Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group*. Recommendations from the EGAPP Working Group: does the use of Oncotype DX tumor gene expression profiling to guide treatment decisions improve outcomes in patients with breast cancer?

Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature

The diagnosis of breast cancer—including determination of prognosis and prediction—has been traditionally based on clinical and pathological characteristics such as tumor size, nodal status, and tumor grade. The decision-making process has been expanded by the recent introduction of molecular signatures. These signatures, however, have not reached the highest levels of evidence thus far. Yet they have been brought to clinical practice based on statistical significance in prospective as well as retrospective studies. Intriguingly, it has also been reported that most random sets of genes are significantly associated with disease outcome. These facts raise two highly relevant questions: What information gain do these signatures procure? How can one find a signature that is substantially better than a random set of genes? Our study addresses these questions. To address the latter question, we present a hybrid signature that joins the traditional approach with the molecular one by combining the Nottingham Prognostic Index with gene expressions in a data-driven fashion. To address the issue of information gain, we perform careful statistical analysis and comparison of the hybrid signature, gene expression lists of two commercially available tests as well as signatures selected at random, and introduce the Signature Skill Score—a simple measure to assess improvement on random signatures. Despite being based on in silico data, our research is designed to be useful for the decision-making process of oncologists and strongly supports association of random signatures with outcome. Although our study shows that none of these signatures can be considered as the main candidate for providing prognostic information, it also demonstrates that both the hybrid signature and the gene expression list of the OncotypeDx signature identify patients who may not require adjuvant chemotherapy. More importantly, we show that combining signatures substantially improves the identification of patients who do not need adjuvant chemotherapy.

Pathologist's health-care value in the triage of Oncotype DX® testing: a value-based pathology study of tumour biology with outcomes

AIMS

Pathologists provide expert tissue assessment of breast cancer, yet their value to guide the appropriate use of breast cancer gene expression profile tests (GEPT) is underutilised. The specific aims of this study are to report morpho-immunohistological characteristics of breast tumours with Oncotype DX^® (ODx) recurrence scores (RS) of 10 or fewer (ultra-low risk) and 25 or fewer (low risk) in order to determine if pathologists can identify prospectively patient tumours that do not require ODx testing.

METHODS AND RESULTS

Oncotype DX^® cases with RS < 10 from 2005 to 2010 comprised 441 of 2594 (17%) of clinical cases; this cohort had 5 years' follow-up and was treated with endocrine therapy alone. Tumours were analysed for tumour type, Nottingham grade, mitosis score (MS) semi-quantitative (H-score) hormone receptor content and Magee equation 3. Knowledge derived from this data set was used to develop algorithms in order to identify prospectively tumours with RS of 10 or fewer or 25 or fewer. Thirty-four per cent of tumours were low-grade special types, while the remainder were enriched with high hormone receptor content with MS of 1. These algorithmic selection criteria identified correctly all patient cases below the chemotherapy cut-point, i.e. RS < 25, indicating that these oncotype test orders were an unnecessary cost.

CONCLUSIONS

This unique study demonstrates that (i) pathologists add great value to triage breast cancer for GEPT; and (ii) can identify prospectively low-grade tumour biology with high sensitivity and high specificity for those cases which do not require chemotherapy (RS < 25) using MS and hormone receptor content.

Clinical and economic impact of the 21-gene recurrence score assay in adjuvant therapy decision making in patients with early-stage breast cancer: pooled analysis in 4 Basque Country university hospitals

Purpose

The 21-gene recurrence score (RS) is a genomic test developed as a prognostic and predictive tool to improve the treatment decision making in cases of estrogen receptor-positive and human epidermal growth factor receptor 2-negative early-stage breast cancer. This study examined the clinical and economic impact of its use in 4 Basque Country university hospitals.

Methods

Taking into consideration the RS result, we recorded the recommended initial systemic adjuvant therapy (endocrine therapy with or without chemotherapy) according to standard clinicopathologic factors and the final decision about chemotherapy. Then, if the RS was high, chemotherapy was recommended; it was not recommended if the RS was low; for those with an intermediate RS, clinicopathologic factors were considered, and the initial recommendation based on those factors was maintained. In addition, the probability of switching treatment was calculated. Then, we developed an economic evaluation by measuring the treatment’s incremental short-term budget impact from both the societal perspective and that of the Basque Health System. Patients’ characteristics and chemotherapy use were analyzed using logistic regressions and receiver operating characteristic curves.

Results

Without an RS, chemotherapy would have been prescribed to 56% of 401 patients, but, with RS use, that percentage decreased to 25. The overall rate of decision change was 35.4%. Test inclusion led to a reduction in chemotherapy costs of €922 per patient in the total population. Although this reduction did not entirely offset the cost of the test, the productivity loss per patient was reduced by €1,977.

Conclusion

The 21-gene RS test significantly changed the indication for chemotherapy. As chemotherapy treatments with no benefit were avoided, patients’ quality of life was improved. The short-term economic impact was negative for the Basque Health Service, but savings resulted when sick-leave costs were included.

Uptake of a 21-gene expression assay in breast cancer practice: views of academic and community-based oncologists

PURPOSE

Advances in personalized medicine have produced novel tests and treatment options for women with breast cancer. Relatively little is known about the process by which such tests are adopted into oncology practice. The objectives of the present study were to understand the experiences of medical oncologists with multigene expression profile (gep) tests, including their adoption into practice in early-stage breast cancer, and the perceptions of the oncologists about the influence of test results on treatment decision-making.

METHODS

We conducted a qualitative descriptive study involving interviews with medical oncologists from academic and community cancer centres or hospitals in 8 communities in Ontario. A 21-gene breast cancer assay was used as the example of gep testing. Qualitative analytic techniques were used to identify the main themes.

RESULTS

Of 28 oncologists who were approached, 21 (75%) participated in the study [median age: 43 years; 12 women (57%)]. Awareness and knowledge of gep testing were derived from several sources: international scientific meetings, participation in clinical studies, discussions with respected colleagues, and manufacturer-sponsored meetings. Oncologists observed that incorporating gep testing into their clinical practice resulted in several changes, including longer consultation times, second visits, and taking steps to minimize treatment delays. Oncologists expressed divergent opinions about the strength of evidence and added value of gep testing in guiding treatment decisions.

CONCLUSIONS

Incorporation of gep testing into clinical practice in early-stage breast cancer required oncologists to make changes to their usual routines. The opinions of oncologists about the quality of evidence underpinning the test affected how much weight they gave to test results in treatment decision-making.

Clinical Utility of the 12-Gene DCIS Score Assay: Impact on Radiotherapy Recommendations for Patients with Ductal Carcinoma In Situ

Objective

The aim of this study was to determine the impact of the results of the 12-gene DCIS Score assay on (i) radiotherapy recommendations for patients with pure ductal carcinoma in situ (DCIS) following breast-conserving surgery (BCS), and (ii) patient decisional conflict and state anxiety.

Methods

Thirteen sites across the US enrolled patients (March 2014–August 2015) with pure DCIS undergoing BCS. Prospectively collected data included clinicopathologic factors, physician estimates of local recurrence risk, DCIS Score results, and pre-/post-assay radiotherapy recommendations for each patient made by a surgeon and a radiation oncologist. Patients completed pre-/post-assay decisional conflict scale and state-trait anxiety inventory instruments.

Results

The analysis cohort included 127 patients: median age 60 years, 80 % postmenopausal, median size 8 mm (39 % ≤5 mm), 70 % grade 1/2, 88 % estrogen receptor-positive, 75 % progesterone receptor-positive, 54 % with comedo necrosis, and 18 % multifocal. Sixty-six percent of patients had low DCIS Score results, 20 % had intermediate DCIS Score results, and 14 % had high DCIS Score results; the median result was 21 (range 0–84). Pre-assay, surgeons and radiation oncologists recommended radiotherapy for 70.9 and 72.4 % of patients, respectively. Post-assay, 26.4 % of overall recommendations changed, including 30.7 and 22.0 % of recommendations by surgeons and radiation oncologists, respectively. Among patients with confirmed completed questionnaires (n = 32), decision conflict (p = 0.004) and state anxiety (p = 0.042) decreased significantly from pre- to post-assay.

Conclusions

Individualized risk estimates from the DCIS Score assay provide valuable information to physicians and patients. Post-assay, in response to DCIS Score results, surgeons changed treatment recommendations more often than radiation oncologists. Further investigation is needed to better understand how such treatment changes may affect clinical outcomes.

Electronic supplementary material

The online version of this article (doi:10.1245/s10434-016-5583-7) contains supplementary material, which is available to authorized users.

The future of clinical cancer genomics

The current and future applications of genomics to the practice of preventive oncology are being impacted by a number of challenges. These include rapid advances in genomic science and technology that allow massively parallel sequencing of both tumors and the germline, a diminishing of intellectual property restrictions on diagnostic genetic applications, rapid expansion of access to the internet which includes mobile access to both genomic data and tools to communicate and interpret genetic data in a medical context, the expansion of for-profit diagnostic companies seeking to monetize genetic information, and a simultaneous effort to depict medical professionals as barriers to rather than facilitators of understanding one's genome. Addressing each of these issues will be required to bring "personalized" germline genomics to cancer prevention and care. A profound future challenge will be whether clinical cancer genomics will be "de-medicalized" by commercial interests and their advocates, or whether the future course of this field can be modulated in a responsible way that protects the public health while implementing powerful new medical tools for cancer prevention and early detection.

Statistical controversies in clinical research: prognostic gene signatures are not (yet) useful in clinical practice

With the genomic revolution and the era of targeted therapy, prognostic and predictive gene signatures are becoming increasingly important in clinical research. They are expected to assist prognosis assessment and therapeutic decision making. Notwithstanding, an evidence-based approach is needed to bring gene signatures from the laboratory to clinical practice. In early breast cancer, multiple prognostic gene signatures are commercially available without having formally reached the highest levels of evidence-based criteria. We discuss specific concepts for developing and validating a prognostic signature and illustrate them with contemporary examples in breast cancer. When a prognostic signature has not been developed for predicting the magnitude of relative treatment benefit through an interaction effect, it may be wishful thinking to test its predictive value. We propose that new gene signatures be built specifically for predicting treatment effects for future patients and outline an approach for this using a cross-validation scheme in a standard phase III trial. Replication in an independent trial remains essential.

The clinical utility of molecular genetic cancer profiling

INTRODUCTION

Next-Generation-Sequencing (NGS) has enabled gene mutation profiling - cataloguing sequence variants and modifications in clinical assays encompassing tens to thousands of genes in tumors and in germlines. The clinical benefit of applying multi-gene NGS to diverse applications in various malignancies remains to be demonstrated.

AREAS COVERED

Applications of gene mutation profiling in oncology include screening cancer-prone families, classification of malignancies, treatment selection, and monitoring the response to treatment of solid tumors (the 'liquid biopsy'). Google Scholar was used to search PubMed for the period 2011-2016 using combinations of the following search terms: 'clinical utility', NGS, 'molecular diagnostics'. Expert commentary: Clinical studies are in progress pairing mutation profiling with streamlined new trial designs to speed identification of promising drug-target combinations and to see if genotype-informed treatment selection will improve outcome across a spectrum of histologies. The analytical advantages and falling cost of NGS make focused gene panels likely to become the dominant modality in molecular diagnostic testing even if trials eventually discourage use of large panels to test all malignancies.