Genomic profiling in breast cancer

Dr Keo Tabane tells us about genomic profiling tests for breast cancer that are currently available in South Africa.

The ‘one-size-fits-all’ approach is no longer commonplace and oncologists  now need to sub-classify breast cancer into different categories for prognostication, and treatment selection. This is to offer women tailor-made treatment for their individual cancers.

Genomic profiling tests available

There are various kinds of genomic profiling tests worldwide; two of which are available in South Africa: Oncotype DX and MammaPrint.

These can be performed on the breast cancer specimen to assess whether the patient stands to benefit from chemotherapy or not. In addition,     these tests give an estimate of the risk    of relapse – helping both the oncologist    and the patient quantify risks and make appropriate, personalised treatment decisions.

It is important to note that these tests are only appropriate for early stage breast cancer i.e. cancer that has not spread beyond the breast and/or the armpit.

Former methods of treatment selection

Prior to these tests, oncologists used clinical and pathological risk factors to determine whether a patient needed chemotherapy or not, before or after surgery.

The indications for chemotherapy  were tumour size of more than 2 cm;    the presence of cancerous glands in the armpit; patients younger than 40 years; HER2-positive status or triple-negative breast cancer (a particularly aggressive type of breast cancer), amongst others.

Recent findings

New advances have now demonstrated that it is not the size of the cancer that matters, but the biology of the cancer. Furthermore, not all women whose cancers have spread to fewer than      three glands in the armpit require chemotherapy.

These tests do not, however, assist     the oncologist to select the correct chemotherapy. The only indicate is whether chemotherapy would be beneficial or not.

They are mainly performed on cancers that are oestrogen-receptor positive and HER2-negative, although  MammaPrint can be performed on some oestrogen-receptor negative cancers, provided they are progesterone-receptor positive.

Most HER2-positive patients and triple-negative patients are mostly high-risk and require chemotherapy. With the addition of one year of Herceptin in the HER2-positive patient population.

Oncotype DX

This test is a 21-gene recurrence score that is performed on formalin-fixed tissue, following surgery of a breast tumour. The specimen is sent to the USA for testing and the turnaround time is approximately 10 working days.

It assesses 21 genes on the cancer specimen, and assigns a score that relates to risk. The results are reported as low-risk, intermediate-risk and high-risk.

Clinical trials have shown that low-risk patients do not benefit from chemotherapy, and should proceed to treatment with hormonal blockade. High-risk patients have a high risk of cancer recurrence and must be treated with chemotherapy, followed by hormonal blockade.

The challenge with Oncotype DX is that clinicians are not sure how to manage the intermediate-risk group. Clinical trials are ongoing, looking at this group.

Currently, the decision for this group would therefore need to be a shared decision between the oncologist and the patient, using traditional clinical and pathological factors as a guide.

Clinical trials have shown that the Oncotype DX test is able to alter the physician’s decision in approximately 30% of patients. We, at the Sandton Oncology Centre, part of the Morningside Breast Care Unit, presented our Oncotype DX results at a local oncology conference. We found that the physician’s decision was altered in 23% of cases, in line with international data. We are due to present our updated results locally in August this year.


This test is a 70-gene score and is sent to the Netherlands for testing. The turnaround time is around two weeks.

This is reported as either low-risk or high-risk. Unlike Oncotype DX, selected patients with oestrogen-receptor negative breast cancer can still benefit from this test, although they would be in the minority.

A recent study, the MINDACT study, showed that using this test could spare 46% of women, who are perceived by their oncologists to be at high recurrence risk by traditional factors, from unnecessary chemotherapy.

This test can also be used prior to surgery, where chemotherapy is being considered preoperatively, to classify the cancer into low-risk Luminal A, high-risk Luminal B, Basal-like and HER2 enriched. Thus, predicting whether a patient would respond to upfront chemotherapy or not. This is called the blueprint and is reported as part of the MammaPrint test result.

Which test to choose

Neither of these tests have been compared head to head. Therefore, either would be appropriate for use in patients with early stage breast cancer.


Most medical aids do fund these tests. The cost is approximately R30 000. Although the tests are expensive, this needs to be weighed against the physical and emotional costs of potentially unnecessary, toxic chemotherapy.

Dr Keo Tabane


Dr Keo Tabane is a medical oncologist at the Sandton Oncology Centre. She has a special interest in breast cancer care, and is an investigator is several international collaborative clinical trials through the Sandton Oncology Research Group. She is part of the executive committee of the South African Society of Medical Oncology (SASMO), as well as on the executive committee of the Breast Cancer Interest Group of South Africa (BIGOSA).

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