Gene Expression Microarray Improves Prediction of Breast Cancer Outcomes

Flash-frozen samples of surgically removed breast cancer tissue are the key to measuring a patient’s risk of metastasis

Every cell in our bodies contains roughly 25,000 genes. If that is the case, why do we have such widely varying types of tissue, such as the cornea and the fingernail, the nose and the kidney? The reason is that in each type of cell, different combinations of these 25,000 genes are turned “on” or “off” to a certain degree, a term called expression. The “expression” of the genes determines the characteristics of each cell.

In a similar manner, cancer cells express their genes in differing ways. Using this supposition, could we use a gene expression assessment to predict which tumors will become metastatic and eventually lead to death as opposed to becoming relatively silent and allowing the patient to live?

Do we need to look at the expression of all 25,000 genes? Could we use this information to assist clinicians in determining who should receive more aggressive therapy early on?

The five-year survival for localized breast cancer is excellent — 98 percent. But once the disease becomes invasive and metastasizes, survival drops significantly. The strongest current clinical predictors for metastasis are age, axillary lymph node status, histological type and grade, tumor size, and hormone receptor status.


MammaPrint is the first FDA-approved gene expression microarray that can improve the prediction of breast cancer outcomes. (A microarray is a collection of up to tens of thousands of genes printed onto a glass slide with each spot on the slide containing a unique gene sequence). The manufacturer has discovered that there is no need to analyze all 25,000 genes. MammaPrint tests the activity of 70 genes that have been statistically determined to be useful in identifying women with early-stage breast cancer who are unlikely to have new evidence of disease over five to 10 years. This test has been available in the Netherlands since 2005.

Not so good for high risk

The test uses flash-frozen samples of the surgically removed breast tumor and relies on microarray technology to measure the amount of RNA expression of the 70 different genes. The level of activity for each of the 70 genes is factored into the equation to produce a “signature score” that classifies the patient as either high or low risk for metastasis. The low probability group has about half the likelihood of recurrence as the high probability group. The negative predictive value for those in the low risk population is 95 percent at 5 years and 90 percent at 10 years making a negative test (or low risk) very accurate. Unfortunately, the positive predictive value for the group with a high risk is only 23 percent and 29 percent for 5 and 10 years respectively.

The basis for the test is a study published in the January 2002 issue of Nature that involved 117 young breast cancer patients. Investigators identified 70 genes that seemed to predict metastasis. The study involved tissue bank material from patients with both sporadic and hereditary (BRCA1 and BRCA2 positive) genes. The researchers derived small amounts of RNA from tumor material that was flash-frozen with liquid nitrogen within one hour after surgery and looked for activated genes. The first step in gene activation research found that about 5,000 genes were active in this group of tumors.

The researchers then looked at the different gene activity levels, comparing those women who had no recurrence within five years to those who had distant metastasis within five years. They calculated an activity correlation coefficient of the expression for each gene with disease progression, and after a series of statistical challenges and calculations, chose 70 genes that appeared to be most likely to predict the development of metastatic disease over the next five years.

Reinforces current clinical practice

This study reinforced current clinical practice as it identified those genes known to be involved in breast cancer prognosis such as progesterone and estrogen receptors, cell cycle, invasion, signal transduction, metalloproteinases and VEGF activity.

This set of 70 genes was then validated in another set of 19 patients. Seven remained free of metastasis for five years and 12 developed metastasis within five years.

The researchers then studied samples in the tissue bank of the Netherlands Cancer Institute. This involved samples of 295 women with tumors less than 5 cm in size from lymph node positive and negative breast carcinoma. They extracted follow-up information from the medical registry and included a mean follow-up of 7.8 years. The researchers determined that the 70-gene profile was more accurate in predicting disease-free survival than the NIH criteria or the St. Gallen criteria, both of which are commonly used.

Final clinical validation involved 326 patients at five clinical sites who were followed for a median of 14 years. These data were published in 2006 in the Journal of the National Cancer Institute.

A major conclusion of all of these studies was that the ability to metastasize to distant sites is an early and inherent genetic property of breast cancer and “argues against the widely accepted idea that metastatic potential is acquired relatively late during multistep tumorigenesis.”

Overall, the results indicated that breast cancer prognosis could be derived from a gene expression analysis, hence the commercialization of this test. The developers feel that the use of this test can more accurately identify those patients who will and will not benefit from adjuvant systemic therapy.

There are limitations. Virtually all of the patients in the second study who were lymph node positive received adjuvant therapy, limiting the prognostic value of the profile for patients who do not receive adjuvant therapy.

Also, as noted above, the positive predictive value is poor and will cause some people to feel that metastasis is inevitable when the predictive value of a high risk result is actually quite low.

The analysis cannot be performed on formalin-fixed paraffin embedded tumor tissue as the formalin causes RNA degradation. MammaPrint requires flash freezing of the biopsy tissue, which is uncommon in surgical suites in the United States.

This test only applies to Stage I or II invasive breast cancer (ER + or ER-) with no lymph node involvement. According to the FDA, it should be used in patients who are under 61, with tumor size of less than 5 cm.

Unavoidable questions

Managed care decision makers will now face not only payment options, but must decide whether to use MammaPrint results to manage adjuvant therapy. The cost of the test was not available at the time of this publication.

Will patients trust a statistical model to determine their options? Will the test be used to enhance or change clinical decisions? Is the test likely to supplant current clinical indicators of survival?

These questions and others just as pressing will constantly face us as we all move toward Tomorrow’s Medicine!

Thomas Morrow, MD, is the immediate past president of the National Association of Managed Care Physicians. He has 21 years of managed care experience at the payer or health plan level.
The author is a director in the value-based health department at Genentech Inc. During the last three years, before taking the Genentech position, he received honoraria or other financial benefits from: Amgen, Amylin Pharmaceuticals, AstraZeneca, Biogen Idec, Centocor, Galderma, GlaxoSmithKline, Johnson & Johnson, Merck, Novartis, Novo Nordisk, Pfizer, Procter & Gamble, Q-Med, Sanofi-Aventis, Teva Pharmaceuticals Industries, UCB, and Wyeth. The views expressed in Tomorrow’s Medicine are the author’s alone.

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