of Texas Red, fluorescein, phycocrytherin, rhodamine, phycocyanin, dansyl, umbelliferone, a green fluorophore, and an orange fluorophore. 33. The method of claim 15, wherein the first nucleic acid probe is labeled with a fluorescent label, further comprising the step of using a filter set that passes only one color at a time. 34. The kit of claim 16, wherein the first nucleic acid probe is labeled with a fluorescent label, the kit further comprising a filter set having a filter that passes only one color at a time. 35. A method for detecting the presence of a cellular target protein and a cellular target nucleic acid in a tissue sample, comprising the steps of: (a) contacting a section of the tissue sample with an antibody which specifically binds to the target protein; (b) determining binding of the antibody to the section of tissue sample; (c) hybridizing a labeled nucleic acid probe to the target nucleic acid in the same section of tissue sample; (d) detecting the presence of the labeled nucleic acid probe in the section of tissue sample; (e) comparing the results of step (b) with the results of step (d); and (f) staining the section of tissue sample with a morphological stain. 36. The method of claim 35 wherein the label is a fluorescent dye. 37. The method of claim 35, wherein the nucleic acid probe is constructed to hybridize to the target nucleic cid sequence indicating a genetic abnormality selected from the group consisting of amplification, addition, substitution, translocation and deletion. 38. The method of claim 35, wherein the target nucleic acid is a HER2/neu gene. 39. The method of claim 35, wherein the target protein is a HER2 protein. 40. The method of claim 35, wherein the tissue sample is selected from the group consisting of breast, prostate, ovary, colon, lung, endometrium, stomach, salivary gland and pancreas tissue samples. 41. The method of claim 35, wherein the section of tissue sample is obtained from fixed, paraffin-embedded tissue sample. 42. The method of claim 35 wherein the staining is performed before step (a). 43. The method of claim 35 wherein the staining is performed with a morphological stain comprising methylene blue, xanthine dye, or thiazine dye. 44. The method of claim 43 wherein the morphological stain comprises xanthine dye and thiazine dye.