The value of genetic testing: beyond clinical utility

The Landscape of Genomic Services for Inherited Retinal Degenerations (IRDs) Across Europe

Purpose

To map the existing genomic services available for patients with IRDs across Europe.

Methods

A survey was conducted to 24 ophthalmic and/or genetic specialists across 19 European countries. The survey was conducted in an interview style via zoom for participants from 17 out of 19 countries. Interviewees were clinical/medical/ophthalmic geneticists, ophthalmologists/retina specialists and internal medicine specialists. The survey focused on referral pathways, genetic counseling, insurance coverage, awareness of genetic testing and counseling for IRDs among practitioners and patients, and preferred testing methodologies.

Results

Genomic services (testing and counselling) for IRDs vary among countries from an awareness, availability and insurance coverage perspective. Affordability could be a barrier for patients in countries without any payment scheme (eg, Poland) and in countries where only a targeted population is covered (eg, Bulgaria). Genetic counseling via qualified genetic counsellors did not exist in many countries. The level of awareness regarding the benefits of genetic testing in IRDs among healthcare professionals (HCPs) and patients was perceived as low in some countries. Panel-based next-generation sequencing (NGS) was the first test of choice for genetic testing in 68% of the studied countries.

Conclusion

There is some disparity in the approach to genetic testing for IRDs across Europe. Greater awareness of genetic testing services is required among the eye care professional community. A revised approach to the provision of genetic testing services such as centralized free genetic testing with associated interpretation and genetic counselling may help in ensuring equitable access and reimbursement, which will empower patients through improved access to clinical trials, expedite innovation, improve access to therapy and the delivery of care.

Genetic Testing Experiences of People Living with Inherited Retinal Degenerations: Results of a Global Survey

INTRODUCTION

Obtaining a genetic diagnosis via genetic testing (GT) is a fundamental step in determining the eligibility of a patient to be enrolled in emerging clinical trials and research studies. Besides, the knowledge of genetic outcome allows patients to plan for significant life choices. However, critical barriers exist to an equitable access to genetic services globally. The objective of this study was to explore patient experiences while seeking genomic services for inherited retinal degenerations (IRDs).

METHODS

An online survey was designed based on a focus group conducted by Retina International and including people affected by IRDs and their families living in different regions around the world. The survey was then circulated to 43 Retina International member organisations globally via email newsletters and social networks. The survey involved questions in relation to the accessibility, affordability, and timeliness of genomic services for IRDs as well as patient perceived awareness of genomic services for IRDs among healthcare professionals.

RESULTS

A total of 410 respondents (IRD patients and caregivers) from over 30 countries across all continents responded to the survey. A considerable number of the patients had to go through a long and arduous journey to access GT and counselling services, wherein 40% had to visit more than 5 physicians, 27% had to visit more than 5 clinics, and 57% had to wait for more than 3 years before obtaining a genetic diagnosis. Furthermore, 46% of respondents reported not receiving genetic counselling prior to undergoing GT, and 39% reported not receiving genetic counselling after undergoing GT. Over 3/4th of the participants reported that they did not have to pay for their genomic services for IRDs. Thirty-seven percent of the respondents reported that their eye care professionals (ECPs) were either not aware of GT, remained neutral, or did not encourage them to undergo GT.

CONCLUSION

Patients with IRDs do not have equitable access to best practice GT and counselling services. Greater awareness and training regarding IRDs and the benefits of GT and genetic counselling for patients and families are needed among ECPs. A best practice model on access to genomic services for IRDs is required.

Impact of providing genetics-based future cardiovascular risk on LDL-C in patients with familial hypercholesterolemia

BACKGROUND

Familial hypercholesterolemia (FH) is an autosomal dominant monogenic disease characterized by high low-density lipoprotein cholesterol (LDL-C) levels. Although carrying causative FH variants is associated with coronary heart disease (CHD), it remains unclear whether disclosing its associated cardiovascular risk affects outcomes in patients with FH.

OBJECTIVE

We aimed to evaluate the efficacy of providing future cardiovascular risk based on genetic testing in addition to a standard FH education program.

METHODS

We conducted a randomized, wait-list controlled, open-label, single-center trial. In the intervention group, we reported a future cardiovascular risk based on the genetic testing adding to standard FH education at week 0. In the wait-list control group, we only disseminated standard FH education according to the guidelines at week 0; they later received a genetic testing-based cardiovascular risk assessment at week 24. The primary endpoint of this study was the plasma LDL-C level at week 24.

RESULTS

Fifty eligible patients with clinically diagnosed FH, without a history of CHD, were allocated to the intervention group (n = 24) or the wait-list control group (n = 26). At week 24, the intervention group had a significantly greater reduction in LDL-C levels than the wait-list control group (mean changes, -13.1 mg/dL vs. 6.6 mg/dL; difference, -19.7 mg/dL; 95% confidence interval, -34 to -5.6; p = 0.009). This interventional effect was consistent with FH causative variant carriers but not with non-carriers.

CONCLUSIONS

In addition to standard FH care, providing future cardiovascular risk based on genetic testing can further reduce plasma LDL-C levels, particularly among FH causal variant carriers.

REGISTRATION

Japan Registry of Clinical Trials (jRCTs04218002). URL: https://jrct.niph.go.jp/latest-detail/jRCTs042180027.

Determining the utility of diagnostic genomics: a conceptual framework

BACKGROUND

Diagnostic efficacy is now well established for diagnostic genomic testing in rare disease. Assessment of overall utility is emerging as a key next step, however ambiguity in the conceptualisation and measurement of utility has impeded its assessment in a comprehensive manner. We propose a conceptual framework to approach determining the broader utility of diagnostic genomics encompassing patients, families, clinicians, health services and health systems to assist future evidence generation and funding decisions. BODY: Building upon previous work, our framework posits that utility of diagnostic genomics consists of three dimensions: the domain or type and extent of utility (what), the relationship and perspective of utility (who), and the time horizon of utility (when). Across the description, assessment, and summation of these three proposed dimensions of utility, one could potentially triangulate a singular point of utility axes of type, relationship, and time. Collectively, the multiple different points of individual utility might be inferred to relate to a concept of aggregate utility.

CONCLUSION

This ontological framework requires retrospective and prospective application to enable refinement and validation. Moving forward our framework, and others which have preceded it, promote a better characterisation and description of genomic utility to inform decision-making and optimise the benefits of genomic diagnostic testing.

A Modern Approach to Dyslipidemia

Lipid disorders involving derangements in serum cholesterol, triglycerides, or both are commonly encountered in clinical practice and often have implications for cardiovascular risk and overall health. Recent advances in knowledge, recommendations, and treatment options have necessitated an updated approach to these disorders. Older classification schemes have outlived their usefulness, yielding to an approach based on the primary lipid disturbance identified on a routine lipid panel as a practical starting point. Although monogenic dyslipidemias exist and are important to identify, most individuals with lipid disorders have polygenic predisposition, often in the context of secondary factors such as obesity and type 2 diabetes. With regard to cardiovascular disease, elevated low-density lipoprotein cholesterol is essentially causal, and clinical practice guidelines worldwide have recommended treatment thresholds and targets for this variable. Furthermore, recent studies have established elevated triglycerides as a cardiovascular risk factor, whereas depressed high-density lipoprotein cholesterol now appears less contributory than was previously believed. An updated approach to diagnosis and risk assessment may include measurement of secondary lipid variables such as apolipoprotein B and lipoprotein(a), together with selective use of genetic testing to diagnose rare monogenic dyslipidemias such as familial hypercholesterolemia or familial chylomicronemia syndrome. The ongoing development of new agents-especially antisense RNA and monoclonal antibodies-targeting dyslipidemias will provide additional management options, which in turn motivates discussion on how best to incorporate them into current treatment algorithms.

Preanalytical DNA assessment for downstream applications: How to optimize the management of human biospecimens to support molecular diagnosis-An experimental study

Background

The development of next‐generation sequencing approaches has accelerated the diagnostic process, although at present, there is a lack of a clear consensus on efficient management of human samples for downstream applications. This study aims to investigate timeframe (in terms of short preservation), temperature, and additional preservation procedures (i.e., freeze and thaw cycles) for human biospecimens to implement the reliability and reproducibility of molecular investigations.

Methods

Overall, 45 whole peripheral bloods, 22 peripheral blood mononuclear cells samples, 15 saliva, and 15 buccal swab biospecimens (through the extracted DNA) were investigated, assessing yield, integrity, amplifiability, and sizing accuracy via the most common molecular techniques.

Results

Based on the overall evaluation criteria, the results indicate that DNA extracted from all samples, shortly preserved, have suitable quality and reliable reproducibility to be used in diagnostic activities and biomedical research, even if DNA from peripheral blood mononuclear cells is more affected by the experimental conditions.

Conclusion

Our findings confirm the reliability of peripheral blood samples in almost all the experimental conditions. Saliva and buccal swabs are efficient almost as well, while peripheral blood mononuclear cells, albeit remain a primary source of DNA for molecular screenings, represent a less efficient source.

Clinical application of fetal genome-wide sequencing during pregnancy: position statement of the Canadian College of Medical Geneticists

Purpose and scope

The aim of this position statement is to provide recommendations for Canadian healthcare professionals regarding the use of genome-wide sequencing (GWS) in the context of diagnostic testing of the fetus during pregnancy. This statement was developed to facilitate clinical translation of GWS as a prenatal diagnostic test and the development of best practices in Canada, but the applicability of this document is broader and aims to help professionals in other healthcare systems.

Methods of statement development

A multidisciplinary group was assembled to review existing literature on fetal GWS for genetic diagnosis in the context of suspected monogenic diseases and to make recommendations relevant to the Canadian context. The statement was circulated for comments to the Canadian College of Medical Geneticists (CCMG) membership-at-large and, following incorporation of feedback, approved by the CCMG Board of Directors on 19 February 2021.

Results and conclusions

The use of prenatal GWS is indicated for the investigation of multiple fetal anomalies. Its use in the context of isolated fetal anomaly should be guided by available resources and current evidence, which is continually changing. During pregnancy, GWS should be ordered by, or in collaboration with, a medical geneticist. It should be used following detailed phenotyping to interrogate known disease genes, preferably using a trio approach, following detailed fetal phenotyping. Testing should be done with an overall aim to help in the management of the pregnancy, delivery and postnatal care. It should be guided by personal utility of the test for the pregnant person and clinical utility for pregnancy and birth management, as outlined herein. Genetic counselling is crucial in making the parental decision an informed decision. Chromosomal microarray analysis should be completed in parallel or prior to GWS and should be preceded by Quantitative Fluorescent PCR (QF-PCR) for detection of common aneuploidies. In normal circumstances, only pathogenic and likely pathogenic variants with a high likelihood of being associated with the identified fetal anomalies should be reported. Reporting of secondary findings, defined as purposeful analysis of variants in a set of medically actionable genes, should not, by default, be performed in the prenatal context. Laboratories should only report incidental findings that reveal risk of a significant Mendelian condition during infancy and childhood. Should a laboratory have a policy for reporting incidental findings in medically actionable adult-onset conditions, they should only be reported with explicit opt-in consent signed by the tested individuals. Genetic counselling is crucial in disclosing the test results and the implications the results may have for the fetus. It should be emphasised that negative results do not rule out a genetic diagnosis nor guarantee a good prognosis. Postnatal phenotyping and reanalysis of existing data should be considered. Families should be given the opportunity to participate in research studies as appropriate. These recommendations will be routinely re-evaluated as knowledge of the diagnostic and clinical utility of fetal GWS during pregnancy improves.

Worldwide barriers to genetic testing for movement disorders

BACKGROUND AND PURPOSE

Despite enormous advances in identifying genetic variants responsible for many neurological diseases, access to genetic testing may be limited in clinical practice. The objective of this study was to assess worldwide access to genetic tests for movement disorders and factors impacting their utilization.

METHODS

The Rare Movement Disorders Study Group of the International Parkinson and Movement Disorder Society designed an online survey electronically mailed to all 7815 members.

RESULTS

Survey data completed by 1269 participants from 109 countries were analysed. Limited access to geneticists and genetic counsellors was reported in many world regions compared to Europe and North America. Availability of genetic testing was limited, with rates of access lower than 50%. Genetic testing for chorea was the most commonly available. For parkinsonism, dystonia, ataxia, hereditary spastic paraplegias and metabolic disorders, there was limited access to genetic testing in all countries compared to Europe and North America, with significant differences found for Africa, Central/South America, Asia. In many regions, genetic testing was supported by either private or public funding. Genetic testing was free of charge in Europe according to 63.5% of respondents. In North America, Africa, Central/South America, Asia and the Middle East access to free of charge genetic testing was by far significantly lower compared to Europe.

CONCLUSIONS

This survey highlights difficulties in accessing genetic testing and individuals with expertise in genetics at the worldwide level. In addition, major disparities in genetic testing amongst world regions are highlighted, probably due to a variety of factors including financial barriers.

High Rates of Genetic Diagnosis in Psychiatric Patients with and without Neurodevelopmental Disorders: Toward Improved Genetic Diagnosis in Psychiatric Populations

OBJECTIVE

There is a paucity of literature on genetic diagnosis in psychiatric populations, particularly the vulnerable population of patients with concomitant neurodevelopmental disorder (NDD). In this cross-sectional study, we investigated the genetic diagnostic rate in 151 adult psychiatric patients from two centers in Ontario, Canada, including a large subset (73.5%) with concurrent NDD, and performed phenotypic analysis to determine the strongest predictors for the presence of a genetic diagnosis.

METHOD

Patients 16 years of age or older and affected with a psychiatric disorder plus at least one of NDD, neurological disorder, congenital anomaly, dysmorphic features, or family history of NDD were recruited through the genetics clinics between 2012 and 2016. Patients underwent genetic assessment and testing according to clinical standards. Chi-squared test was used for phenotypic comparisons. Multivariate logistic regression analysis was performed to determine which phenotypic features were predictive of genetic diagnosis types.

RESULTS

Overall, 45.7% of patients in the total cohort were diagnosed with genetic disorders with the vast majority of diagnoses (89.9%) comprising single gene and chromosomal disorders. There were management and treatment implications for almost two-thirds (63.8%) of diagnosed patients. Presence of a single gene disorder or chromosomal diagnosis was predicted by differing combinations of neurological, NDD, and psychiatric phenotypes.

CONCLUSION

The results of this study highlight the frequency and impact of genetic diagnosis in psychiatric populations, particularly those with concomitant NDD. Genetic assessment should be considered in psychiatric patients, particularly those with multiple brain phenotypes (psychiatric, neurodevelopmental, neurological).

Primary Care Physician Experiences with Integrated Population-Scale Genetic Testing: A Mixed-Methods Assessment

The scalable delivery of genomic medicine requires collaboration between genetics and non-genetics providers. Thus, it is essential to investigate and address the perceived value of and barriers to incorporating genetic testing into the clinical practice of primary care providers (PCPs). We used a mixed-methods approach of qualitative interviews and surveys to explore the experience of PCPs involved in the pilot DNA-10K population genetic testing program. Similar to previous research, PCPs reported low confidence with tasks related to ordering, interpreting and managing the results of genetic tests, and identified the need for additional education. PCPs endorsed high levels of utility for patients and their families but noted logistical challenges to incorporating genetic testing into their practice. Overall PCPs were not familiar with the United States' Genetic Information Nondiscrimination Act and they expressed high levels of concern for patient data privacy and potential insurance discrimination. This PCP feedback led to the development and implementation of several processes to improve the PCP experience with the DNA-10K program. These results contribute to the knowledge base regarding genomic implementation using a mixed provider model and may be beneficial for institutions developing similar clinical programs.

Can genetic testing help in the management of dyslipidaemias?

PURPOSE OF REVIEW

The aim of this study was to evaluate the potential role of genetic testing, particularly next-generation DNA sequencing, in diagnosing and managing dyslipidaemias, particularly monogenic dyslipidaemias.

RECENT FINDINGS

Targeted DNA sequencing of the genes causing monogenic dyslipidaemias is becoming more accessible. Some societies' position statements advise selective utilization of DNA testing in combination with clinical and biochemical assessment. However, high-quality peer-reviewed evidence showing that a DNA-based diagnosis impacts upon long-term patient outcomes is currently lacking. Nonetheless, we show anecdotal examples of tangible clinical actions following from a genetic diagnosis. In any event, care must be taken when interpreting genetic reports. We strongly feel that expertise in both genetics and dyslipidaemias is required to adequately interpret and report results to patients, as well as to make informed treatment decisions that can have a potential lifelong impact.

SUMMARY

There are some examples of monogenic dyslipidaemias for which having a molecular diagnosis might beneficially affect patient outcomes, for example certain cases of suspected familial hypercholesterolemia, familial chylomicronemia syndrome, sitosterolemia or lysosomal acid lipase deficiency. In general, we recommend limiting genetic testing to selected cases of monogenic dyslipidaemias. Finally, we advise that there is currently no proven clinical benefit in testing for polygenic dyslipidaemias.

Primary care physician experiences utilizing a family health history tool with electronic health record-integrated clinical decision support: an implementation process assessment

Family health history (FHH) screening plays a key role in disease risk identification and tailored disease prevention strategies. Primary care physicians (PCPs) are in a frontline position to provide personalized medicine recommendations identified through FHH screening; however, adoption of FHH screening tools has been slow and inconsistent in practice. Information is also lacking on PCP facilitators and barriers of utilizing family history tools with clinical decision support (CDS) embedded in the electronic health record (EHR). This study reports on PCPs' initial experiences with the Genetic and Wellness Assessment (GWA), a patient-administered FHH screening tool utilizing the EHR and CDS. Semi-structured interviews were conducted with 24 PCPs who use the GWA in a network of community-based practices. Four main themes regarding GWA implementation emerged: benefits to clinical care, challenges in practice, CDS-specific issues, and physician-recommended improvements. Sub-themes included value in improving patient access to genetic services, inadequate time to discuss GWA recommendations, lack of patient follow-through with recommendations, and alert fatigue. While PCPs valued the GWA's clinical utility, a number of challenges were identified in the administration and use of the GWA in practice. Based on participants' recommendations, iterative changes have been made to the GWA and workflow to increase efficiency, upgrade the CDS process, and provide additional education to PCPs and patients. Future studies are needed to assess a diverse sample of physicians' and patients' perspectives on the utility of FHH screening utilizing EHR-based genomics recommendations.

Physician Experience with Direct-To-Consumer Genetic Testing in Kaiser Permanente

Health systems and physicians nationwide aspire to consistently and reliably apply genetic and genomic information to guide disease prevention, management, and treatment. However, clinical information, including genetics/genomics data from within and outside of the care delivery system, is expanding rapidly. Between November 2017 and April 2018, we surveyed 1502 Permanente Medical Group primary care and specialist physicians to assess the degree to which direct-to-consumer genetic test results were being presented to physicians and identify genetics educational needs among physicians (response rate 15%). Adjusted logistic regression (according to respondent characteristics) was used to calculate adjusted odds ratios (ORs) and 95% confidence intervals (CIs) comparing responses within groups. Results showed 35% and 12% of respondents reported receiving at least one direct-to-consumer health risk genetic result (DTC-health risk) or direct-to-consumer pharmacogenomic test result (DTC-PGx), respectively, from a patient in the past year. Of those receiving at least one test result, 40% (DTC-health risk) and 39% (DTC-PGx) of physicians reported 1+ referral(s); 78% (DTC-health risk) and 42% (DTC-PGx) of referrals were to clinical genetics. In total, 85% of physicians would spend ≥2 h/year on genetics/genomics education.

Delivering genomic medicine in the United Kingdom National Health Service: a systematic review and narrative synthesis

PURPOSE

We sought to assess the readiness of the United Kingdom (UK) National Health Service to implement a Genomic Medicine Service. We conducted a systematic literature review to identify what is known about factors related to the implementation of genomic medicine in routine health care and to draw out the implications for the UK and other settings.

METHODS

Relevant studies were identified in Web of Science and PubMed from their date of inception to April 2018. The review included primary research studies using quantitative, qualitative, or mixed methods, and systematic reviews. A narrative synthesis was conducted.

RESULTS

Fifty-five studies met our inclusion criteria. The majority of studies reviewed were conducted in the United States. We identified four domains: (1) systems, (2) training and workforce needs, (3) professional attitudes and values, and (4) the role of patients and the public.

CONCLUSION

Mainstreaming genomic medicine into routine clinical practice requires actions at each level of the health-care system. Our synthesis emphasized the organizational, social, and cultural implications of reforming practice, highlighting that demonstration of clinical utility and cost-effectiveness, attending to the compatibility of genomic medicine with clinical principles, and involving and engaging patients are key to successful implementation.

Stakeholders' views on the value of outcomes from clinical genetic and genomic interventions

PURPOSE

Robust evidence about the value of clinical genomic interventions (CGIs), such as genetic/genomic testing or clinical genetic evaluation, is limited. We obtained stakeholders' perspectives on outcomes from CGIs to help inform their value.

METHODS

We used an adapted Delphi expert panel process. Two anonymous survey rounds assessed the value of 44 CGI outcomes and whether a third party should pay for them, with discussion in between rounds.

RESULTS

Sixty-six panelists responded to the first-round survey and 60 to the second. Policy-makers/payers gave the lowest ratings for value and researchers gave the highest. Patients/consumers had the most uncertainty about value and payment by a third party. Uncertainty about value was observed when evidence of proven health benefit was lacking, potential harms outweighed benefits for reproductive outcomes, and outcomes had only personal utility for individuals or family members. Agreement about outcomes for which a third party should not pay included prevention through surgery with unproven health benefits, establishing ancestry, parental consanguinity, and paternity.

CONCLUSION

Research is needed to understand factors contributing to uncertainty and stakeholder differences about the value of CGI outcomes. Reaching consensus will accelerate the creation of metrics to generate the evidence needed to inform value and guide policies that promote availability, uptake, and coverage of CGIs.

Primary care physician experiences with integrated pharmacogenomic testing in a community health system

Aim: To explore primary care physicians’ views of the utility and delivery of direct access to pharmacogenomics (PGx) testing in a community health system. Methods: This descriptive study assessed the perspectives of 15 healthcare providers utilizing qualitative individual interviews. Results: Three main themes emerged: perceived value and utility of PGx testing; challenges to implementation in practice; and provider as well as patient needs. Conclusion: While providers in this study viewed benefits of PGx testing as avoiding side effects, titrating doses more quickly, improving shared decision-making and providing psychological reassurance, challenges will need to be addressed such as privacy concerns, cost, insurance coverage and understanding the complexity of PGx test results.

Pulmonary arterial hypertension: Specialists' knowledge, practices, and attitudes of genetic counseling and genetic testing in the USA

Pulmonary arterial hypertension (PAH) is characterized by obstruction of pre-capillary pulmonary arteries, which leads to sustained elevation of pulmonary arterial pressure. Identifying those at risk through early interventions, such as genetic testing, may mitigate disease course. Current practice guidelines recommend genetic counseling and offering genetic testing to individuals with heritable PAH, idiopathic PAH, and their family members. However, it is unclear if PAH specialists follow these recommendations. Thus, our research objective was to determine PAH specialists' knowledge, utilization, and perceptions about genetic counseling and genetic testing. A survey was designed and distributed to PAH specialists who primarily work in the USA to assess their knowledge, practices, and attitudes about the genetics of PAH. Participants' responses were analyzed using parametric and non-parametric statistics and groups were compared using the Wilcoxon rank sum test. PAH specialists had low perceived and actual knowledge of the genetics of PAH, with 13.2% perceiving themselves as knowledgeable and 27% actually being knowledgeable. Although these specialists had positive or ambivalent attitudes about genetic testing and genetic counseling, they had poor utilization of these genetic services, with almost 80% of participants never or rarely ordering genetic testing or referring their patients with PAH for genetic counseling. Physicians were more knowledgeable, but had lower perceptions of the value of genetic testing and genetic counseling compared to non-physicians ( P < 0.05). The results suggest that increased education and awareness is needed about the genetics of PAH as well as the benefits of genetic testing and genetic counseling for individuals who treat patients with PAH.