Controversy and debate on clinical genomics sequencing—paper 1: genomics is not exceptional: rigorous evaluations are necessary for clinical applications of genomic sequencing

A scoping review of the assessment reports of genetic or genomic tests reveals inconsistent consideration of key dimensions of clinical utility

OBJECTIVES

Genetic and genomic tests are the cornerstone of personalized preventive approaches. Inconsistency in evaluating their clinical utility is often cited as a reason for their limited implementation in clinical practice. Previous reviews have primarily focused on theoretical frameworks used for clinical utility evaluations of genetic tests, rather than actual assessments and examined dimensions, rather than specific indicators within these dimensions. We aimed to review the dimensions and the specific indicators measured in published assessment reports of genetic or genomic tests.

STUDY DESIGN AND SETTING

We conducted a scoping review of assessment reports of genetic and genomic tests used for prevention, searching through PubMed, Web of Science, Scopus, the websites of 20 different organizations, Google, and Google Scholar. From the included assessments, we extracted the reported indicators of clinical utility, compiling a list of disease-specific indicators that detailed their numerator, denominator, and calculation methods. We analyzed the extracted indicators by stratifying them according to ten comprehensive dimensions of clinical utility, the assessment framework used, and the type of indicator (categorized as quantitative, qualitative, reference, or no evidence reported). From these indicators, we then distilled a list of general indicators.

RESULTS

We reviewed 3054 unique references and 12,000 results from gray literature searches, ultimately selecting 57 assessment reports. The reference frameworks used were health technology assessment (HTA) (42%), Evaluation of Genomic Applications in Practice and Prevention (EGAPP) (25%), ACCE (21%), and others (12%). We identified 951 disease-specific indicators. The dimensions most frequently evaluated (ie, had at least one indicator) were analytic validity (60%), clinical validity (79%), clinical efficacy (79%), and economic impact (58%). Only 12 assessments compared health outcomes between tested and untested groups, and fewer than 15% of the assessments addressed equity, acceptability, legitimacy, and personal value.

CONCLUSION

Our study illustrates that, although dimensions such as equity and acceptability, are significantly emphasized in traditional evaluation frameworks, these are often not considered in the assessments. Additionally, our study has underscored a significant dearth of reported primary evidence concerning the clinical efficacy of these tests.

PLAIN LANGUAGE SUMMARY

Genetic and genomic tests analyze a person's genes to predict health risks and guide healthcare decisions, potentially identifying who might benefit from certain treatments or check-ups. However, determining whether these tests are genuinely useful for wide use in health services is complex, because there is no standard way to define "clinical utility" of a genetic test. To understand how these tests are evaluated, we reviewed 57 evaluation reports from high-income countries, most of which focused on cancer-related genetic tests. We found that many evaluations looked mainly at how well a test predicted a condition (validity) and considered some form of effectiveness, yet often failed to measure whether the test truly improved patient health outcomes, such as lowering death rates or enhancing the quality of life. Moreover, factors like patient acceptance, equity, and personal relevance (eg, reducing anxiety) were frequently overlooked. Without including these broader considerations, evaluations risk missing critical evidence that would indicate whether a test is helpful, fair, and worth using. From over 900 unique indicators used to measure clinical utility, we created a simpler list of about 150 general indicators that can guide future evaluations. This consolidated list can help test developers decide which factors to investigate, evaluators determine what to measure, and policymakers identify what might be missing before deciding if a test should be adopted in healthcare. By highlighting the gaps-areas that should be assessed but currently are not-our study encourages a more comprehensive approach to evaluating genetic tests. If we fail to consider issues like equity, patient preferences, and proven health benefits, we risk investing in tests that may do little good or even harm patients. Ultimately, recognizing these shortcomings can lead to better-informed decisions, ensuring that genetic testing is used in ways that truly benefit patients and deliver safer, more personalized, and fairer healthcare for everyone.

Strength of evidence underlying the CMS-FDA parallel review of comprehensive genomic profiling tests in the cancer setting

BACKGROUND

Although use of comprehensive genomic profiling was approved by a novel Centers for Medicare & Medicaid Services-US Food and Drug Administration parallel review process, the quality of the supporting evidence is unclear. We evaluated the rigor of the peer-reviewed literature cited in the National Coverage Determination Memorandum for the FoundationOneCDx (Foundation Medicine, Inc, Cambridge, MA).

METHODS

We identified studies cited in the memorandum. Two independent researchers evaluated each study and applied a modified version of the Fryback and Thornbury hierarchy, an established framework for evaluating the efficacy of diagnostic tests. Studies focused on clinical outcomes were then categorized by study design, guided by recommendations from the Center for Medical Technology Policy.

RESULTS

The sample included 113 scientific studies. The majority (60/113 [53.1%]) used comprehensive genomic profiling outside the course of clinical care, and there was substantive heterogeneity in the cancer types assessed and the sequencing depth. We found 8 (7.1%) studies that assessed whether clinical care had changed due to comprehensive genomic profiling testing, and 38 (33.6%) assessed clinical outcomes. After excluding studies that tested for 5 or fewer genomic alterations, 25 remained in the clinical outcomes sample: Of these, only 1 included a comparator group that did not receive comprehensive genomic profiling testing. Only 4 studies used FoundationOneCDx as the primary genomic test, none of which compared the outcomes of patients who did vs did not receive the test.

CONCLUSIONS

The findings indicate gaps in the supporting evidence for broad comprehensive genomic profiling use in patients with solid tumors. More rigorous studies that assess clinical utility would better inform the approval process for novel diagnostic tests.

The Future of Newborn Genomic Testing

Genome sequencing (GS) provides exciting opportunities to rapidly identify a diagnosis in critically ill newborns and children with rare genetic conditions. Nevertheless, there are reasons to remain cautious about the use of GS. Studies to date have been mostly in highly selected populations of babies with unusual clinical presentations. GS leads to diagnoses in many such infants. More rarely, it leads to beneficial changes in management. Parents and physicians whose babies meet these criteria and for whom GS is performed both find these results useful. The concern is this: we do not know how useful such testing will be in the general population. We can speculate that a number of problems will arise as the use of GS expands. First, the percentage of cases in which a valid molecular diagnosis is made will likely go down. The number of ambiguous results or false positives will rise. Genetic counseling will become more complex and challenging. We do not know the relative cost-effectiveness of whole genome, whole exome, or targeted panels in different populations. We do not know the relative contribution of a molecular diagnosis to the decision to withdraw life support. We will have to carefully evaluate the use of such testing in order to understand whether it truly improves outcome and survival or reduces symptoms in babies who are tested. Each of these concerns will require careful study of both the technology and the ethical issues to allow us to harness the potential of these new technologies while avoiding foreseeable problems. Studies are underway to see how the tests are used in general populations. These studies should generate important information to guide clinicians and policymakers. As part of informed consent, doctors should explain to parents that genetic results are not always straightforward. Sometimes, they confirm a diagnosis that was already suspected. Sometimes, they rule out a possible diagnosis. Sometimes, the results are ambiguous and difficult to interpret. Anticipatory discussions should try to give parents a realistic understanding of the likely impact of a genetic diagnosis. Diagnostic genomic testing for newborns is a science that is still in its infancy. More research is essential in order to establish how to personalize this promising but sometimes problematic tool.

The Consultant's intermediary role in the regulation of molecular diagnostics in the US

Molecular diagnostics are fast becoming a big business, with the promise of personalized medicine fueling the growth of "blockbuster" tests with high expectations for health system impact and commercial success. We investigate the polycentric regulatory regime for molecular diagnostics in the US, drawing attention to the prominent role of coverage and reimbursement systems in setting regulatory standards for this industry. We hone in on the private consultants who assist molecular diagnostics companies to gain broad clinical uptake of their products. Through a web-based search of consulting companies, analysis of their online materials, and 13 qualitative interviews with consultants, we describe the role of these actors in the coverage and reimbursement of novel diagnostics and highlight the production of evidence as a critical part of the process. We argue that consultants operate as regulatory intermediaries, helping to develop the evidentiary standards for payment decisions that ultimately benefit their clients, the manufacturers. We suggest that public policy discussions over how best to realize the promise of personalized medicine should be re-oriented to consider whose interests are represented in the regulatory regime governing access to these technologies.

The promise of public health ethics for precision medicine: the case of newborn preventive genomic sequencing

Precision medicine aims to tailor medical treatment to match individual characteristics and to stratify individuals to concentrate benefits and avoid harm. It has recently been joined by precision public health-the application of precision medicine at population scale to decrease morbidity and optimise population health. Newborn preventive genomic sequencing (NPGS) provides a helpful case study to consider how we should approach ethical questions in precision public health. In this paper, I use NPGS as a case in point to argue that both precision medicine and precision public health need public health ethics. I make this argument in two parts. First, I claim that discussions of ethics in precision medicine and NPGS tend to focus on predominantly individualistic concepts from medical ethics such as autonomy and empowerment. This highlights some deficiencies, including overlooking that choice is subject to constraints and that an individual's place in the world might impact their capacity to 'be responsible'. Second, I make the case for using a public health ethics approach when considering ethics and NPGS, and thus precision public health more broadly. I discuss how precision public health needs to be construed as a collective enterprise and not just as an aggregation of individual interests. I also show how analysing collective values and interests through concepts such as solidarity can enrich ethical discussion of NPGS and highlight previously overlooked issues. With this approach, bioethics can contribute to more just and more appropriate applications of precision medicine and precision public health, including NPGS.

Quality of life drives patients' preferences for secondary findings from genomic sequencing

There is growing impetus to include measures of personal utility, the nonmedical value of information, in addition to clinical utility in health technology assessment (HTA) of genomic tests such as genomic sequencing (GS). However, personal utility and clinical utility are challenging to define and measure. This study aimed to explore what drives patients' preferences for hypothetically learning medically actionable and non-medically actionable secondary findings (SF), capturing clinical and personal utility; this may inform development of measures to evaluate patient outcomes following return of SF. Semi-structured interviews were conducted with adults with a personal or family cancer history participating in a trial of a decision aid for selection of SF from genomic sequencing (GS) ( www.GenomicsADvISER.com ). Interviews were analyzed thematically using constant comparison. Preserving health-related and non-health-related quality of life was an overarching motivator for both learning and not learning SF. Some participants perceived that learning SF would help them "have a good quality of life" through informing actions to maintain physical health or leading to psychological benefits such as emotional preparation for disease. Other participants preferred not to learn SF because results "could ruin your quality of life," such as by causing negative psychological impacts. Measuring health-related and non-health-related quality of life may capture outcomes related to clinical and personal utility of GS and SF, which have previously been challenging to measure. Without appropriate measures, generating and synthesizing evidence to evaluate genomic technologies such as GS will continue to be a challenge, and will undervalue potential benefits of GS and SF.

Mind the gap: Knowledge deficits in evaluating young sudden cardiac death

Sudden cardiac arrest affects around half a million people aged under 50 years old annually, with a 90% mortality rate. Despite high patient numbers and clear clinical need to improve outcomes, many gaps exist in the evidence underpinning patients' management. Domains identifying the greatest barriers to conducting trials are the prehospital and forensic settings, which also provide care to the majority of patients. Addressing gaps in evidence along each point of the cardiac arrest trajectory is a key clinical priority.

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).

Bibliometric Analysis of Research on Telomere Length in Children: A Review of Scientific Literature

Telomere length in early life has been recently associated with biological aging and development of negative consequences in later adult life. A relevant area of research has emerged to understand the factors that impact telomere length in children. We conducted a bibliometric analysis to track research output and identify global trends and gaps in the knowledge of telomere length in children. Bibliographic data were retrieved from the Web of Science database and then analyzed by using Bibliometrix R package. A total of 840 publications were yielded from 1991 to 2019. The references were prominently published in journals, with 20 high ranked journals contributing to 30% of literature on telomere length in children. The USA was the most productive country (35.7%), followed by Europe (12.1%), and Asia (11.9%). A knowledge map of telomere length in children through keyword analyses revealed that there were two potential main lines of research based on two different approaches: genomic research and epidemiological research. This study shows that telomere length in children is a topic of research that has gained significant relevance in the last decade. This bibliometric study may be helpful in identifying research trends and finding research hot spots and gaps in this research field.

Do next-generation sequencing results drive diagnostic and therapeutic decisions in MDS?

This article has a companion Point by Thol and Platzbecker.

What did we learn from multiple omics studies in asthma?

More than a decade has passed since the finalization of the Human Genome Project. Omics technologies made a huge leap from trendy and very expensive to routinely executed and relatively cheap assays. Simultaneously, we understood that omics is not a panacea for every problem in the area of human health and personalized medicine. Whilst in some areas of research omics showed immediate results, in other fields, including asthma, it only allowed us to identify the incredibly complicated molecular processes. Along with their possibilities, omics technologies also bring many issues connected to sample collection, analyses and interpretation. It is often impossible to separate the intrinsic imperfection of omics from asthma heterogeneity. Still, many insights and directions from applied omics were acquired-presumable phenotypic clusters of patients, plausible biomarkers and potential pathways involved. Omics technologies develop rapidly, bringing improvements also to asthma research. These improvements, together with our growing understanding of asthma subphenotypes and underlying cellular processes, will likely play a role in asthma management strategies.

Genetic Diagnostic Testing for Inherited Cardiomyopathies: Considerations for Offering Multi-Gene Tests in a Health Care Setting

Inherited cardiomyopathies (ICs) are a major cause of heart disease. Given their marked clinical and genetic heterogeneity, the content and clinical utility of IC multi-gene panels has been the topic of continuous debate. Our genetics diagnostic laboratory has been providing clinical diagnostic testing for ICs since 2012. We began by testing nine genes and expanded our panel by fivefold in 2015. Here, we describe the implementation of a cost-effective next-generation sequencing (NGS)-based assay for testing of IC genes, including a protocol that minimizes the amount of Sanger sequencing required to confirm variants identified by NGS, which reduces the cost and time of testing. The NGS assay was developed for the simultaneous analysis of 45 IC genes and was assessed for the impact of panel expansion on variant detection, turnaround time, and cost of testing in a cohort of 993 patients. The assay led to a considerable reduction in test cost and turnaround time. However, only a marginal increase was observed in the diagnostic yield, whereas the rate of inconclusive findings increased considerably. These findings suggest that the ongoing evaluation of gene content and monitoring of clinical utility for multi-gene tests are essential to achieve maximum clinical utility of multi-gene tests in a publicly funded health care setting.

Genome-wide sequencing in acutely ill infants: genomic medicine's critical application?

Diagnostic genome-wide sequencing (exome or genome sequencing and data analysis for high-penetrance disease-causing variants) in acutely ill infants appears to be clinically useful, but the value of this diagnostic test should be rigorously demonstrated before it is accepted as a standard of care. This white paper was developed by the Paediatric Task Team of the Global Alliance for Genomics and Health's Regulatory and Ethics Work Stream to address the question of how we can determine the clinical value of genome-wide sequencing in infants in an intensive care setting. After reviewing available clinical and ethics literature on this question, we conclude that evaluating diagnostic genome-wide sequencing as a comprehensive scan for major genetic disease (rather than as a large panel of single-gene tests) provides a practical approach to assessing its clinical value in acutely ill infants. Comparing the clinical value of diagnostic genome-wide sequencing to chromosomal microarray analysis, the current evidence-based standard of care, per case of serious genetic disease diagnosed provides a practical means of assessing clinical value. Scientifically rigorous studies of this kind are needed to determine if clinical genome-wide sequencing should be established as a standard of care supported by healthcare systems and insurers for diagnosis of genetic disease in seriously ill newborn infants.

Integrating Genomics into Healthcare: A Global Responsibility

Genomic sequencing is rapidly transitioning into clinical practice, and implementation into healthcare systems has been supported by substantial government investment, totaling over US$4 billion, in at least 14 countries. These national genomic-medicine initiatives are driving transformative change under real-life conditions while simultaneously addressing barriers to implementation and gathering evidence for wider adoption. We review the diversity of approaches and current progress made by national genomic-medicine initiatives in the UK, France, Australia, and US and provide a roadmap for sharing strategies, standards, and data internationally to accelerate implementation.