Defining purpose: a key step in genetic test evaluation

Beyond severity: utility as a criterion for setting the scope of RGCS

Reproductive genetic carrier screening (RGCS) allows prospective parents to identify and act upon their chances of having a child with a genetic condition. In deciding which genetic conditions to include in RGCS, severity is often used as a criterion. However, the concept is inherently complex, subjective and multidimensional, and determinations of severity will remain intractably contested. We propose the concept of utility as a criterion for setting the scope of RGCS, and put forward two central arguments for doing so. First, utility is a more appropriate and effective concept as it responds to context and makes an explicit connection between the purpose of RGCS and the value of information obtained for that purpose: namely, to facilitate reproductive decision-making. Utility comprises both clinical and personal utility, and varies according to the availability and accessibility of reproductive options, including pre-implantation genetic testing, prenatal genetic diagnosis, and termination of pregnancy. Second, there are ethical reasons for preferring utility over severity. Utility is a property of the information gleaned from RGCS, while severity is a property of a genetic condition or of an instance of this condition in a person. While consideration of the severity of genetic conditions is not lost when focusing on utility, the need to rely on value judgements regarding the quality of life of people who live with genetic conditions is circumvented. Therefore, utility should replace severity as justification for the inclusion of genetic conditions in RGCS programmes.

How can we address the uncertainties regarding the potential clinical utility of polygenic score-based tests?

As common low penetrance variants associated with diseases are uncovered, attempts continue to be made to harness this knowledge for improving healthcare. Polygenic scores have been developed as the mechanism by which knowledge of common variants can be used to investigate genetic contributions to disease risk. They serve as a biomarker to provide an estimate of the genetic liability for a particular disease. Discussion continues as to whether polygenic scores are a useful biomarker and their readiness for incorporation into clinical and public health practice. In this paper, we investigate the key challenges that need to be addressed, in the description and assessment of the clinical utility of polygenic score-based tests for use in clinical and public health practice.

Knowledge of genetic eye diseases and genetic services and attitudes toward genetic testing and gene therapy

PURPOSE:

Genetic eye diseases are among the top ten causes of ocular health burden. Asia accounts for nearly two-thirds of the global burden of genetic eye diseases. A great deal of resources is being invested in genetic research and development of genetic services including gene testing laboratories and genetic counseling in India. These efforts will be meaningful only if the public and clinicians are aware of their existence. This study aimed to understand the level of knowledge about genetic eye diseases and genetic services and attitudes toward genetic testing and gene therapy in four groups of participants (undergraduate medical students, paramedical staff, non-ophthalmologist doctors, and the general public).

MATERIALS AND METHODS:

This was a cross-sectional survey in India. Four hundred questionnaires were analyzed from the four groups of participants. Knowledge score was calculated for the different questions. To bring out the differences across the groups, Chi-square test was done with a post hoc Mann–Whitney U-test and Kruskal–Wallis test. P < 0.05 was taken as statistically significant.

RESULTS:

The level of awareness about genetic eye diseases was better among undergraduate students, doctors, and paramedical staff compared to the general public (P < 0.001). The majority across all three groups had a positive attitude toward genetic testing and gene therapy. However, most of the participants across all groups were not aware of the genetic facilities available in our country.

CONCLUSION:

This study shows a positive attitude toward genetic medicine. However, there is a need to improve public awareness about genetic eye diseases and facilities available for genetic testing and gene therapy.

Utility and Diversity: Challenges for Genomic Medicine

Genomic information is poised to play an increasing role in clinical care, extending beyond highly penetrant genetic conditions to less penetrant genotypes and common disorders. But with this shift, the question of clinical utility becomes a major challenge. A collaborative effort is necessary to determine the information needed to evaluate different uses of genomic information and then acquire that information. Another challenge must also be addressed if that process is to provide equitable benefits: the lack of diversity of genomic data. Current genomic knowledge comes primarily from populations of European descent, which poses the risk that most of the human population will be shortchanged when health benefits of genomics emerge. These two challenges have defined my career as a geneticist and have taught me that solutions must start with dialogue across disciplinary and social divides.

Understanding polygenic models, their development and the potential application of polygenic scores in healthcare

The use of genomic information to better understand and prevent common complex diseases has been an ongoing goal of genetic research. Over the past few years, research in this area has proliferated with several proposed methods of generating polygenic scores. This has been driven by the availability of larger data sets, primarily from genome-wide association studies and concomitant developments in statistical methodologies. Here we provide an overview of the methodological aspects of polygenic model construction. In addition, we consider the state of the field and implications for potential applications of polygenic scores for risk estimation within healthcare.

Healthcare System Priorities for Successful Integration of Genomics: An Australian Focus

This paper examines key considerations for the successful integration of genomic technologies into healthcare systems. All healthcare systems strive to introduce new technologies that are effective and affordable, but genomics offers particular challenges, given the rapid evolution of the technology. In this context we frame internationally relevant discussion points relating to effective and sustainable implementation of genomic testing within the strategic priority areas of the recently endorsed Australian National Health Genomics Policy Framework. The priority areas are services, data, workforce, finances, and person-centred care. In addition, we outline recommendations from a government perspective through the lens of the Australian health system, and argue that resources should be allocated not to just genomic testing alone, but across the five strategic priority areas for full effectiveness.

The Spectrum of Genetic Testing

OBJECTIVE

To introduce genetic testing as it relates to oncology and nursing.

DATA SOURCES

Peer-reviewed journals, government web sites and resources, published recommendations, and professional experience as a genetic counselor.

CONCLUSION

Genetic testing is a major component of oncology health care and with the continued expansion of the application of genetic testing, many patients will have genetic testing throughout their cancer journey.

IMPLICATIONS FOR NURSING PRACTICE

To provide supportive care for patients with cancer or at risk for cancer, oncology nurses need to appreciate the many and varied genetic testing platforms and testing strategies. Oncology nurses can be a resource for patients and family members regarding testing options, insurance coverage, and understanding medical management decisions.

From vascular biology to vascular medicine

Cardiovascular disorders include various conditions characterized by morphological and functional defects of the heart and vascular system. Molecular biology techniques (in particular DNA sequencing) have recently offered new insights into the etiology of cardiovascular defects, revealing their association with germline as well as somatic mutations.

Genetic tests are evaluated on the basis of their analytical and clinical validity, clinical utility, and ethical, legal and social implications. Next generation sequencing is so far the best approach for molecular diagnosis of congenital heart defects and vascular anomalies, the genetic and phenotypic heterogeneity of which makes them difficult to diagnose. Understanding the molecular causes of congenital heart defects and vascular anomalies has permitted clinical trials of drugs targeting affected genes and pathways.

The articles in this Special Issue aim to provide guidance for those concerned with diagnosis and research in the field of cardiovascular defects. The approach to genetic testing is discussed.

Integrative omics for health and disease

Advances in omics technologies - such as genomics, transcriptomics, proteomics and metabolomics - have begun to enable personalized medicine at an extraordinarily detailed molecular level. Individually, these technologies have contributed medical advances that have begun to enter clinical practice. However, each technology individually cannot capture the entire biological complexity of most human diseases. Integration of multiple technologies has emerged as an approach to provide a more comprehensive view of biology and disease. In this Review, we discuss the potential for combining diverse types of data and the utility of this approach in human health and disease. We provide examples of data integration to understand, diagnose and inform treatment of diseases, including rare and common diseases as well as cancer and transplant biology. Finally, we discuss technical and other challenges to clinical implementation of integrative omics.

Paediatricians underuse recommended genetic tests in children with global developmental delay

Objectives

To assess paediatricians' use of genetic testing for children with global developmental delay (GDD).

Study Design

We developed and piloted a questionnaire assessing the use of genetic tests in children with GDD and awareness of relevant guidelines. All practicing Quebec paediatricians were contacted. Paediatricians who did not evaluate children with GDD in their practice were excluded. Descriptive and statistical analyses were performed with SPSS.

Results

Of the 651 paediatricians, 225 answered (34.5%) and 141 were eligible. Only 31.9% were familiar with at least one guideline about genetic tests for the investigation of children with GDD, but 93.6% had ordered genetic testing for children with GDD (Fragile X testing [92.9%], karyotype [87.2%] and chromosomal microarray [63.8%]). Based on vignettes, 20.6% of participants would order genetic tests for isolated GDD and 95.0% for GDD with dysmorphic features and microcephaly. Only 56.7% ordered Fragile X testing for a girl with GDD and a known family history of Fragile X syndrome. Use of tests for isolated GDD was increased in presence of maternal pregnancy, compared with absence of pregnancy (44.7% and 27.7%, respectively). More participants would order genetic tests for a child with GDD and fetal exposure to alcohol (69.5%) than isolated GDD (20.6%).

Conclusions

Even though paediatricians often order genetic testing for children with GDD, practices and knowledge regarding testing are not optimal. As new and more complex genetic tests are developed, up-to-date training about the use of genetic tests for children with GDD needs to be integrated into paediatrics residency programs and continuous medical education.

Giving and withholding of information following genomic screening: challenges identified in a study of primary care physicians in Estonia

The use of predictive genomic information to improve medical care remains a contentious topic. However, it is generally agreed that the potential of genomics to improve medicine relies on medical care providers' ability to effectively communicate and put in context the meaning of test results. As the amount of information available increasingly outstrips providers' ability to offer qualified judgments on what the information means, consumers inevitably will be faced with test results of uncertain significance, as well as difficult questions about what they do or do not wish to know. Results of this survey of 64 primary care doctors in Estonia suggests that it may be inherently difficult for physicians to withhold genetic information obtained by genome scans or sequencing, even when they believe that having that information is not in the best interests of their patient. The descriptive data suggest introducing genomic medicine through primary care physicians, as proposed by the Estonian Genome Center of the University of Tartu, will require further genetics education as well as a carefully developed set of guidelines for determining where, when and how to use test results.

A formal risk-benefit framework for genomic tests: facilitating the appropriate translation of genomics into clinical practice

PURPOSE

Evaluation of genomic tests is often challenging because of the lack of direct evidence of clinical benefit compared with usual care and unclear evidence requirements. To address these issues, this study presents a risk-benefit framework for assessing the health-related utility of genomic tests.

METHODS

We incorporated approaches from a variety of established fields including decision science, outcomes research, and health technology assessment to develop the framework. Additionally, we considered genomic test stakeholder perspectives and case studies.

RESULTS

We developed a three-tiered framework: first, we use decision-analytic modeling techniques to synthesize data, project incidence of clinical events, and assess uncertainty. Second, we defined the health-related utility of genomic tests as improvement in health outcomes as measured by clinical event rates, life expectancy, and quality-adjusted life-years. Finally, we displayed results using a risk-benefit policy matrix to facilitate the interpretation and implementation of findings from these analyses.

CONCLUSION

A formal risk-benefit framework may accelerate the utilization and practice-based evidence development of genomic tests that pose low risk and offer plausible clinical benefit, while discouraging premature use of tests that provide little benefit or pose significant health risks compared with usual care.

Development and description of GETT: a genetic testing evidence tracking tool

BACKGROUND

The completion of the Human Genome Project has increased the pace of discovery of genetic markers for disease. Despite tremendous efforts in fundamental research, clinical applications still lag behind expectations, partly due to the lack of effective tools to systematically search for and summarize published data relative to the clinical assessment of new diagnostic molecular tests.

METHODS

Through a collaborative process using published tools and an expert panel, we developed a detailed checklist of the evidence that needs to be collected or produced to evaluate the potential usefulness of a new molecular diagnostic test. This tool is called GETT, for Genetic testing Evidence Tracking Tool.

RESULTS

GETT allows 1) researchers to summarize the current evidence and to identify knowledge gaps for further research and; 2) stakeholders to collect data related to a given molecular test and improve their decision-making process. GETT comprises 72 clearly defined items/questions, grouped into 10 categories and 26 sub-themes, including an overview of disease epidemiology and genetics, the available diagnostic tools, and their analytical and clinical performances, availability of quality control programs, laboratory and clinical best practice guidelines, clinical utility, and impact on health care and psycho-social, ethical and legal implications. It also includes a summary of the evidence available and attempts to prioritise knowledge gaps related to the testing. We also compare GETT to other existing frameworks.

CONCLUSIONS

This systematic evidence-based tracking tool, which is more detailed than existing frameworks and provides clear definition for each item, will help streamline collection of the available evidence to appraise the potential for clinical application of new molecular diagnostic tests and prioritize research to produce the evidence-base relative to the clinical implementation of molecular diagnostic tests.

Debating clinical utility

The clinical utility of genetic tests is determined by the outcomes following test use. Like other measures of value, it is often contested. Stakeholders may have different views about benefits and risks and about the importance of social versus health outcomes. They also commonly disagree about the evidence needed to determine whether a test is effective in achieving a specific outcome. Questions may be presented as factual disagreements, when they are actually debates about what information matters or how facts should be interpreted and used in clinical decision-making. Defining the different issues at stake is therefore an important element of policy-making. Key issues include evidence standards for test use, and in particular, the circumstances under which prospective controlled data should be required, as well as evidence on feasibility, cost and equitable delivery of testing; the goals of population-based screening programs, and in particular, the role of social outcomes in evaluating test value; and the appropriate uses and funding of tests that inform non-medical actions. Addressing each of these issues requires attention to stakeholder values and methods for effective deliberation that incorporate consumer as well as health professional perspectives.

Usefulness of factor V Leiden mutation testing in clinical practice

We have investigated the clinical usefulness of the activated protein C resistance (APCR)/factor V Leiden mutation (FVL) test by sending out questionnaires to all Norwegian physicians who ordered these tests from our publicly funded service laboratory during a 3-month period, and of whom 70% (267/383) responded. Indications for testing, patient follow-up, the use of APCR versus FVL tests and differences in practice between hospital doctors and GPs were examined. We found that 46% of the tests were predictive, ordered for risk assessment in healthy individuals with no previous history of venous thromboembolism (VTE). Among these, 42% of the tests were taken on the initiative of the patient and 24% were screening tests before prescription of oral contraceptives. In total, 54% of the tests were classified as diagnostic, among which 42% were ordered owing to a previous history of VTE and 22% to a history of brain stroke or myocardial infarction. The prevalence of FVL heterozygotes was not significantly different between the predictive and diagnostic test groups, that is, 26 and 20%, respectively. Only the predictive tests influenced patient follow-up. Here, the physician's advice to patients depended on the test result. In general, the clinical usefulness of APCR/FVL testing was low. Many tests were performed on unsubstantiated or vague indications. Furthermore, normal test results led to unwarranted refrain from giving advice about antithrombotic measures, leading to potential harm to the patient.

Evaluation of the validity and utility of genetic testing for rare diseases

The conventional criteria for evaluating genetic tests include analytic validity, clinical validity, and clinical utility. Analytical validity refers to a test's ability to measure the genotype of interest accurately and reliably. Clinical validity refers to a test's ability to detect or predict the clinical disorder or phenotype associated with the genotype. Clinical utility of a test is a measure of its usefulness in the clinic and resulting changes in clinical endpoints. In addition, the utility to individuals and families of genomic information, or personal utility, should be considered. This chapter identifies methodological and data issues involved in assessing each type of validity or utility. The validity and utility of a test must be considered in a specific context, which include diagnostic testing, newborn screening, prenatal carrier screening, and family or cascade screening. Specific rare disorders addressed include cystic fibrosis, fragile X syndrome, Duchenne and Becker muscular dystrophy, spinal muscular atrophy, Huntington disease, as well as cancer associated with BRCA mutations.

'Over-the-counter' genetic testing: what does it really mean for primary care?

The publication of More Genes Direct by the Human Genetics Commission is a timely reminder of the potential impact that 'over-the-counter' genetic testing (that is, a direct genetic test without the need for a medical referral) may have on the NHS. This article considers the relevance of current genetic research on complex common diseases and how this might translate into risk estimates for developing conditions such as dementia, cancer, and cardiovascular disease. The implications for primary care include the need to understand the current limitations of genetic testing and its commercial application over the counter, and the importance of continuing to make risk assessments using family history. The authors recommend caution in the premature introduction of over-the-counter testing without a sound evidence base.

Guidance for considering ethical, legal, and social issues in health technology assessment: application to genetic screening

OBJECTIVES AND METHODS

Many authors have argued that ethical, legal, and social issues ("ELSIs") should be explicitly integrated into health technology assessment (HTA), yet doing so poses challenges. This discussion may be particularly salient for technologies viewed as ethically complex, such as genetic screening. Here we provide a brief overview of contemporary discussions of the issues from the HTA literature. We then describe key existing policy evaluation frameworks in the fields of disease screening and public health genomics. Finally, we map the insights from the HTA literature to the policy evaluation frameworks, with discussion of the implications for HTA in genetic screening.

RESULTS AND CONCLUSIONS

A critical discussion in the HTA literature considers the definition of ELSIs in HTA, highlighting the importance of thinking beyond ELSIs as impacts of technology. Existing HTA guidance on integrating ELSIs relates to three broad approaches: literature synthesis, involvement of experts, and consideration of stakeholder values. The thirteen key policy evaluation frameworks relating to disease screening and public health genomics identified a range of ELSIs relevant to genetic screening. Beyond straightforward impacts of screening, these ELSIs require consideration of factors such as the social and political context surrounding policy decisions. The three broad approaches to addressing ELSIs described above are apparent in the screening/genomics literatures. In integrating these findings we suggest that the method chosen for addressing ELSIs in HTA for genetic screening may determine which ELSIs are prioritized; and that an important challenge is the lack of guidance for evaluating such methods.

Ethical, legal, and social issues in health technology assessment for prenatal/preconceptional and newborn screening: a workshop report

Prenatal/preconceptional and newborn screening programs have been a focus of recent policy debates that have included attention to ethical, legal, and social issues (ELSIs). In parallel, there has been an ongoing discussion about whether and how ELSIs may be addressed in health technology assessment (HTA). We conducted a knowledge synthesis study to explore both guidance and current practice regarding the consideration of ELSIs in HTA for prenatal/preconceptional and newborn screening. As the concluding activity for this project, we held a Canadian workshop to discuss the issues with a diverse group of stakeholders. Based on key workshop themes integrated with our study results, we suggest that population-based genetic screening programs may present particular types of ELSIs and that a public health ethics perspective is potentially highly relevant when considering them. We also suggest that approaches to addressing ELSIs in HTA for prenatal/preconceptional and newborn screening may need to be flexible enough to respond to diversity in HTA organizations, cultural values, stakeholder communities, and contextual factors. Finally, we highlight a need for transparency in the way that HTA producers move from evidence to conclusions and the ways in which screening policy decisions are made.

Ethical and social implications of genetic testing for communication disorders

Advances in genetics and genomics have quickly led to clinical applications to human health which have far-reaching consequences at the individual and societal levels. These new technologies have allowed a better understanding of the genetic factors involved in a wide range of disorders. During the past decade, incredible progress has been made in the identification of genes involved in the normal process of hearing. The resulting clinical applications have presented consumers with new information and choices. Many of the same gene identification techniques are increasingly being applied to the investigation of complex disorders of speech and language. In parallel with gene identification, studies of the legal, ethical and psychosocial impacts of the clinical application of these advances and their influence on specific behaviors of individuals with communication disorders are paramount, but often lag behind. These studies will help to ensure that new technologies are introduced into clinical practice in a responsible manner.

LEARNING OUTCOMES

As a result of this activity, the participant will be able to (1) explain the differences between Mendelian and complex forms of inheritance and why these differences complicate the ethical impact of genetic testing, (2) explain how publicly funded genome research through the Human Genome Project, the International HapMap Project and others have examined the ethical, legal and social implications of genome research, (3) list some of the ethical complexities of prenatal, newborn and predictive testing for various genetic disorders and (4) discuss the importance of evidence-based practice to the development of public policy for the introduction and clinical use of genetic tests.