Gene expression markers for breast cancer prognosis

1. A method of predicting the likelihood of long-term survival of a breast cancer patient without the recurrence of breast cancer, comprising:

quantitatively determining a level of an RNA transcript of CD68 in a breast cancer tissue sample obtained from said patient using a primer comprising the nucleotide sequence of SEQ ID NO:162,

normalizing said level against the expression level of a reference set of RNA transcripts to obtain a normalized CD68 expression level;

comparing the normalized CD68 expression level to a normalized CD68 expression level in reference breast tumor samples; and

predicting a likelihood of long-term survival without recurrence of breast cancer of the patient,

wherein increased normalized CD68 expression level indicates a decreased likelihood of long-term survival without breast cancer recurrence.

2. The method of claim 1 wherein the breast cancer is invasive breast carcinoma.

3. The method of claim 1 wherein said RNA is isolated from core biopsy tissue or fine needle aspirate cells.

4. A method of predicting the likelihood of long-term survival of a patient diagnosed with estrogen receptor (ER)-positive breast cancer, without the recurrence of breast cancer, comprising the steps of:

(1) quantitatively determining the level of an RNA transcript of CD68 in a breast cancer tissue sample obtained from said patient using a primer comprising the nucleotide sequence of SEQ ID NO:162,

(2) normalizing the level of the RNA transcript of CD68 against a reference set of RNA transcripts to obtain a normalized CD68 expression level;

(3) comparing the normalized CD68 expression level to a normalized CD68 expression level in reference breast tumor samples;

(4) subjecting the normalized CD68 expression level obtained in step (2) to statistical analysis; and

(5) determining whether the patient has an increased or decreased likelihood of said long-term survival without recurrence of breast cancer, wherein increased normalized CD68 expression level is indicative of a reduced likelihood of long-term survival without recurrence of breast cancer.

5. The method of claim 4 , wherein said sample is a tissue sample from fine needle, core, or other types of biopsy.

6. The method of claim 4 , wherein the level of the RNA transcript of CD68 is determined by quantitative reverse transcription polymerase chain reaction (qRT-PCR).

7. The method of claim 4 , further comprising the step of preparing a report indicating that the patient has an increased or decreased likelihood of long-term survival without breast cancer recurrence.

8. The method of claim 1 , wherein the level of the RNA transcript of CD68 is determined by quantitative reverse transcription polymerase chain reaction (qRT-PCR).

9. The method of claim 1 , further comprising the step of preparing a report indicating that the patient has an increased or decreased likelihood of long-term survival without breast cancer recurrence.

10. A method of predicting the likelihood of long-term survival of a breast cancer patient without the recurrence of breast cancer, comprising:

isolating RNA from a tissue sample obtained from a breast tumor of the patient;

reverse transcribing an RNA transcript of CD68 to produce a cDNA of CD68 using a primer comprising the nucleotide sequence of SEQ ID NO:162;

amplifying the cDNA of CD68;

producing an amplicon of the RNA transcript of CD68;

qauntitatively assaying a level of the amplicon of the RNA transcript of CD68;

normalizing said level against a level of an amplicon of at least one reference RNA transcript in said tissue sample to provide a normalized CD68 amplicon level;

comparing the normalized CD68 amplicon level to a normalized CD68 amplicon level in reference breast tumor samples; and

predicting the likelihood of long-term survival without the recurrence of breast cancer, wherein increased normalized CD68 amplicon level is indicative of a reduced likelihood of long-term survival without recurrence of breast cancer.

11. The method of claim 10 , wherein the breast cancer is invasive breast cancer.

12. The method of claim 10 , wherein the breast cancer is estrogen receptor (ER) positive breast cancer.

13. The method of claim 10 , wherein the cDNA of CD68 is amplified by polymerase chain reaction.

14. The method of claim 10 , further comprising the step of preparing a report indicating that the patient has an increased or decreased likelihood of long-term survival without breast cancer recurrence.

15. The method of claim 10 , wherein the level of the amplicon of the RNA transcript of CD68 is a threshold cycle (Ct) value and the normalized CD68 amplicon level is a normalized Ct value.

16. The method of claim 10 , wherein the reference breast cancer samples comprise at least 40 breast cancer samples.

17. The method of claim 1 , wherein the breast cancer tissue sample is a fixed, wax-embedded breast cancer tissue sample.

18. The method of claim 4 , wherein the breast cancer tissue sample is a fixed, wax-embedded breast cancer tissue sample.

19. The method of claim 10 , wherein the tissue sample is a fixed, wax-embedded tissue sample.