Is it research or is it clinical? Revisiting an old frontier through the lens of next-generation sequencing technologies

European Reference Networks: challenges and opportunities

European Reference Networks (ERNs) were founded on the principle that many rare disease (RD) issues are pan-European and any single Member State cannot solve them alone. In 2021, ERNs are already in the deployment stage; however, their day-to-day functioning and realization of their potential are still severely hampered by many challenges, including issues in governance and regulation, lack of legal status, insufficient and unsustainable funding, lack of ERN integration into national systems, endangered collaboration with UK RD experts due to Brexit, insufficient exploitation of ERN potential in RD research, underappreciation of highly qualified human resources, problems with the involvement of patient representatives, and still unclear place of ERNs in the overall European RD and digital ecosystem. Bold and innovative solutions that must be taken to solve these challenges inevitably involve pan-European collaboration across several sectors and among multistakeholder RD communities and in many cases crucially rely on the constructive dialogue and coherent, united decisions of national and European authorities that are based on common EU values. Importantly, unresolved challenges may have a strong impact on the further sustainability of ERNs and their ability to realize full potential in addressing huge unmet needs of RD patients and their families.

Impact of Next Generation Sequencing on Clinical Practice in Oncology in France: Better Genetic Profiles for Patients Improve Access to Experimental Treatments

OBJECTIVES

We evaluated how next generation sequencing (NGS) can modify care pathways in an observational impact study in France.

METHODS

All patients with lung cancer, colorectal cancer, or melanoma who had NGS analyses of somatic genomic alterations done in 1 of 7 biomolecular platforms certified by the French National Cancer Institute (INCa) between 2013 and 2016 were eligible. We compared patients' pathways before and after their NGS results. Endpoints consisted of the turnaround time in obtaining results, the number of patients with at least 1 genomic alteration identified, the number of actionable alterations, the impact of the genomic multidisciplinary tumor board on care pathways, the number of changes in the treatment plan, and the survival outcome up to 1 year after NGS analyses.

RESULTS

1213 patients with a request for NGS analysis were included. NGS was performed for 1155 patients, identified at least 1 genomic alteration for 867 (75%), and provided an actionable alteration for 614 (53%). Turnaround time between analyses and results was on average 8 days (Min: 0; Max: 95) for all cancer types. Before NGS analysis, 33 of 614 patients (5%) were prescribed a targeted therapy compared with 54 of 614 patients (8%) after NGS analysis. Proposition of inclusion in clinical trials with experimental treatments increased from 5% (n = 31 of 614) before to 28% (n = 178 of 614) after NGS analysis. Patients who benefited from a genotype matched treatment after NGS analysis tended to have a better survival outcome at 1 year than patients with nonmatched treatment: 258 days (±107) compared with 234 days (±106), (P = .41).

CONCLUSIONS

NGS analyses resulted in a change in patients' care pathways for 20% of patients (n = 232 of 1155).

Genomic testing in healthcare: a hybrid space where clinical practice and research need to co-exist

Introduction: Clinical practice and research are traditionally seen as distinct activities that are governed by different principles and processes. Innovative technologies such as genomic testing challenge this model, involving many activities that cannot be easily categorized as purely research, or purely clinical care. Areas covered: We discuss the interdependence of research and clinical practice in the context of genomics, for example, when determining the significance of rare genetic variants, or diagnosing newly described rare diseases. We highlight the potential of the symbiotic relationship between clinical practice and research. Expert opinion: In the context of genomics, it is not appropriate to treat clinical practice and research as entirely separable. Forcing binary categorization of activities as one or the other risks losing the many benefits that derive from their integration. We need to explore the hybrid area where clinical practice and research coincide, developing governance that allows us to maximize its potential, rather than insisting that hybrid clinical-research activities conform to processes built for 'pure clinical practice' or 'pure research'. We argue the need for a renegotiation of the contract around genomic testing, recognizing, valuing and facilitating the hybrid space where clinical practice and research co-exist.

Model consent clauses for rare disease research

Background

Rare Disease research has seen tremendous advancements over the last decades, with the development of new technologies, various global collaborative efforts and improved data sharing. To maximize the impact of and to further build on these developments, there is a need for model consent clauses for rare diseases research, in order to improve data interoperability, to meet the informational needs of participants, and to ensure proper ethical and legal use of data sources and participants’ overall protection.

Methods

A global Task Force was set up to develop model consent clauses specific to rare diseases research, that are comprehensive, harmonized, readily accessible, and internationally applicable, facilitating the recruitment and consent of rare disease research participants around the world. Existing consent forms and notices of consent were analyzed and classified under different consent themes, which were used as background to develop the model consent clauses.

Results

The IRDiRC-GA4GH MCC Task Force met in September 2018, to discuss and design model consent clauses. Based on analyzed consent forms, they listed generic core elements and designed the following rare disease research specific core elements; Rare Disease Research Introductory Clause, Familial Participation, Audio/Visual Imaging, Collecting, storing, sharing of rare disease data, Recontact for matching, Data Linkage, Return of Results to Family Members, Incapacity/Death, and Benefits.

Conclusion

The model consent clauses presented in this article have been drafted to highlight consent elements that bear in mind the trends in rare disease research, while providing a tool to help foster harmonization and collaborative efforts.

Electronic supplementary material

The online version of this article (10.1186/s12910-019-0390-x) contains supplementary material, which is available to authorized users.

Privacy and ethical challenges in next-generation sequencing

INTRODUCTION

Next-generation sequencing (NGS) is expected to revolutionize health care. NGS allows for sequencing of the whole genome more cheaply and quickly than previous techniques. NGS offers opportunities to advance medical diagnostics and treatments, but also raises complicated ethical questions that need to be addressed.

AREAS CONSIDERED

This article draws from the literature on research and clinical ethics, as well as next-generation sequencing, in order to provide an overview of the ethical challenges involved in next-generation sequencing. This article includes a discussion of the ethics of NGS in research and clinical contexts.

EXPERT OPINION

The use of NGS in clinical and research contexts has features that pose challenges for traditional ethical frameworks for protecting research participants and patients. NGS generates massive amounts of data and results that vary in terms of known clinical relevance. It is important to determine appropriate processes for protecting, managing and communicating the data. The use of machine learning for sequencing and interpretation of genomic data also raises concerns in terms of the potential for bias and potential implications for fiduciary obligations. NGS poses particular challenges in three main ethical areas: privacy, informed consent, and return of results.