Clinical evidence supporting genomic tests in early breast cancer: Do all genomic tests provide the same information?

Markopoulos, Christos; Velde, Cjh van de; Zarca, D.; Özmen, Vahit; Masetti, Riccardo

doi:10.1016/j.ejso.2016.08.012

Cited by 39 publications

(34 citation statements)

References 76 publications

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“…One of the most widely utilized signatures is Oncotype DX, which predicts NCT response in ERpositive breast cancer patients based on the expression of 21 genes. [14][15][16][17][18] Patients with high Oncotype DX risk scores are more likely to respond to the NCT. 17 Other gene assays, such as EndoPredict and PROSIGNA, were also introduced to predict the NCT response in ER-positive patients.…”

Section: Introductionmentioning

confidence: 99%

Gene signature‐based prediction of triple‐negative breast cancer patient response to Neoadjuvant chemotherapy

2020

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Neoadjuvant chemotherapy is the current standard of care for large, advanced, and/or inoperable tumors, including triple‐negative breast cancer. Although the clinical benefits of neoadjuvant chemotherapy have been illustrated through numerous clinical trials, more than half of the patients do not experience therapeutic benefit and needlessly suffer from side effects. Currently, no clinically applicable biomarkers are available for predicting neoadjuvant chemotherapy response in triple‐negative breast cancer; the discovery of such a predictive biomarker or marker profile is an unmet need. In this study, we introduce a generic computational framework to calculate a response‐probability score (RPS), based on patient transcriptomic profiles, to predict their response to neoadjuvant chemotherapy. We first validated this framework in ER‐positive breast cancer patients and showed that it predicted neoadjuvant chemotherapy response with equal performance to several clinically used gene signatures, including Oncotype DX and MammaPrint. Then, we applied this framework to triple‐negative breast cancer data and, for each patient, we calculated a response probability score (TNBC‐RPS). Our results indicate that the TNBC‐RPS achieved the highest accuracy for predicting neoadjuvant chemotherapy response compared to previously proposed 143 gene signatures. When combined with additional clinical factors, the TNBC‐RPS achieved a high prediction accuracy for triple‐negative breast cancer patients, which was comparable to the prediction accuracy of Oncotype DX and MammaPrint in ER‐positive patients. In conclusion, the TNBC‐RPS accurately predicts neoadjuvant chemotherapy response in triple‐negative breast cancer patients and has the potential to be clinically used to aid physicians in stratifying patients for more effective neoadjuvant chemotherapy.

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Section: Introductionmentioning

confidence: 99%

Gene signature‐based prediction of triple‐negative breast cancer patient response to Neoadjuvant chemotherapy

2020

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“…15 For example, in patients with breast cancer, high-throughput gene expression profiling studies have enabled the development of commercial prognostic kits, such as MammaPrint-DX, Oncotype-DX, EndoPredict, and Prosigna, to aid clinical decision. 16 In patients with FA, successful oral immunotherapy (OIT) in patients with peanut allergy has been associated with conversion of allergen-specific T cells to anergic T cells. 17 These findings, along with technological developments that allow real-time monitoring, could have therapeutic implications and enable personalized medicine.…”

Section: What Are Omics?mentioning

confidence: 99%

Food allergy and omics

Dhondalay

Rael

Acharya

et al. 2018

Journal of Allergy and Clinical Immunology

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Food allergy (FA) prevalence has been increasing over the last few decades and is now a global health concern. Current diagnostic methods for FA result in a high number of false-positive results, and the standard of care is either allergen avoidance or use of epinephrine on accidental exposure, although currently with no other approved treatments. The increasing prevalence of FA, lack of robust biomarkers, and inadequate treatments warrants further research into the mechanism underlying food allergies. Recent technological advances have made it possible to move beyond traditional biological techniques to more sophisticated high-throughput approaches. These technologies have created the burgeoning field of omics sciences, which permit a more systematic investigation of biological problems. Omics sciences, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, and exposomics, have enabled the construction of regulatory networks and biological pathway models. Parallel advances in bioinformatics and computational techniques have enabled the integration, analysis, and interpretation of these exponentially growing data sets and opens the possibility of personalized or precision medicine for FA.

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“…The optimal selection of neoadjuvant therapy (NAC or NET) in post-menopausal patients with ER positive disease remains to be determined. The role of molecular assays has yet to be fully elucidated 33 although early results with the 21 gene assay suggest possible clinical utility 34 . Likewise, a 4-gene signature has recently been proposed to allow patients to be classed as likely long-term responders or non-responders within 2 weeks of starting endocrine therapy 35 .…”

Section: Identifying Patients Who May Benefit From Neoadjuvant Therapymentioning

confidence: 99%

Opportunities and priorities for breast surgical research

Cutress

McIntosh

Potter

et al. 2018

The Lancet Oncology

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Background: The Breast Cancer Campaign Gap analysis (2013) established breast cancer research priorities without specific focus on surgical research nor the role of surgeons. The majority of breast cancer patients encounter a surgeon at diagnosis or during treatment, thus surgical involvement in design and delivery of high-quality research to improve patient care is critical. This review aims to identify opportunities and priorities for breast surgical research to complement the previous gap analysis. Methods: Research-active breast surgeons met and identified topic areas for breast surgical research which mapped to the patient pathway. These included diagnosis, neoadjuvant treatment, surgery, adjuvant therapy and special groups (e.g. risk-reducing surgery). Section leads were identified based on research interests with invited input from experts in specific areas, supported by consultation with the Association of Breast Surgery (ABS) membership and Independent Cancer Patients' Voice (ICPV). The document was iteratively modified until participants were satisfied that key priorities for surgical research were clear. Results: Key research gaps were identified for each topic area including: (1) issues surrounding overdiagnosis and treatment; (2) optimising selection for neoadjuvant therapies and subsequent surgery; (3) reducing re-operation rates for breast conserving surgery; (4) generating evidence for the clinical and cost-effectiveness of breast reconstruction and mechanisms for evaluating novel interventions; (5) determining optimal axillary management, especially post-neoadjuvant treatment; (6) defining and standardising indications for risk-reducing surgery. Strategies for resolving these knowledge gaps are proposed. Conclusions: Surgeons are ideally placed for a central role in breast cancer research and should foster a culture of engagement and participation in research to benefit patients and the NHS. Development of infrastructure and surgical research capacity together with appropriate allocation of research funding will be needed to successfully address the key clinical and translational research gaps highlighted in this analysis within the next two decades.

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Clinical evidence supporting genomic tests in early breast cancer: Do all genomic tests provide the same information?

Cited by 39 publications

References 76 publications

Gene signature‐based prediction of triple‐negative breast cancer patient response to Neoadjuvant chemotherapy

Gene signature‐based prediction of triple‐negative breast cancer patient response to Neoadjuvant chemotherapy

Food allergy and omics

Opportunities and priorities for breast surgical research

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