Assessing Genomic Assays in Early-Stage Invasive Breast Cancer

Genomic assays have become indispensable tools in the management of early-stage invasive breast cancer, helping oncologists move beyond traditional pathologic staging to make more individualized treatment decisions. Several validated tests are currently available, each with distinct methodologies, gene signatures, and clinical applications, and knowing when and how to use them can meaningfully change a patient's course of care.

During a Case-Based Roundtable event, Laura Huppert, MD, medical oncologist at UCSF Health, discusses decision-making factors and considerations with currently available genomic assays.

The Leading Assays: MammaPrint and Oncotype DX

Among the available options, 2 assays dominate everyday clinical practice. "The top two that I'm using on a regular basis are the MammaPrint and Oncotype assays," said Huppert.

MammaPrint is a 70-gene signature test that can be performed on formalin-fixed paraffin-embedded (FFPE) or fresh-frozen tissue using microarray technology. It generates a genomic risk score ranging from −1 to +1, where scores from −1 to 0 indicate higher genomic risk and scores from 0 to +1 indicate lower genomic risk.

Oncotype DX s a 21-gene signature test performed on FFPE samples using quantitative PCR (qPCR). Interpretation of its recurrence score requires consideration of both nodal status and menopausal status, and it is widely available in the United States.

Additional Assays Used in Select Cases

Three other tests play a role in specific clinical situations. Prosigna (formerly PAM50) uses a 50-gene signature to predict recurrence risk. EndoPredict is a 12-gene qPCR-based assay that likewise predicts recurrence. Breast Cancer Index (BCI) serves a somewhat different purpose: It is primarily used to guide decisions about extended adjuvant endocrine therapy, often deployed around the 5-year mark to determine whether a patient should continue treatment beyond the standard duration.

NCCN Guidelines and Preferred Tests

The NCCN Breast Cancer Guidelines incorporate all 5 assays, but not equally. Oncotype DX holds a critical distinction: it is both predictive (informing whether chemotherapy will provide benefit) and prognostic (estimating the likelihood of recurrence). MammaPrint, while clearly prognostic, has somewhat less data supporting its predictive utility. Both Oncotype DX and MammaPrint carry NCCN Category 1 preferred status. Prosigna, EndoPredict, and BCI receive NCCN Category 2A designations.

A Biomarker-Driven Algorithm for Adjuvant Therapy Decisions

These assays are indicated only in hormone receptor (ER)-positive, HER2-negative breast cancer. For triple-negative and HER2-positive disease, there is no established evidence supporting their use.

For premenopausal women with node-negative disease, Oncotype DX is the standard first choice. Node-positive disease introduces more complexity. The RxPONDER trial (NCT01272037)¹ demonstrated chemotherapy benefit across the board in node-positive patients, though Huppert noted nuances in interpreting its findings. "Sometimes I do send Oncotype DX or MammaPrint in select node-positive patients to help me have at least a sense of their biology and help make decisions," she explained, "although there is insufficient evidence at the moment" to recommend this routinely.

For postmenopausal women, the picture is clearer. Both Oncotype DX and MammaPrint are reasonable choices for node-negative and node-positive disease with 1 to 3 positive nodes. Patients with 4 or more positive nodes are generally recommended to receive chemotherapy regardless of genomic score, so testing is typically not pursued in that group.

Clarifying Menopausal Status with Hormonal Markers

Accurate menopausal status determination is essential for test interpretation, yet it can be clinically ambiguous. "It can sometimes be unclear for women—if they just had their IUD removed, when was their last period," Huppert observesd She routinely checks FSH and LH levels and, in uncertain cases, also considers serum anti-Müllerian hormone (AMH), a marker of ovarian reserve.

AMH levels decline in advance of the final menstrual period, making it a potentially useful indicator of menopausal trajectory. A retrospective analysis of the RxPONDER trial found that AMH correlated with chemotherapy benefit among women classified as premenopausal: those with serum AMH below 10 ng/mL showed no benefit from adding chemotherapy. Notably, approximately 21% of women enrolled as premenopausal in that trial had very low AMH levels consistent with a postmenopausal biology.² "If they're in the low range, that does suggest they're more likely postmenopausal," Huppert said. However, she cautioned that AMH was not prospectively collected in the trial and she does not check it routinely, "but it is something I've done a few times when I'm really not sure."

When menopausal status remains uncertain, she defaults to a conservative approach: "I would lean on calling them pre- or perimenopausal and group the perimenopausal patients in that category."

The Anthracycline Question

One area of ongoing debate involves high-risk patients and whether anthracycline-based regimens should be preferentially used. "Should we use anthracyclines for the very high Oncotype scores? Should we use anthracyclines for the high-2s vs the high-1s?" These questions, Huppert acknowledged, were not what the landmark genomic trials were designed to answer definitively. Nonetheless, she leans toward incorporating anthracyclines for very high Oncotype scores and high-2 results. "It's not a strict rule in my mind," she noted, "but I lean towards using anthracyclines for the high-2s and the very high Oncotype types based on these data."

Clinical Judgment Remains Central

Even with robust genomic data in hand, the assays are one input among many. Tumor size, nodal burden, and other high-risk pathologic features may drive a chemotherapy recommendation regardless of a favorable genomic score. "There are patients, regardless of the score, where they have high enough risk features—big enough tumors, enough things—where we want to give chemo no matter what," Huppert said. Still, she credits Oncotype DX with a particularly strong influence on her clinical thinking: "I do really think that the Oncotype helps guide my thinking about patients more strongly than most other clinical features."

As the field continues to evolve, these assays represent one of the clearest examples of precision oncology applied at scale: translating tumor biology into actionable, individualized treatment plans.

REFERENCES

1. Kalinsky K, Barlow WE, Gralow JR, et al. 21-Gene Assay to Inform Chemotherapy Benefit in Node-Positive Breast Cancer. N Engl J Med. 2021 Dec 16;385(25):2336-2347. doi: 10.1056/NEJMoa2108873. Epub 2021 Dec 1. PMID: 34914339; PMCID: PMC9096864.

2. Kalinsky K, Barlow WE, Pathak HB, Gralow JR, Albain KS, Hayes DF, et al. Correlation of serum anti-Müllerian hormone (AMH) levels on identification of premenopausal patients (pts) with hormone receptor positive (HR+), HER2-negative, node-positive breast cancer most likely to benefit from adjuvant chemotherapy in SWOG S1007 (RxPONDER) J Clin Oncol. 2024;42:505. doi: 10.1200/JCO.2024.42.16_suppl.505