Compositions, kits, and methods for identification, assessment, prevention, and therapy of breast cancer

A method of assessing whether a patient is afflicted with breast cancer, the method comprising:

• a) determining the level of expression in a patient sample of at least two markers independently selected from the markers listed in Table 1 and Table 2;
• b) determining the level of expression of each of the markers in a control sample;
• and
• c) comparing the level of expression of the marker in the patient sample and the level of expression of the marker in the control sample;
• wherein a difference in the level of expression of more than one of the markers in the patient sample as compared to the corresponding level of expression of the markers in the control sample, is an indication that the patient is afflicted with breast cancer.

A method for assessing whether a patient has breast cancer that has metastasized or is likely to metastasize, comprising:

• a) determining the level of expression of a marker in a patient sample, wherein the marker is selected from the markers listed in Table 2,
• b) determining the level of expression of the marker in a control sample, and
• c) comparing the level of expression of the marker in the patient sample and the level of expression of the marker in the control sample;
• wherein a higher level of expression in the patient sample as compared to the level of expression of the marker in the control sample is an indication that the breast cancer has metastasized or is likely to metastasize.

A method for predicting the clinical outcome of a breast cancer patient, the method comprising:

• a) determining the level of expression of a marker in a patient sample, wherein the marker is selected from the markers listed in Table 2,
• b) determining the level of expression of the marker in a sample from a control subject having a good clinical outcome;
• and
• c) comparing the level of expression of the marker in the patient sample and the level of expression of the marker in the sample from the control subject;
• wherein a higher level of expression of the marker in the patient sample as compared to the level of expression of the marker in the sample from the control subject is an indication that the patient has a poor clinical outcome.

A method for monitoring the progression of breast cancer in a patient, the method comprising:

• a) determining the level of expression of a marker in a patient sample from a first point in time, wherein the marker is selected from the group consisting of the markers listed in Table 1 and the markers listed in Table 2;
• b) determining the level of expression of the marker in a sample from the patient at a subsequent point in time;
• and
• c) comparing the level of expression detected in steps a) and b), thereby monitoring the progression of breast cancer in the patient,
• wherein a change in the level of expression of the marker is indicative of either progression or regression of breast cancer.

A method of assessing the efficacy of a therapy for inhibiting breast cancer in a patient, the method comprising:

• a) determining the level of expression of a marker in a first sample obtained from the patient prior to administering at least a portion of the therapy to the patient, wherein the marker is selected from the group consisting of the markers listed in Table 1 and the markers listed in Table 2,
• b) determining the level of expression of the marker in a second sample obtained from the patient subsequent to administering the portion of the therapy;
• c) comparing the level of expression of the marker in the first sample as compared to the level of expression of the marker in the second sample;
• and
• d) determining that the therapy is efficacious for inhibiting breast cancer in the patient when there is a lower level of expression of the marker in the second sample, relative to the first sample.