Inclusion Criteria:

Part I

1. Women with HER2-negative breast cancer, as defined by FISH testing. (FISH testing may
have been performed on the primary tumor, or subsequently on a biopsy of a metastatic
lesion.)

2. Patients should be currently receiving chemotherapy, or scheduled to start
chemotherapy (second-line or subsequent), for HER2-negative metastatic breast cancer.

3. To begin protocol treatment, patients must have progressed after at least 1 previous
chemotherapy regimen for metastatic breast cancer.

4. Patients who are ER/PR positive or negative are eligible. ER/PR positive patients
should be refractory to hormonal therapy, or not good candidates for hormonal therapy
due to clinical features.

5. ECOG performance status of 0, 1 or 2 (see Appendix A).

6. Adequate recovery from recent surgery. ≥ 1 week must have elapsed from the time of a
minor surgery; ≥ 4 weeks must have elapsed from the time of a major surgery.

7. Patients must have measurable disease per RECIST criteria (see Section 9).

8. Laboratory values as follows: Absolute neutrophil count (ANC) ≥1500/μL Hemoglobin
(Hgb) ≥10 g/dL Platelets ≥100,000/L AST or ALT and alkaline phosphatase (ALP) must be
<2.5 x ULN, or <5 x ULN in patients with liver metastases. Total bilirubin <1.5 x the
institutional ULN Serum creatinine <1.5 x institutional ULN or calculated creatinine
clearance ≥45 mL/min Patients from Part 1 who have HER2 overexpression/activation
identified by the PRO Onc Assay may enter the treatment portion of Part 2, if they
meet all Part 2 eligibility criteria.

BRE 166 Protocol 20JAN2010 Page 19 of 63 9. Patients must be 18 years of age. 10. Life
expectancy of ≥ 12 weeks. 11. Patient must be accessible for treatment and follow-up. 12.
Patients must be able to understand the investigational nature of this study and give
written informed consent prior to study entry.

Part II

1. Women with HER2-negative breast cancer, as defined by FISH testing. (FISH testing
may have been performed on the primary tumor, or subsequently on a biopsy of a
metastatic lesion.)

2. Patients should be currently receiving chemotherapy, or scheduled to start
chemotherapy, for HER2-negative metastatic breast cancer.

3. Patients who are ER/PR positive or negative are eligible. ER/PR positive patients
should be refractory to hormonal therapy, or not good candidates for hormonal therapy
due to clinical features.

4. ECOG performance status of 0, 1 or 2.

5. Adequate recovery from recent surgery. ≥ 1 week must have elapsed from the time of a
minor surgery; ≥ 4 weeks must have elapsed from the time of a major surgery.

6. Patients must have measurable disease per RECIST criteria.

7. Laboratory values as follows:

• Absolute neutrophil count (ANC) ≥1500/μL

- Hemoglobin (Hgb) ≥10 g/dL

- Platelets ≥100,000/uL

- AST or ALT and alkaline phosphatase (ALP) must be <2.5 x ULN, or <5 x ULN in
patients with liver metastases.

- Total bilirubin <1.5 x the institutional ULN

- Serum creatinine <1.5 x institutional ULN or calculated creatinine clearance ≥45
mL/min

8. Patients must be ≥18 years of age.

9. Life expectancy of ≥ 12 weeks.

10. Patient must be accessible for treatment and follow-up.

11. Patients must be able to understand the investigational nature of this study and give
written informed consent prior to study entry.

12. Patients who are eligible for HER2-targeted treatment will begin this treatment at
the first time a treatment change is necessary (i.e. at the next progression of
metastatic breast cancer). This may occur immediately after PRO Onc assay results
are received, or may be several months later, for patients responding well to their
current chemotherapy.

13. Patients must continue to meet all inclusion and exclusion criteria for the Part 2
screening population at the time they are ready to start HER2-targeted treatment.

14. Ejection fraction ≥ 50%, as measured by echocardiogram (ECHO) or MUGA.

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Exclusion Criteria:

Part I

1. Patients currently responding to hormonal therapy.

2. Previous treatment with any HER2-targeted agent.

3. Patients with meningeal metastases.

4. Patients who are not considered likely candidates for subsequent therapy after next
progression of metastatic breast cancer.

5. Women who are pregnant or lactating.

6. Patients with New York Heart Association class II or greater congestive heart
failure.

7. Any of the following ≤6 months prior to starting study treatment:

• myocardial infarction;

• severe unstable angina;

• ongoing cardiac dysrhythmia

8. Concurrent severe, intercurrent illness including, but not limited to, ongoing or
active infection, or psychiatric illness/social situations that would limit safety
and compliance with study requirements.

9. Mental condition that would prevent patient comprehension of the nature of, and risk
associated with, the study.

10. Use of any non-approved or investigational agent ≤ 30 days of administration of the
first dose of study drug. Patients may not receive any other investigational or
anti-cancer treatments while participating in this study.

Part II

1. Patients currently responding to hormonal therapy.

2. Previous treatment with any HER2-targeted agent.

3. Patients with meningeal metastases.

4. Patients with active brain metastases. Patients who have received radiation or
surgery for brain metastases are eligible if there is no evidence of central nervous
system (CNS) disease progression, and at least 4 weeks have elapsed since treatment.
Ideally, patients should not still require use of seizure medication or steroids.

5. Patients who are not considered likely candidates for subsequent therapy after next
progression of metastatic breast cancer.

6. Women who are pregnant or lactating.

7. Patients with New York Heart Association class II or greater congestive heart
failure.

8. Any of the following ≤6 months prior to starting study treatment:

• myocardial infarction;

• severe unstable angina;

• ongoing cardiac dysrhythmia.

9. Concurrent severe, intercurrent illness including, but not limited to, ongoing or
active infection, or psychiatric illness/social situations that would limit safety
and compliance with study requirements.

10. Mental condition that would prevent patient comprehension of the nature of, and risk
associated with, the study.

11. Use of any non-approved or investigational agent ≤ 30 days of administration of the
first dose of study drug. Patients may not receive any other investigational or
anti-cancer treatments while participating in this study.

12. Past or current history of neoplasm other than the entry diagnosis with the exception
of treated non-melanoma skin cancer or carcinoma in situ of the cervix, or other
cancers cured by local therapy alone and a DFS ≥5 years.

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