Molecular Testing for Breast Cancer

Author: Marisa Healy, BSN, RN
Last Reviewed: October 05, 2022

When breast cancer is diagnosed, the tumor tissue is tested for "biomarkers.” Biomarkers are substances or abnormalities that can be found in the tumor tissue. These markers tell us what is happening in the cells in your body. They are used to predict how your body will respond to treatment and can help guide your treatment options. The use of biomarkers to customize treatment may also be called "personalized medicine.” These tests let your treatment team choose the right treatment for your tumor.

Molecular testing for breast cancer includes:

  • Hormone receptor status:
    • This test reports if the tumor has extra estrogen and/or progesterone receptors. One or both receptors may be positive. A positive result is called ER+/PR+, though how the result is reported varies depending on the test. Results may be reported as:
      • A percentage of the cells that tested positive for receptors (from 0% to 100%).
      • A number between 0 and 3, with 0 being no receptors and 3 being the most receptors.
      • An Allred score is a combination of the percent positive and their intensity. The score is from 0-9, with 9 being the most strongly receptor positive.
      • Positive or negative.
    • ER+ and/or PR+ tumors may be treated with hormone therapy, which works by blocking the tumor cells from getting the estrogen and progesterone they need to grow.
  • HER2/neu Status:
    • HER2/neu stands for human epidermal growth factor receptor 2, which is a protein that is found on the surface of some patient's breast cancer cells.
    • The HER2/neu test result may be reported as positive or negative (FISH test) OR as a score between 0 and +3 (IHC test), depending on the type of test used.
    • If the IHC test is used, a score of 0 or +1 is considered HER2 negative. A score of +3 is HER2 positive. A score of +2 is unclear and should be sent for the FISH test to confirm the HER2 status.
    • Tumors that are HER2 positive may be treated with medications that target this receptor.
  • OncoType Dx Test:
    • This test looks at the activity of 21 genes found in the tumor cells. It then uses that information to predict the risk of recurrence (the cancer coming back after treatment), how likely a patient is to benefit from chemotherapy treatment after surgery in early stage cancer, or the benefit of radiation therapy after DCIS surgery.
    • This test may be used for DCIS or stage I or II invasive breast cancers that are ER+ (estrogen receptor positive) that have not spread to the lymph nodes.
    • The result is reported as a "Recurrence Score," which is a number from 0 to 100 that reflects a low, intermediate, or high risk of recurrence. This score can be used, along with other tumor traits, to decide the best treatment for you.
  • MammaPrint Test:
    • This tests the activity of 70 genes found in the tumor cells to predict the risk of recurrence (the risk of the cancer coming back after treatment).
    • This test may be used for stage I and II breast cancers that are smaller than 5 centimeters and that have not spread to the lymph nodes.
    • The results are reported as either low risk or high risk. This result, along with other traits of the tumor may be used to choose treatment.
  • Urokinase plasminogen activator (uPA) and plasminogen activator inhibitor (PAI-1) tests:
    • Higher levels of these biomarkers in the tumor tissue may mean that it is more aggressive (grows faster).
    • These tests may be used in early stage breast cancers that has not spread to the lymph nodes to predict prognosis. A very good prognosis may mean patient can avoid chemotherapy treatment.
  • Prosigna (PAM50) Breast Cancer Prognostic Gene Signature Assay:
    • This is a genomic test that looks at the activity of 58 genes to estimate the risk of recurrence of hormone-receptor positive breast cancer.
    • The results are reported as a risk of recurrence score from 0 to 100 in 2 ways.
      • Node-negative cancers are either low (0-40), intermediate (41-60), or high (61-100).
      • Node-positive cancers are classified as low (0-40) or high (41-100).
    • Knowing if you have a high or low risk of distant recurrence more than 5 years after diagnosis can help decide whether 5 or 10 years of hormonal therapy is best for your treatment.

There are many different tests used to learn more about a breast cancer tumor. The tests that are ordered for you depend on your specific cancer. These tests and results can help guide your treatment. Ask your provider which tests are right for you.

References MammaPrint Test. 2020. Found at OncoType Dx Test. 20202. Found at

Hagemann, I.S. (2016). Molecular Testing in Breast Cancer. Arch Pathol Lab Med, 140, 815-824.

Harris, L. N., Ismaila, N., McShane, L. M., Andre, F., Collyar, D. E., Gonzalez-Angulo, A. M., ... & Van Poznak, C. (2016). Use of biomarkers to guide decisions on adjuvant systemic therapy for women with early-stage invasive breast cancer: American Society of Clinical Oncology clinical practice guideline. Journal of Clinical Oncology, JCO652289.

Cancer.Net. Breast Cancer: Diagnosis. 2020. Found at Prosigna Breast Cancer Prognostic Gene Signature Assay. 2020. Found at


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