CAM 278

Gene Expression Testing for Breast Cancer Prognosis

Category:Laboratory   Last Reviewed:April 2021
Department(s):Medical Affairs   Next Review:April 2022
Original Date:July 2004    

Gene expression assays measure the number of specific mRNAs being transcribed to assess the genes that are active in a particular cell or tissue. Analyses of gene expression can be clinically useful for disease classification, diagnosis, prognosis, and tailoring treatment to underlying genetic determinants of pharmacologic response (Steiling, 2019).

Adjuvant systemic therapy has reduced mortality from breast cancer (Davies et al., 2011; Peto et al., 2012){Harris, 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}. Several breast tumor gene expression assays have been developed to guide decisions on adjuvant systemic therapy for women with early-stage invasive breast cancer (Harris et al., 2016; Theodoros & Bergh, 2020)

Regulatory Status
MammaPrint® was U.S. Food and Drug Association (FDA)-approved on June 22, 2007. MammaPrint® is performed in Agendia laboratories in the Netherlands and in California. MammaPrint is FDA cleared for use in women under 61, with stage 1 or 2 breast cancer, invasive carcinoma, tumor size ≤5 cm, and lymph node negative (FDA, 2007).

Prosigna™ received 510(k) clearance from FDA based on substantial equivalence to MammaPrint® on September 6, 2013 (FDA, 2013).

Additionally, many labs have developed specific tests that they must validate and perform in house. These laboratory-developed tests (LDTs) are regulated by the Centers for Medicare and Medicaid (CMS) as high-complexity tests under the Clinical Laboratory Improvement Amendments of 1988 (CLIA ’88). As an LDT, the U. S. Food and Drug Administration has not approved or cleared this test; however, FDA clearance or approval is not currently required for clinical use.

Application of coverage criteria is dependent upon an individual’s benefit coverage at the time of the request.

  1. Use of the Oncotype DX 21-gene expression, EndoPredict, or PAM50 (Prosigna) assay is considered MEDICALLY NECESSARY for the determination of the recurrence of risk for deciding whether or not to undergo adjuvant chemotherapy in individuals with primary, invasive breast cancer who meet all of the following criteria:
    1. Node-negative (lymph nodes with micrometastases (less than two mm in size) are considered node negative for this policy statement) OR with 1-3 involved axillary lymph nodes when test results would impact treatment decisions
    2. Hormone receptor positive (either estrogen-receptor (ER) or progesterone-receptor (PR) positive)
    3. Human epidermal growth factor receptor two (HER2) negative
    4. Tumor size > 0.5 cm
    5. Histology is ductal/NST (see Note 1), lobular, mixed or micropapillary
    6. Staging pT1, pT2, or pT3; and pN0 or pN1mi (≤2mm axillary node metastasis) or pN1 (<4 nodes)
      • The assay should only be ordered on a tissue specimen obtained during surgical removal of the tumor and after subsequent pathology examination of the tumor has been completed and determined to meet the above criteria (i.e., the test should not be ordered on a preliminary core biopsy).
      • For patients who otherwise meet the above characteristics but who have multiple primary tumors, a specimen from the tumor with the most aggressive histological characteristics should be submitted for testing. It is not necessary to conduct testing on each tumor; treatment is based on the most aggressive lesion.
  2. Use of Mammaprint to determine recurrence risk for deciding whether to undergo adjuvant chemotherapy is considered MEDICALLY NECESSARY in women with high clinical risk per MINDACT categorization with primary, invasive breast cancer with the same characteristics as considered medically necessary for Oncotype DX (1a – 1f).
  3. Tumor testing for hormone receptor (Estrogen Receptor and Progesterone Receptor) expression and Human Epidermal Growth Factor Receptor 2 (HER2) overexpression is considered MEDICALLY NECESSARY for all women with newly diagnosed, non-metastatic breast cancer.
  4. Use of Breast Cancer Index (BCI) test to determine benefit of extended adjuvant endocrine therapy is considered MEDICALLY NECESSARY in individuals with T1 and T2 HR-positive, HER2-negative, and lymph node-negative tumors.
  5. Use of Mammaprint to determine recurrence risk for deciding whether to undergo adjuvant chemotherapy is considered NOT MEDICALLY NECESSARY in women with low clinical risk per MINDACT categorization with primary, invasive breast cancer.

The following is considered NOT MEDICALLY NECESSARY due to a lack of available published scientific literature confirming that the test(s) is/are required and beneficial for the diagnosis and treatment of a patient’s illness.

  1. In males, use of gene expression assays other than 21-gene RT-PCR-based assays is considered NOT MEDICALLY NECESSARY.
  2. Use of other gene expression assays including, but not limited to Mammostrat, is considered NOT MEDICALLY NECESSARY.
  3. The use of Oncotype DX for DCIS is considered NOT MEDICALLY NECESSARY.
  4. Use of all other tests than 21-gene Oncotype Dx for pN0 or Node-negative or Breast Cancer Index (BCI) for predictive purposes is considered NOT MEDICALLY NECESSARY.
  5. Use of gene expression assays for any other indications or in any other situations not mentioned above is considered NOT MEDICALLY NECESSARY.

Note 1: From NCCN (2021) “According to WHO, carcinoma of NST (no special type) encompasses multiple patterns including medullary pattern, cancers with neuroendocrine expression, and other rare patterns” (NCCN, 2021).

Globally, breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death in women. In the United States, breast cancer is the most diagnosed cancer and the second most common cause of cancer death in women. Approximately 1 in 8 women will develop breast cancer in their lifetime (Siegel, Miller, & Jemal, 2019; Taghian & Merajver, 2020).  

Adjuvant systemic therapy has reduced mortality from breast cancer (Darby et al., 2011; Davies et al., 2011; Forouzanfar et al., 2011; Peto et al., 2012). However, adjuvant therapy is not without its risks and costs. Reliable prognostic profiles for recurrence and clinically applicable predictive factors would be of great value in the use of adjuvant therapy by identifying which therapies would be most likely of benefit to patients and which patients would not benefit (Theodoros & Bergh, 2020).

Several biology-based prognostic profiles have been developed, validated, and are in clinical use to predict breast cancer response to chemotherapy. Intensive research efforts are ongoing to refine the clinical utility and the indications for these prognostic profiles (Simon, Paik, & Hayes, 2009). In addition, as next generation sequencing of tumor genomes progresses, these profiles will be improved or replaced by the next generation of molecular profiles (Theodoros & Bergh, 2020).

Chen et al. examined the association of genomic methylation and the changes in the subsequent transcriptome. The authors desired to observe how a chronic condition influenced epigenomic changes. A human volunteer provided peripheral blood samples over 36 months, and the authors created 28 methylome datasets as well as 57 transcriptome datasets. During this period, the human volunteer experienced 6 viral infections and two elevated periods of fasting glucose and glycated hemoglobin A1c. The authors noted that the methylome changes correlated with the glucose level changes, and that the gene expression levels varied greatly, often during the viral infections. The authors proposed that the DNA methylation was the primary gene expression mechanism for chronic conditions, as it was generally a stable epigenetic marker (Chen et al., 2018).

Rueda et al. presented a disease model that stratifies distinct stages and incorporated factors such as “locoregional recurrence, distant recurrence, breast-cancer-related death and death from other causes”. This model integrated these features into an individual risk-of-recurrence prediction. This model was applied to 3,240 patients, of which 1,980 had molecular data. From this model, the authors identified four late-recurring “integrative subtypes, comprising about one quarter (26%) of tumours that are both positive for ER and negative for human epidermal growth factor receptor 2, each with characteristic tumour-driving alterations in genomic copy number and a high risk of recurrence (mean 47–62%) up to 20 years after diagnosis”. These four subtypes were “enriched” in copy number alterations, and these alterations were labeled the “likely drivers” of each subgroup. A triple negative subgroup “IntCluster 10” was found to be largely relapse-free after 5 years whereas the “IntCluster4 ER negative” subgroup was found to have a large risk of recurrence (Rueda et al., 2019).

However, innovative ideas continue to spread as the field burgeons, not limiting its inspiration to etiology. Savci-Heijink, Halfwerk, Koster, Horlings, and van de Vijver (2019) believe in the clinical value of identifying a gene expression profile in tumors that selects a subpopulation of patients that is more likely to develop visceral organ metastases due to their association with poor survival outcomes in breast cancers. The researchers analyzed the genetic profiles of 157 primary tumors from breast cancer patients who developed distant metastases and differentially expressed genes between the group of tumors with visceral metastasis and those without visceral metastases were noted. The results yielded fourteen differentially expressed genes (WDR6, CDYL, ATP6V0A4, CHAD, IDUA, MYL5, PREP, RTN4IP1, BTG2, TPRG1, ABHD14A, KIF18A, S100PBP and BEND3) between the tumors with visceral metastasis and those without visceral metastases. According to the data, five of the genes (CDYL, ATP6V0A4, PREP, RTN4IP1 and KIF18A) were upregulated while the other genes were downregulated, creating a list of biomarkers and genetic signatures of interest that may result in earlier diagnosis and treatment (Savci-Heijink et al., 2019).

OncoType DX
The Oncotype Dx 21-gene recurrence score (RS) is the best-validated prognostic assay and may identify patients who are most and least likely to derive benefit from adjuvant chemotherapy. The expression levels of 16 genes (plus five reference genes) are measured by quantitative reverse transcription polymerase chain reaction (RT-PCR). The sum of this calculation is known as the RS to optimize prediction of distant relapse despite tamoxifen therapy. At this time, it is indicated for women with node-negative, estrogen receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancer to determine the prognosis in patients recommended to proceed with at least a five-year course of endocrine therapy. The optimal RS cutoff for omission of chemotherapy remains unclear given that the different studies have used different cutoffs (Mamounas et al., 2010; Paik et al., 2004; Paik et al., 2006; Sparano et al., 2015). However, it may be reasonable not to administer adjuvant chemotherapy for patients with node-negative, ER-positive breast cancer and an RS of <15 (Theodoros & Bergh, 2019, 2020).

Sparano et al. (2018) performed a prospective trial to assess the utility of the recurrence score based on the 21 gene breast cancer assay to predict chemotherapy in patients who have a midrange score.  “Of the 9,719 eligible patients with follow-up information, 6,711 (69%) had a midrange recurrence score of 11 to 25 and were randomly assigned to receive either chemoendocrine therapy or endocrine therapy alone. The trial was designed to show noninferiority of endocrine therapy alone for invasive disease-free survival (defined as freedom from invasive disease recurrence, second primary cancer, or death).” They found that “Endocrine therapy was noninferior to chemoendocrine therapy in the analysis of invasive disease-free survival (hazard ratio for invasive disease recurrence, second primary cancer, or death [endocrine vs. chemoendocrine therapy], 1.08; 95% confidence interval, 0.94 to 1.24; P=0.26). At 9 years, the two treatment groups had similar rates of invasive disease-free survival (83.3% in the endocrine-therapy group and 84.3% in the chemoendocrine-therapy group), freedom from disease recurrence at a distant site (94.5% and 95.0%) or at a distant or local-regional site (92.2% and 92.9%), and overall survival (93.9% and 93.8%). The chemotherapy benefit for invasive disease-free survival varied with the combination of recurrence score and age (P=0.004), with some benefit of chemotherapy found in women 50 years of age or younger with a recurrence score of 16 to 25.” They concluded that “Adjuvant endocrine therapy and chemoendocrine therapy had similar efficacy in women with hormone-receptor-positive, HER2-negative, axillary node-negative breast cancer who had a midrange 21-gene recurrence score, although some benefit of chemotherapy was found in some women 50 years of age or younger (Sparano et al., 2018).”

In a prospective, randomized trial of endocrine therapy (ET) versus chemoendocrine therapy (CET), Kalinsky et al. (2021) attempted to gather support for the potential prognostic and predictive role of the RS for CT benefit in postmenopausal patients with 1 to 3 lymph node-positive breast cancer using Oncotype Dx in the RxPonder Trial. In the study, women with a RS less than 25 were randomized to receive ET or CET in 1:1 randomization using 3 stratification factors—RS (0-13 vs.14-25), menopausal status, and axillary nodal dissection vs. sentinel node biopsy—with the end goal of ascertaining whether the effect of CT on invasive disease-free survival (IDFS) was a function of RS. Of 9,383 patients screened in the study, 5,083 patients were randomized based on having met eligibility criteria, and with a median follow-up period of 5.1 years, the authors observed 447 IDFS events. It was reported that in a model with CT, RS, and menopausal status (no interaction term), higher continuous RS was associated with worse IDFS (hazard ratio HR 1.06, 2-sided p<0) and that and CT was associated with an improvement in IDFS (HR 0.81, p=0.026). Moreover, a distinction exists between postmenopausal and premenopausal patients in their reception of chemoendocrine versus endocrine therapy based on their RS: in postmenopausal patients (n=3,350), the HR for CET vs. ET was not significant (HR=0.97, p=0.82, indicating no benefit from CT, whereas in premenopausal patients (N=1,665, 33%), the HR (0.54) was statistically significant (p=0.0004), suggesting CT benefit. In other words, postmenopausal patients in this situation may be spared adjuvant chemotherapy, while premenopausal patients have much to benefit from the same. Therefore, the authors concluded that “the current data show that adjuvant therapy can be de-escalated to ET alone in postmenopausal pts with a RS < 25 and 1-3 +LN” (Kalinsky et al., 2021).

EndoPredict® (Myriad Genetic, Inc.) is a breast cancer prognostic test that assesses the expression of eight target genes as compared to three housekeeping (normalization) genes and one additional control gene to detect contamination by residual DNA. The results of this testing are combined to produce a clinical score to determine whether the breast cancer is at high- or low-risk of possible recurrence within ten years (Myriad, 2020; Warf et al., 2017).

According to the Myriad EndoPredict® Technical Specifications (Effective Date: 12/10/2019), if the test is used on resected tissue, the 12-gene molecular score is then “combined with tumor size and lymph node status to generate an EPclin Risk Score associated recurrence risks and estimated absolute benefit of chemotherapy” whereas “the molecular score and its associated 10-year risk of distance recurrence…are provided” if the sample is a biopsy specimen (Myriad, 2019). The target genes in the EndoPredict® test include the following (Filipits et al., 2019; Warf et al., 2017):

  • BIRC5
  • DHCR7
  • UBE2C
  • AZGP1
  • IL6ST
  • MGP
  • RBBP8
  • STC2

Filipits et al. (2017) validated EP’s 11 gene version (only missing the one gene to control for DNA contamination, HBB). The investigators combined these gene expression results with nodal status and tumor size into a risk score (“EPClin”). Two cohorts of 378 and 1,324 samples were used in this study, and both cohorts demonstrated that the risk score produced was an independent predictor of distant recurrence. The investigators calculated that EPClin had superior prognostic power compared to solely clinicopathologic factors. EPClin was also found to result in a 4% rate of recurrence for both low-risk cohorts in each sample, a 28% recurrence rate in the “high risk” portion of the 378-item sample, and a 22% recurrence rate in the “high risk” portion of the 1324-item sample. The authors concluded that “the multigene EP risk score provided additional prognostic information to the risk of distant recurrence of breast cancer patients, independent from clinicopathologic parameters. The EPclin score outperformed all conventional clinicopathologic risk factors (Filipits et al., 2011; Myriad, 2017).” 

Two recent studies by Sestak and colleagues (2018) have also shown the clinical validity and utility of EndoPredict® testing in women with node-positive breast cancer (Sestak et al., 2018; Sestak et al., 2019). One study consisted of both node-positive and node-negative women (n=3,746) to compare the performance of EPclin for predicting distant recurrence in women who had either received endocrine therapy (ET) alone or ET with chemotherapy (ET+C). “In this comparative non-randomised analysis, the rate of increase in DR with EPclin score was significantly reduced in women who received ET + C versus ET alone. Our indirect comparisons suggest that a high EPclin score can predict chemotherapy benefit in women with ER-positive, HER2-negative disease (Sestak et al., 2019).” In the other study, the researchers compared the performance of six different prognostic signatures for ER-positive breast cancer in two different patient groups—node-negative and node-positive. The six tests include EndoPredict®, Breast Cancer Index (BCI), Clinical Treatment Score (CTS), IHC4, ROR, and RS. Within the node-positive cohort (n=277), the authors report the highest univariate hazard ratio (HR) for EPclin (1.69) compared to 1.39 for RS (Sestak et al., 2018).

Another study (n=1,702) compared the use of EndoPredict® in node-positive and node-negative women treated with endocrine therapy only.  This study assessed both the 10- and 15-year distant recurrence-free rate (DRFR). Similar to the node-negative individuals, the 10-year DRFR for patients with 1 – 3 positive nodes improved significantly higher than for the full cohort (95.6% versus 80.9%, respectively). “The molecular and EPclin scores were significant predictors of DRFR after adjusting for clinical variables, regardless of nodal status (Filipits et al., 2019).”

Evidence of EndoPredict’s ability to produce a change in therapeutic management abound. For example, Villarreal-Garza et al. (2020) enrolled 99 premenopausal women with a median age of 43 and with hormone receptor-positive, HER2-negative, T1-T2, and N0-N1 breast cancer, and the cases were presented to a multidisciplinary tumor board. The researchers reported that a “change in chemotherapy or endocrine therapy regimen was suggested in 19% and 20% of cases” when EPclin results were made available. Moreover, it was reported that a significant difference could be “found in the median EPclin score between patients with a low- vs. high-intensity chemotherapy and endocrine therapy regimen recommendation (p = 0.049 and p = 0.0001, respectively)”, which may have contributed to high final treatment adherence (93%) in premenopausal patients (Villarreal-Garza et al., 2020).

Dubsky et al. (2020) used hormone receptor (HR)-positive, HER2-negative samples from patients in the ABCSG-34 randomized phase II trial to generate a 12-gene molecular score with the goal of assessing EndoPredict’s ability to predict response to neoadjuvant chemotherapy (NaCT) or neoadjuvant endocrine therapy (NET). The patients in the study were assigned to receive either NaCT or NET based on menopausal status, HR expression, grade and Ki67, and their responses to their assigned therapies were measured by using residual cancer burden (RCB). It was reported that the 12-gene molecular score significantly predicted treatment response for NaCT and NET, boasting areas under the curve (AUC) of 0.736 and 0.726 respectively. Based on these results, it was concluded that “Tumours with low MS were unlikely to benefit from NaCT, whereas a high MS predicted resistance to NET”, further motivating the use of EndoPredict to provide personalized treatment to patients (Dubsky et al., 2020).

Breast Cancer Index
The Breast Cancer Index (BCI) is a combination of two profiles, the HOXB13-to-IL17BR expression ratio (H:I ratio) and the Molecular Grade Index (MGI). This combination is intended to report “the individualized likelihood of benefit from extended endocrine therapy” and “the individualized risk of late distant recurrence of breast cancer (Years 5 - 10)”. The five genes the MGI examines are BUB1B, CENPA, NEK2, RACGAP1, and RRM2 (Biotheranostics, 2018). Using genome-wide microarray analysis, three differentially expressed genes that were associated with an increased risk of progression among ER-positive patients treated with tamoxifen were: the antiapoptotic homeobox B13 (HOXB13, overexpressed in tamoxifen recurrent cases) and both interleukin 17B receptor (IL17BR) and EST AI240933 (both overexpressed in tamoxifen nonrecurrent cases) (Theodoros & Bergh, 2019).

This test was validated by Ma et al. (2008). The MGI was validated by separate 410-sample and 323-sample cohorts, and its interaction with the H:I ratio was evaluated. The authors found that “high MGI was associated with significantly worse outcome only in combination with high HOXB13:IL17BR, and likewise, high HOXB13:IL17BR was significantly associated with poor outcome only in combination with high MGI.” The investigators concluded that “the combination of MGI and HOXB13:IL17BR outperforms either alone and identifies a subgroup (∼30%) of early stage estrogen receptor–positive breast cancer patients with very poor outcome despite endocrine therapy (Ma et al., 2008).

The BCI has been recently demonstrated to be discerning in other respects. The IDEAL trial attempted to answer the pressing question of the optimal duration of extended endocrine therapy (EET), after completing 5 years of initial aromatase inhibitor (AI)–based adjuvant therapy (Liefers et al., 2020). The IDEAL trial assessed the ability of BCI (H/I) to predict endocrine benefit of 2.5 vs. 5 years of extended letrozole using available tumor specimen samples from 908 HR+ patients (73% lymph node-positive, disease free at 2.5 years), with 88% and 68% of which were receiving prior treatment with an aromatase inhibitor (AI) or chemotherapy, respectively. It was found that BCI by H/I status (High vs. Low) was “significantly predictive of response from extended letrozole in the overall (N = 908) and pN+ [lymph node-positive] (N = 664) cohorts”, leading the researchers to exalt the BCI as an important genomic tool for future use (Liefers et al., 2020). 

Notably, BCI (H/I) predicted EET benefit in patients that received any primary adjuvant therapy with an AI (N = 794)

Predictor Analysis of Microarray 50
The Predictor Analysis of Microarray 50 (PAM50, by Prosigna) is a 50-gene test that characterizes an individual tumor by intrinsic subtype. It was designed to determine the intrinsic subtype of a cancer using only 50 prespecified genes. The four subtypes are “luminal A, luminal B, HER2-enriched, and basal-like” (Parker et al., 2009). Results from the PAM50 are used to generate the risk of recurrence (ROR) score, which can stratify patients with ER-positive disease into high, medium, and low subsets. The test can be performed on formalin-fixed, paraffin-embedded tissue with a high degree of analytical validity (Nielsen et al., 2010; Theodoros & Bergh, 2019).

This test was validated by Parker et al. The investigators developed this 50-gene set from 189 prototype samples and evaluated 761 patients for prognosis. The four discrete subtypes were found to be prognostically significant and predicted neoadjuvant chemotherapy efficacy with a negative predictive value for pathologic complete response (to a taxane and anthracycline regimen) of 97%. The authors concluded “diagnosis by intrinsic subtype adds significant prognostic and predictive information to standard parameters for patients with breast cancer (Parker et al., 2009).”

Recently, the intrinsic molecular subtype generated by the Prosigna assay has been demonstrated to be useful in guiding the inclusion and exclusion of an anthracycline to CMF-based chemotherapy. The DBCG89D trial randomized 980 high-risk early breast cancer patients to adjuvant CMF (cyclophosphamide, methotrexate and fluorouracil) or CEF (cyclophosphamide, epirubicin and fluorouracil), ultimately using the data from 686 tumor samples. Continuous ROR score was associated with distant recurrence for CMF and CEF (hazard ratios of 1.20 and 1.04, respectively), and distant recurrence was reported to be significantly longer in those patients with HER2-enriched tumors treated with CEF than with CMF. The results suggested that the benefit of CEF as compared to CMF correlate with an increasing ROR score, and so “patients with Her2-enriched breast cancer derived substantial benefit from anthracycline chemotherapy whereas anthracyclines are not an essential component of chemotherapy for patients with luminal subtypes”, and, similarly, “A benefit from substituting methotrexate with epirubicin is observed among patients with Her2-enriched or Basal-like subtypes whereas there is a lack of such benefit among patients with a Luminal A or Luminal B subtypes” (Jensen et al., 2020). However, the authors admit that the results of the study may potentially be skewed by the retrospective evaluation’s use of only a small subset of patients’ data and the lack of optimal instrumentation and testing, since one-third of the patients were ER-positive but endocrine therapies were not employed (Jensen et al., 2020).

MammaPrint is a 70-gene test that assesses the risk of recurrence within the first 5-10 years of diagnosis. The test reports risk in one of two categories, “low” and “high”. MammaPrint’s validation places “low” risk at a 1.3% chance (95% confidence interval: 0-3.1%) that cancer will recur in 5 years whereas those classified as “high” risk have a 11.7% chance for the cancer to recur in 5 years (95% confidence interval: 6.6%-16.8%) (Agendia, 2015, 2018). Agendia offers other breast cancer assessments, such as BluePrint. BluePrint is an 80-gene molecular subtyping assay, which “analyzes the activity” of its genes. It is proposed to identify a tumor’s molecular “subtype”: luminal A/B, basal, or HER2. Each subtype has varying molecular characteristics (ER-positive or negative, HER2-positive or negative, et al.), which is proposed to help clinicians provide targeted treatment for a patient (Agendia, 2019).

MammaPrint was validated by Cardoso et al. The authors determined the risk recurrence of 6,693 patients. Of these 6,693 patients, 1,550 of them were found to have high clinical risk and low genomic risk, and the rate of survival without distant metastasis in this cohort was 94.7% among those not receiving chemotherapy. The difference in survival rate between these patients and those receiving chemotherapy was 1.5%. The authors estimated that “given these findings, approximately 46% of women with breast cancer who are at high clinical risk might not require chemotherapy” (Fatima Cardoso et al., 2016).

However, it may be possible that new prognostic assays are beginning to make their foray.   

Prat et al. (2020) derived a prognostic assay that integrates multiple data types for predicting survival outcome in patients with newly diagnosed HER2-positive breast cancer to aid treatment decisions for those with early-stage HER2-positive breast cancer, where escalation or de-escalation of systemic therapy is a point of contention. Using clinical-pathological data on stromal tumor-infiltrating lymphocytes, PAM50 subtypes, and expression of 55 genes obtained from patients who participated in the Short-HER phase 3 trial, Prat et al. (2020) then evaluated their model based on a combined dataset of 267 patients with early-stage HER2-positive breast cancer treated with different neoadjuvant and adjuvant anti-HER2-based combinations and from four other studies (PAMELA, CHER-LOB, Hospital Clinic, and Padova) with disease-free survival outcome data. The final model, named HER2DX, was comprised of data from 435 (35%) of 1254 patients for tumor size (T1 vs rest), nodal status (N0 vs rest), number of tumor-infiltrating lymphocytes (continuous variable), subtype (HER2-enriched and basal-like vs rest), and 13 genes. The authors exalt the analytical power of HER2DX by reporting that it was “significantly associated with disease-free survival as a continuous variable” and reported that the 5-year disease-free survival in the HER2DX low-risk group was 93.5% (89.0-98.3%) whereas the high-risk group reported 81.1% (71.5-92.1). The researchers assert that HER2DX “identifies patients with early-stage, HER2-positive breast cancer who might be candidates for escalated or de-escalated systemic treatment” and that “Future clinical validation of HER2DX seems warranted to establish its use in different scenarios, especially in the neoadjuvant setting” (Prat et al., 2020).

Clinical Utility
Blok et al. (2018) performed a meta-analysis of the MammaPrint, OncotypeDX, PAM50/Prosigna and Endopredict assays. The authors investigated the evidence available on both the clinical utility and economic value of these assays. Most of the observed studies concluded that genomic profiling contributed to less chemotherapy use. However, the authors caution that “absolute numbers should be interpreted carefully, since some tests are less frequently studied than others” especially as “the clinical consensus on adjuvant chemotherapy is that we are most likely over-treating our patients, since we are not capable of identifying patients that will or will not benefit from chemotherapy using the current clinicopathological parameters". The authors note that Petkov et al. retrospectively matched OncoType DX use with SEER registry data for over 40,000 patients and found that “patients with node negative, HR+, HER2- breast cancer which underwent testing (n = 40,134, 22.7% chemotherapy) had no lower chemotherapy use compared to patients that were not tested (n = 144,056, 22.2% chemotherapy)”. The authors noted that 90% of the 44 economic analyses concluded that genomic testing was cost-effective; although, various biases are mentioned (publication bias, publications using overlapping samples, and more) (Blok et al., 2018).

Gustavsen et al. (2014) performed an economic analysis of the Breast Cancer Index. “Costs associated with adjuvant chemotherapy, toxicity, followup, endocrine therapy, and recurrence were modeled over 10 years. The models examined cost utility compared with standard practice when used at diagnosis and in patients disease-free at 5 years post diagnosis.” The authors calculated BCI to save approximately $3,803 per patient for the newly diagnosed population and $1,803 per patient in the 5 years post diagnosis population. These savings were projected to come from “adjuvant chemotherapy use, extended endocrine therapy use, and endocrine therapy compliance” (Gustavsen et al., 2014).

Camp et al. (2019) investigated a new reinterpretative technique of the PAM50 assay. The authors reorganized the gene expression data provided by the assay into five “quantitative, orthogonal, multi-gene breast tumor traits” and stated that these “dimensions” better represented breast cancer pedigrees. They re-assessed the data of the GEICAM/9906 clinical trial with these dimensions. After reorganization, the authors concluded that dimensions “PC1 and PC5” were associated with disease-free survival, and low “PC3 and PC4” indicated response to paclitaxel. However, high PC3 or PC4 did not show survival advantage (Camp et al., 2019).

Wuerstlein et al. (2019) evaluated the clinical utility of MammaPrint and its intended adjunct test, BluePrint. Physicians were asked to provide initial therapy recommendations (based on clinicopathological factors), then were provided results of MammaPrint/BluePrint risk stratifiers. Then the same physicians provided new treatment recommendations, and the subsequent treatment was recorded. The authors identified a switch in treatment in 29.1% of cases. Physician adherence to MammaPrint risk assessment was over 90% in both groups of risk (low and high). Even when physicians and risk stratifiers disagreed, the physicians tended to recommend treatments based on the risk stratifier. Overall, the authors concluded that “MammaPrint and BluePrint test results strongly impacted physicians’ therapy decisions in luminal EBC with up to three involved lymph nodes” (Wuerstlein et al., 2019).

Toole et al. (2014) evaluated the similarities and differences in genetic profiles between primary breast cancers in patients with multiple primaries. The authors also evaluated whether obtaining genetic profiling scores (OncoType DX) on each primary affected chemotherapy decisions. 22 patients had multiple tumor samples sent for analysis, and the authors found that 6 patients had their chemotherapy recommendations changed based on differing OncoType scores (between their samples). The authors also noted that scores tended to differ more between tumors appearing simultaneously on different breasts compared to multiple tumors on the same breast (Toole, Kidwell, & Van Poznak, 2014).

Another study published in 2016 compared the use of EndoPredict® (EPclin) and PAM50 risk of recurrence (ROR) scores in node-positive breast cancer to predict distant metastasis-free survival (MFS). ROR scores can be based using subtype (ROR-S); subtype and proliferation (ROR-P); subtype and tumor size (ROR-T); and subtype, proliferation, and tumor size combined (ROR-PT). “Predictors including clinical information showed superior prognostic performance compared to molecular scores alone (10-year MFS, low-risk group: ROR-T 88 %; ROR-PT 92 %; EPclin 100 %). The EPclin-based risk stratification achieved a significantly improved prediction of MFS compared to ROR-T, but not ROR-PT (Martin et al., 2016).”

A recent study by Ding et al. (Ding et al., 2019) specifically used the 21-gene recurrence score for patients with pure mucinous breast cancer (PMBC). This multi-year study of 8,048 female PMBC patients categorized the patients based on RS risk groups of low, intermediate, and high RS risk groups. They found the distribution to be 64.9%, 31.9%, and 3.2%, respectively.  For PMBC patients, the authors note that PMBC patients do show significantly different 5-year survival rates based on ER status. They do conclude that RS can be used with PMBC patients…”age, progesterone receptor status, and grade could independently predict RS” (Ding et al., 2019). These data support the findings of a considerably smaller comparative study (n=35 PMBC patients and n=70 IDC patients) that show on average PMBC patients score lower than IDC patients (average RS 21.26 and 24.40, respectively); however, they authors do conclude that “patients with high RS in the PMBC group might be recommended to receive adjuvant chemotherapy” since 8.57% of PMBC patients have RS scores within the highest risk stratification (W. Wang et al., 2018). Both studies contradict an earlier, smaller study (n=10 TC patients and n=33 MC patients) that reported no patients within the high-risk RS category (Turashvili et al., 2017).

A large retrospective study of various subtypes of T1-T2N0 estrogen receptor-positive breast cancer (n=83,665) was published in 2018. Both mucinous and tubular histologies were included in the study. The authors note considerable differences in RS scores between the various histologies; for example, they found that 1.0% and 28.5% of tubular adenocarcinoma patients had RS scores in the high and intermediate ranges, respectively, whereas mucinous adenocarcinoma patients fared worse with 3.4% and 28.8%, respectively. It should be noted, however, that only 2.1% of the patients included in the study had been diagnosed with mucinous adenocarcinoma and 0.6% with tubular adenocarcinoma (J. Wang et al., 2018). Similarly, a study by Kizy et al. also reports that 4% of tubular carcinoma patients were classified as high risk based on the Trial Assigning Individualized Options for Treatment RS criteria (Kizy et al., 2018).

An in-depth systemic review of the effectiveness and cost-effectiveness of Oncotype DX®, MammaPrint®, Prosigna®, EndoPredict®, and immunohistochemistry 4 (IHC4) was released in 2019 (Harnan et al., 2019). For this review, the authors included a total of 153 studies, including the MINDACT RCT for MammaPrint. The authors note that a limitation of this systemic review, and of the current field in general, is that only one RCT has been completed to date. Their results include the following:

  • “There is limited and varying evidence that oncotype DX and MammaPrint can predict benefit from chemotherapy.”
  • “The health economic analysis suggests that the incremental cost-effectiveness ratios for the tests versus current practice are broadly favourable for the following scenarios: (1) oncotype DX, for the LN0 subgroup with a Nottingham Prognostic Index (NPI) of > 3.4 and the one to three positive lymph nodes (LN1–3) subgroup (if a predictive benefit is assumed); (2) IHC4 plus clinical factors (IHC4+C), for all patient subgroups; (3) Prosigna, for the LN0 subgroup with a NPI of > 3.4 and the LN1–3 subgroup; (4) EndoPredict Clinical, for the LN1–3 subgroup only [emphasis added]; and (5) MammaPrint, for no subgroups (Harnan et al., 2019).”

American Society of Clinical Oncology (ASCO)
In 2016, ASCO provided recommendations on appropriate use of breast tumor biomarker assay results to guide decisions on adjuvant systemic therapy for women with early-stage invasive breast cancer. ASCO recommends that “in addition to estrogen and progesterone receptors and human epidermal growth factor receptor 2, the panel found sufficient evidence of clinical utility for the biomarker assays Oncotype DX, EndoPredict, PAM50, Breast Cancer Index, and urokinase plasminogen activator and plasminogen activator inhibitor type 1 in specific subgroups of breast cancer (Harris et al., 2016).”

ASCO also made the following recommendations:

  • If a patient has ER/PgR-positive, HER2-negative (node-negative) breast cancer, the clinician may use the 21-gene recurrence score to guide decisions on adjuvant systemic chemotherapy. Type: evidence based. Evidence quality: high. Strength of recommendation: strong.
  • If a patient has ER/PgR-positive, HER2-negative (node-positive) breast cancer, the clinician should not use the 21-gene RS to guide decisions on adjuvant systemic chemotherapy. Type: evidence based. Evidence quality: intermediate. Strength of recommendation: moderate.
  • If a patient has HER2-positive breast cancer or TN breast cancer, the clinician should not use the 21-gene RS to guide decisions on adjuvant systemic therapy. Type: informal consensus. Evidence quality: insufficient. Strength of recommendation: strong
  • If a patient has ER/PgR-positive, HER2-negative (node-positive) breast cancer, the clinician should not use the Breast Cancer Index, the PAM50-ROR, the 12-gene risk score, or the 21-gene RS, (EndoPredict), to guide decisions on adjuvant systemic therapy.
  • If a patient has ER/PgR-positive, HER2-negative (node-negative) breast cancer, the clinician may use urokinase plasminogen activator (uPA), plasminogen activator inhibitor type 1 (PAI-1), the Breast Cancer Index, the PAM50 risk of recurrence (ROR) score, the 12-gene risk score (EndoPredict), and the 21-gene recurrence score (Oncotype DX) to guide decisions on adjuvant systemic therapy. If the patient has had 5 years of endocrine therapy without evidence of recurrence, the clinician should not use multiparameter gene expression or protein assays (Oncotype DX, EndoPredict, PAM50, Breast Cancer Index, or IHC4) to guide decisions on extended endocrine therapy.
  • If a patient has HER2-positive breast cancer or TN breast cancer, the clinician should not use uPA, IHC4, the 12-gene risk score (EndoPredict), PAI-1, the 21-gene RS (Oncotype DX), the five-protein assay (Mammostrat), the Breast Cancer Index or TILs to guide decisions on adjuvant systemic therapy. The clinician should not use circulating tumor cells (CTCs) to guide decisions on adjuvant systemic therapy
  • If a patient has HER2-positive breast cancer, the clinician should not use the PAM50-ROR to guide decisions on adjuvant systemic therapy.
  • If a patient has TN breast cancer, the clinician should not use the PAM50-ROR to guide decisions on adjuvant systemic therapy (Harris et al., 2016).

In 2017 the ASCO (Krop et al., 2017), based on a review of the MINDACT study publication, revised their guidelines on Use of Biomarkers to Guide Decisions on Adjuvant Systemic Therapy for Women With Early-Stage Invasive Breast Cancer to state:

Recommendation 1.1.1 (update of Recommendation 1.7).
If a patient has ER/PgR–positive, HER2-negative, node-negative, breast cancer, the MammaPrint assay may be used in those with high clinical risk per MINDACT categorization to inform decisions on withholding adjuvant systemic chemotherapy due to its ability to identify a good prognosis population with potentially limited chemotherapy benefit (Type: evidence based; Evidence quality: high; Strength of recommendation: strong).

Recommendation 1.1.2 (update of Recommendation 1.7).
If a patient has ER/PgR–positive, HER2-negative, node-negative, breast cancer, the MammaPrint assay should not be used in those with low clinical risk per MINDACT categorization to inform decisions on withholding adjuvant systemic chemotherapy as women in the low clinical risk category had excellent outcomes and did not appear to benefit from chemotherapy even with a genomic high-risk cancer (Type: evidence based; Evidence quality: high; Strength of recommendation: strong).”

Recommendation 1.2.2: (update of 2016 recommendation 1.7): If a patient has ER/PgR–positive, HER2-negative, node-positive, breast cancer, the MammaPrint assay should not be used in patients with one to three positive nodes and at low clinical risk per MINDACT categorization to inform decisions on withholding adjuvant systemic chemotherapy. There are insufficient data on the clinical utility of MammaPrint in this specific patient population (Type: informal consensus; Evidence quality: low; Strength of recommendation: moderate).

Recommendation 1.3: (update of 2016 recommendation 1.8): If a patient has HER2-positive breast cancer, the clinician should not use the MammaPrint assay to guide decisions on adjuvant systemic therapy. Additional studies are required to address the role of MammaPrint in patients with this tumor subtype who are also receiving HER2-targeted therapy (Type: informal consensus; Evidence quality: low; Strength of recommendation: moderate).

Recommendation 1.4: (update of 2016 recommendation 1.9): If a patient has ER/PgR negative and HER2-negative (triple negative) breast cancer, the clinician should not use the MammaPrint assay to guide decisions on adjuvant systemic chemotherapy (Type: informal consensus; Evidence quality: insufficient; Strength of recommendation: strong) (Krop et al., 2017)”.

ASCO published an update regarding the “Role of Patient and Disease Factors in Adjuvant Systemic Therapy Decision Making for Early-Stage, Operable Breast Cancer”, which was released in response to the results of two phase III trials, MINDACT and TAILORx. The updated guidelines state that the clinical trials found evidence of clinical utility for both node-positive and node-negative patients, but only for patients determined to be at high clinical risk. Therefore, the Panel did not recommend use of MammaPrint for patients determined to be of low clinical risk (Henry et al., 2019).

In a focused update published in 2019, the ASCO addressed the use of Oncotype DX in the following recommendation:

“For patients with hormone receptor–positive, axillary node–negative breast cancer whose tumors have Oncotype DX recurrence scores of less than 26, there is little to no benefit from chemotherapy, especially for patients older than age 50 years. Clinicians may recommend endocrine therapy alone for women older than age 50 years. For patients 50 years of age or younger with recurrence scores of 16 to 25, clinicians may offer chemoendocrine therapy. Patients with recurrence scores greater than 30 should be considered candidates for chemoendocrine therapy. Based on informal consensus, the panel recommends that oncologists may offer chemoendocrine therapy to these patients with recurrence scores of 26 to 30” (Andre et al., 2019).

American Joint Committee on Cancer
In 2018, the Expert Panel determined that:

“Multigene panels may provide prognostic and therapy predictive information that complements T, N, M and biomarker information. Use of these assays is not required for staging. The Breast Expert Panel included one multigene panel in Pathological Prognostic Staging, but others may be equally useful for clinical decision making. Inclusion in the staging system does not imply recommendation or endorsement of one multigene panel over any other for use in clinical care (ACS, 2018).”

Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group
In 2009, the EGAPP found “insufficient evidence to make a recommendation for or against the use of tumor gene expression profiles to improve outcomes in defined populations of women with breast cancer (EGAPP, 2009).”

With regard to MammaPrint, EGAPP found “that data were adequate to support an association between the MammaPrint Index and 5- or 10-year metastasis rates, but the relative efficacy of testing in ER-positive and -negative women is not clear. Study subjects were European, and how characteristics of other demographic populations might affect test performance is not known (EGAPP, 2009).”

Also, with regard to the H:I test, EGAPP found that “the evidence available to assess clinical validity is inadequate, with a small number of studies in a variety of heterogeneous populations, and only one study that applies directly to the laboratory-developed test offered by Quest (EGAPP, 2009).”

The 2016 EGAPP Working Group guidelines state that there is “insufficient evidence to recommend for or against the use of Oncotype DX testing to guide chemotherapy treatment decisions in women with hormone receptor–positive, lymph node–negative, or lymph node–positive early breast cancer who are receiving endocrine therapy.” The guidelines further state that “with regard to clinical utility, although there was evidence from prospective retrospective studies that the Oncotype DX test predicts benefit from chemotherapy, and there was adequate evidence that the use of Oncotype DX gene expression profiling in clinical practice changes treatment decisions regarding chemotherapy, no direct evidence was found that the use of Oncotype DX testing leads to improved clinical outcomes (EGAPP, 2015).”

National Comprehensive Cancer Network (NCCN)
The 2021 Version 1 guidelines of NCCN Clinical Practice Guidelines for Breast Cancer considers five gene expression assays for adjuvant systemic therapy. The five are comprised of the 21-gene Oncotype Dx, the 70-gene MammaPrint, the 50-gene PAM50, the 12-gene EndoPredict, and the Breast Cancer Index (BCI). All five gene expression assays achieved the NCCN Category of Evidence and Consensus grade of 2A (consensus of appropriateness of intervention based on lower-level evidence) or higher, with Oncotype Dx achieving grade 1 (consensus based on higher-level evidence) for node-negative and MammaPrint for achieving grade 1 for node-negative and 1 to 3 positive nodes. However, it should be noted that only Oncotype Dx is labeled as predictive assay and the preferred assay of choice for node-negative disease. And BCI is noted as “predictive of benefit of extended adjuvant endocrine therapy.” The NCCN then goes to state that “Other prognostic gene assays can provide additional prognostic information in patients with 1-3 positive lymph nodes but are unknown if predictive of chemotherapy benefit in 1-3 positive lymph nodes” (NCCN, 2021).  

The NCCN Panel “notes that multigene assays provide prognostic and therapy-predictive information that complements TNM and biomarker information”. Below is a summary table adapted from their recommendations based on risk scores and nodal statuses of the multigene assays:Assay

Recurrence Risk

Treatment Implications

21-gene (Oncotype Dx) (for pN0)


“Consideration should be given for the addition of chemotherapy to endocrine therapy in this group”


“Clinicians should consider additional clinical and pathologic factors with regard to the addition of chemotherapy to endocrine therapy in decision-making”


“For patients…the addition of chemotherapy to endocrine therapy is recommended.”

21-gene (Oncotype Dx) (for pN0)

Low (<18)

“…clinicians should be aware that the optimal RS cut-off (<11 vs. <18) is still unknown both for prognosis (risk of recurrence) as well as prediction of chemotherapy benefit.”

Intermediate (18-30) or High (>/=31)

“Because of a higher risk of distant recurrence, patients…should be considered for adjuvant chemotherapy in addition to endocrine therapy.”

70-gene (MammaPrint) (for pN0 and pN+ [1-3 positive nodes])


“…the additional benefit of adjuvant chemotherapy may be small in this group.”


50-gene (PAM50) (for pN0 and pN+ [1-3 positive nodes])

Node-negative: Low (0-40) OR Node-negative: Intermediate (41-60) OR Node-negative High (61-100)

“…a risk of recurrence score in the low range, regardless of T size, places the tumor into the same prognostic category as T1a-T1b,N0,M0.”

Node-positive: Low (0-40) OR Node-positive: High (41-100)

“…the distant recurrence risk was less than 3.5% at 10 years and no distant recurrence was seen at 10 years in the TransATAC study in a similar group.”

12-gene (EndoPredict) (for pN0 and pN+ [1-3 positive nodes])

Low (=/<3.3) OR High (>3.3)

“The assay is prognostic in endocrine and chemo-endocrine treated patients.”

Breast Cancer Index (BCI)

BCI (H/I) Low

“…no significant improvement in DFS or OS compared to the control arm in terms of extending endocrine therapy duration.”

BCI (H/I) High

“…demonstrated significant improvements in DFS when adjuvant endocrine therapy was extended, compared to the control arm.”

The NCCN also had the following to summarize about the assays mentioned above and their respective interpretations and/or rationales:

For Oncotype DX in Node-Negative, HR-positive, HER2-negative disease: “Among patients with T1b/c and T2, lymph node-negative, HR-positive, HER2-negative tumors with RS between 0-10, the risk of distant recurrence is low and these patients derive no incremental benefit from the addition of adjuvant chemotherapy to endocrine therapy. At the other end of the spectrum, patients with lymph node-negative, HR-positive, HER2-negative cancers with high RS (≥31) have a higher risk of distant recurrence and secondary analyses of prospective studies demonstrate a clear benefit from adjuvant chemotherapy.

For those with intermediate RS (11-25), the recently reported TAILORx trial of postmenopausal women (n=6,711) with lymph node-negative, HR-positive, HER-2 negative breast cancer, showed similar disease-free survival rates at 9-years in those who received adjuvant chemotherapy followed by endocrine therapy compared with endocrine therapy alone.”

For Oncotype DX in Node-Positive, HR-positive, HER2-negative disease: Based on secondary analyses, the NCCN state that “These results suggest that in patients with limited nodal disease (1-3 positive lymph nodes) and a low RS [<18], the absolute benefit from chemotherapy is likely to be very small.” On the other hand, “There is a clear benefit from adjuvant chemotherapy in patients with node-positive, HR-positive, HER2-negative tumors, if the RS is high (≥31).” However, “The absolute benefit of chemotherapy in patients with limited lymph node involvement and a RS ≤25 remains to be determined.”

For MammaPrint: The NCCN claims that the “data suggest that the additional benefit of adjuvant chemotherapy in patients with high-clinical risk/low genomic risk is likely to be small” and that the data suggest that “the results of the 70-gene signature do not provide evidence for making recommendations regarding chemotherapy for patients at low clinical risk.”

For PAM50: “For patients with T1 and T2 HR-positive, HER2-positive, and lymph node-negative tumors, a ROR in the low-risk range, regardless of T size, places the tumor into the same prognostic category as T1a-T1b, N0, M0.

In patients with 1-3 lymph-node positive, HR-positive, HER2-negative disease with low-risk of recurrence score, the distant recurrence risk was less than 3.5% at 10 years with endocrine therapy alone.”

For EndoPredict: “Patients with T1 and T2 HR-positive, HER2-positive, and lymph node-negative tumors, a 12-gene low risk score, regardless of T size, places the tumor into the same prognostic category as T1a-T1b, N0, M0.” Citing another study, the NCCN states the following for EndoPredict: “patients with 1-3 positive nodes in the low-risk group had a 5.6% risk of distant recurrence at 10 years, suggesting that chemotherapy would be of limited benefit in these women.”

For the BCI: “For patients with T1 and T2 HR-positive, HER2-positive, and lymph node-negative tumors, a BCI in the low-risk range, regardless of T size, places the tumor into the same prognostic category as T1a-T1b, N0, M0. There are limited data as to the role of BCI in HR-positive, HER2-negative, and lymph node-positive breast cancer” (NCCN, 2021).

The NCCN strongly recommends (Category 1) to consider the use of the 21-gene reverse transcriptase polymerase chain reaction (RT-PCR) assay for determining the use of adjuvant chemotherapy in patients with the following tumor characteristics:

  • Hormone receptor-positive;
  • HER2 [human epidermal growth factor receptor 2]-negative;
  • Ductal/NST, lobular, mixed or micropapillary histology;
  • pT1, pT2 or pT3 stage; and pN0;
  • Tumor >0.5 cm.

“Several commercially-available gene-based assays are useful in determining prognosis by predicting distant recurrence, local recurrence, or survival. Of these, only one, the 21-gene assay (Oncotype Dx) has been clinically validated for predicting the benefit of adding adjuvant chemotherapy to further reduce the risk of recurrence.”

“The panel notes that other prognostic multigene assays may be considered to help estimate risk of recurrence but these assays have not been validated to predict the benefit of systemic chemotherapy” (NCCN, 2021).

Within a section on special considerations for breast cancer in men, the NCCN states (Category 2A), “Data are limited regarding the use of molecular assays to assess prognosis and to predict benefit from chemotherapy in men with breast cancer. Available data suggest 21-gene assay recurrence score provides prognostic information in men with breast cancer” (NCCN, 2021).

NCCN also notes that ER status should be determined for DCIS patients, but do not mention any gene expression tests for evaluation (NCCN, 2020a, 2021).

Regarding tubular or mucinous types of breast cancer, the NCCN notes that the ER and PR status of the tumor is crucial and likely to be positive. The NCCN recommends a re-test if a tubular, mucinous, or papillary subtype is found to be ER- and PR-, but if the tumor is truly ER- and PR-, the tumor should be treated as if it were of usual histology (ductal, lobular, mixed, metaplastic) (NCCN, 2021).

A request from Genomic Health to review OncoType DCIS for potential inclusion in NCCN guidelines was denied in September 2018. The vote was 21 “No” and 7 “Abstain”. A similar request was denied in August 2019, with 24 “No” and 5 “Absent” (NCCN, 2020b).

National Institute for Health and Care Excellence (NICE, 2018)
NICE released three new guidelines regarding gene expression tests, which are as follows:

1. “EndoPredict (EPclin score), Oncotype DX Breast Recurrence Score and Prosigna are recommended as options for guiding adjuvant chemotherapy decisions for people with oestrogen receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative and lymph node (LN)-negative (including micrometastatic disease; see section 5.4) early breast cancer, only if:

  • they have an intermediate risk of distant recurrence using a validated tool such as PREDICT or the Nottingham Prognostic Index
  • information provided by the test would help them choose, with their clinician, whether or not to have adjuvant chemotherapy taking into account their preference
  • the companies provide the tests to the NHS with the discounts agreed in the access proposals and
  • clinicians and companies make timely, complete and linkable record-level test data available to the National Cancer Registration and Analysis Service as described in the data collection arrangements agreed with NICE (see section 5.29).”

2. MammaPrint is not recommended for guiding adjuvant chemotherapy decisions for people with ER-positive, HER2‑negative and LN-negative early breast cancer because it is not cost effective (NICE, 2018).

European Society for Medical Oncology (ESMO)
ESMO notes that “In cases of uncertainty regarding indications for adjuvant chemotherapy (after consideration of other tests), gene expression assays, such as MammaPrint, Oncotype DX, Prosigna and EndoPredict, may be used, where available. These assays can determine the individual’s recurrence risk as well as potentially predict the benefit of chemotherapy”. This point was unchanged in the 2019 update (F. Cardoso et al., 2019; Senkus et al., 2015).”

In a 2019 update, ESMO elaborates on gene expression profiles for breast cancer. They state that “Gene expression profiles, such as MammaPrint, Oncotype DX Recurrence Score, Prosigna and Endopredict, may be used to gain additional prognostic and/or predictive information to complement pathology assessment and to predict the benefit of adjuvant chemotherapy”. They also remark that Prosigna, Endopredict, and Oncotype are intended for ER-positive early breast cancer only and that Mammaprint and OncoType are still being evaluated for clinical utility (F. Cardoso et al., 2019).

European Group on Tumor Markers (EGTM, 2017)
EGTM notes several gene expression profiles as having clinical utility regarding adjuvant chemotherapy.

uPA/PAI-1, Oncotype DX, MammaPrint, Prosigna, EndoPredict and BCI may be used for avoiding adjuvant chemotherapy in ER-positive, HER2-negative and lymph node–negative patients.

Oncotype DX, MammaPrint, Prosigna and EndoPredict may also be used for avoiding adjuvant chemotherapy in ER-positive, HER2-negative and lymph node–positive patients (1–3 positive nodes) (Duffy et al., 2017). 


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Coding Section






Unlisted molecular pathology procedure


81518 (effective 01/01/2019)

Oncology (breast), mRNA, gene expression profiling by real-time RT-PCR of 11 genes (7 content and 4 housekeeping), utilizing formalin-fixed paraffin-embedded tissue, algorithms reported as percentage risk for metastatic recurrence and likelihood of benefit from extended endocrine therapy 



Oncology (breast), mRNA, gene expression profiling by real-time RT-PCR of 21 genes, utilizing formalin-fixed paraffin embedded tissue, algorithm reported as recurrence score



Oncology (breast), mRNA gene expression profiling by hybrid capture of 58 genes (50 content and 8 housekeeping), utilizing formalin-fixed paraffin-embedded tissue, algorithm reported as a recurrence risk score



Oncology (breast), mRNA, microarray gene expression profiling of 70 content genes and 465 housekeeping genes, utilizing fresh frozen or formalin-fixed paraffin-embedded tissue, algorithm reported as index related to risk of distant metastasis



Oncology (breast), mRNA, gene expression profiling by RT-PCR of 12 genes (8 co ntent and 4 housekeeping), utilizing formalin-fixed paraffin-embedded tissue, algorithm reported as recurrence risk score
Proprietary test: EndoPredict®
Lab/Manufacturer: Myriad Genetic Laboratories, Inc.



Unlisted multianalyte assay with algorithmic analysis-EndoPredict



Unlisted chemistry procedure



Morphometric analysis, tumor Immunohistochemistry (eg, Her-2/neu, estrogen receptor/progesterone receptor), quantitative or semiquantitative, per specimen, each single antibody stain procedure; manual 



Morphometric analysis, tumor immunohistochemistry (eg, Her-2/neu, estrogen receptor/progesterone receptor), quantitative or semiquantitative, per specimen, each single antibody stain procedure; using computer-assisted technology 



Morphometric analysis, in situ hybridization (quantitative or semi-quantitative), using computer-assisted technology, per specimen; each multiplex probe stain procedure 



Morphometric analysis, in situ hybridization (quantitative or semi-quantitative), manual, per specimen; initial single probe stain procedure 



Microdissection (ie, sample preparation of microscopically identified target); manual 



Gene expression profiling panel for use in the management of breast cancer treatment 



Oncology (breast ductal carcinoma in situ), mRNA, gene expression profiling by real-time RT-PCR of 12 genes (7 content and 5 housekeeping), utilizing formalin-fixed paraffin-embedded tissue, algorithm reported as recurrence score
Proprietary test: Oncotype DX® Breast DCIS Score™
Lab/manufacturer: Genomic Health, Inc.



Oncology (breast), mRNA, gene expression profiling by next-generation sequencing of 101 genes, utilizing formalin-fixed paraffin-embedded tissue, algorithm reported as a triple negative breast cancer clinical subtype(s) with information on immune cell involvement
Proprietary test: Insight TNBCtype™
Lab/Manufacturer: Insight Molecular Labs 

Procedure and diagnosis codes on Medical Policy documents are included only as a general reference tool for each policy. They may not be all-inclusive.

This medical policy was developed through consideration of peer-reviewed medical literature generally recognized by the relevant medical community, U.S. FDA approval status, nationally accepted standards of medical practice and accepted standards of medical practice in this community, Blue Cross and Blue Shield Association technology assessment program (TEC) and other non-affiliated technology evaluation centers, reference to federal regulations, other plan medical policies, and accredited national guidelines.

"Current Procedural Terminology © American Medical Association.  All Rights Reserved" 

History From 2014 Forward     


Annual review, updating policy to expand coverage ( see new coverage criteria #4. Also updating description, rationale and references. 


Annual review, updating testing covered per NCCN guidelines. 


Interim review, rewriting policy criteria for clarity. Also updating coding. 


Annual review, updating coding and policy. Policy updates are in line with NCCN recommendations and relate to tumor site and type, potential treatment, staging and timing of diagnosis. Updating verbiage related to testing for males for clarity. 


Updating with 2019 codes.  


Annual review, reformatting entire policy. Expanding medical necessity criteria to allow Mammaprint testing for some indications. 


Updating policy with 2018 coding. No other changes. 


Annual review, updating policy criteria related to DX 21 gene expression, otherwise, no change to policy intent. 


Updated category to Laboratory. No other changes


Interim review, adding medical necessity for Prosigna and EndoPredict testing. Updating background, description, guidelines, regulatory status, rationale and references. 


Annual review, no change to policy intent. Updated background, description, guidelines, rationale and references.


Interim review, added additional criteria for medical necessity regarding the histology of the tumor, added additional investigational tests, added that gene expression profiling as a technique of managing the treatment of ductal cardinoma in situ is investigational and that repeat gene expression profiling is investigational.  


Annual review, the following added to policy:The use of other gene expression assays, MammaPrint® 70-gene signature, Mammostrat® Breast Cancer Test, the Breast Cancer Index SM, BreastOncPx™, NexCourse® Breast IHC4, Prosigna™ BreastPRS™, and EndoPredict™ for any indication is considered investigational.


Annual Review

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