Real-world diagnostic outcomes and cost-effectiveness of genome-wide sequencing for developmental and seizure disorders: Evidence from Canada

PURPOSE

To determine real-world diagnostic rates, cost trajectories, and cost-effectiveness of exome sequencing (ES) and genome sequencing (GS) for children with developmental and/or seizure disorders in British Columbia, Canada.

METHODS

Based on medical records review, we estimated real-world costs and outcomes for 491 patients who underwent standard of care (SOC) diagnostic testing at British Columbia Children's Hospital. Results informed a state-transition Markov model examining cost-effectiveness of 3 competing diagnostic strategies: (1) SOC with last-tier access to ES, (2) streamlined ES access, and (3) first-tier GS.

RESULTS

Through SOC, 49.4% (95% CI: 40.6, 58.2) of patients were diagnosed at an average cost of C$11,683 per patient (95% CI: 9200, 14,166). Compared with SOC, earlier ES or GS access yielded similar or improved diagnostic rates and shorter times to genetic diagnosis, with 94% of simulations demonstrating cost savings for streamlined ES and 60% for first-tier GS. Net benefit from the perspective of the health care system was C$2956 (95% CI: -608, 6519) for streamlined ES compared with SOC.

CONCLUSION

Using real-world data, we found earlier access to ES may yield more rapid genetic diagnosis of childhood developmental and seizure disorders and cost savings compared with current practice in a Canadian health care system.

A Rapid Review on the Value of Biobanks Containing Genetic Information

OBJECTIVES

Increasing access to health data through biobanks containing genetic information has the potential to expand the knowledge base and thereby improve screening, diagnosis, and treatment options for many diseases. Nevertheless, although privacy concerns and risks surrounding genetic data sharing are well documented, direct evidence in favor of the hypothesized benefits of data integration is scarce, which complicates decision making in this area. Therefore, the objective of this study is to summarize the available evidence on the research and clinical impacts of biobanks containing genetic information, so as to better understand how to quantify the value of expanding genomic data access.

METHODS

Using a rapid review methodology, we performed a search of MEDLINE/PubMed and Embase databases; and websites of biobanks and genomic initiatives published from 2010 to 2022. We classified findings into 11 indicators including outputs (a direct product of the biobank activities) and outcomes (changes in scientific and clinical capacity).

RESULTS

Of 8479 abstracts and 101 gray literature sources were reviewed, 96 records were included. Although most records did not report key indicators systematically, the available evidence concentrated on research indicators such as publications and gene-disorder association discoveries (63% of studies), followed by research infrastructure (26%), and clinical indicators (11%) such as supporting the diagnosis of individual patients.

CONCLUSIONS

Existing evidence on the benefits of biobanks is skewed toward easily quantifiable research outputs. Measuring a comprehensive set of outputs and outcomes inspired by value frameworks is necessary to generate better evidence on the benefits of genomic data sharing.

Defining Need Amid Exponential Change: Conceptual Challenges in Workforce Planning for Clinical Genetic Services

Rapid growth in the volume of referrals to clinical genetics services in many countries during the past 15 years makes workforce planning a critical policy tool in ensuring that the capacity of the clinical genetics workforce is large enough to meet current and future needs. This article explores the distinctive challenges of workforce planning in clinical genetics and provides recommendations for addressing these challenges using a needs-based planning approach. Specifically, at least 3 features complicate efforts to estimate the need for clinical genetic services: the difficulty in linking many clinical genetic services to concrete health outcomes; the rapidly changing nature of genetic medicine, which creates intrinsic uncertainty about the appropriate level of service; and the heightened relevance of patient preferences in this context. Our recommendations call for needs-based planning studies to include an explicit definition of necessary care, to be flexible in considering nonhealth benefits, to err on the side of including services currently funded by health systems even when evidence about outcomes is limited, and to use scenario analysis and expert input to explore the impact of uncertainty about patients' preferences and future technologies on estimates of workforce requirements.

Workforce Implications of Increased Referrals to Hereditary Cancer Services in Canada: A Scenario-Based Analysis

Over the last decade, utilization of clinical genetics services has grown rapidly, putting increasing pressure on the workforce available to deliver genetic healthcare. To highlight the policy challenges facing Canadian health systems, a needs-based workforce requirements model was developed to determine the number of Canadian patients in 2030 for whom an assessment of hereditary cancer risk would be indicated according to current standards and the numbers of genetic counsellors, clinical geneticists and other physicians with expertise in genetics needed to provide care under a diverse set of scenarios. Our model projects that by 2030, a total of 90 specialist physicians and 326 genetic counsellors (1.7-fold and 1.6-fold increases from 2020, respectively) will be required to provide Canadians with indicated hereditary cancer services if current growth trends and care models remain unchanged. However, if the expansion in eligibility for hereditary cancer assessment accelerates, the need for healthcare providers with expertise in genetics would increase dramatically unless alternative care models are widely adopted. Increasing capacity through service delivery innovation, as well as mainstreaming of cancer genetics care, will be critical to Canadian health systems' ability to meet this challenge.

Frameworks for Health Technology Assessment at an Early Stage of Product Development: A Review and Roadmap to Guide Applications

OBJECTIVES

Early health technology assessment (eHTA) can be used to evaluate and optimize a medical product's value proposition and to inform go/no-go decisions by using health economic modeling, literature scanning, and stakeholder preference studies at an early stage of development. eHTA frameworks offer high-level guidance on conducting this complex, iterative, and multidisciplinary process. The objective of this study was to review and summarize existing eHTA frameworks, understood as systematic approaches to guide early evidence generation and decision making.

METHODS

Using a rapid review methodology, we identified all relevant studies published in English, French, and Spanish from PubMed/MEDLINE and Embase until February 2022. We only included frameworks relevant to the preclinical and early clinical (phase I) stages of medical product development.

RESULTS

From 737 reviewed abstracts, 53 publications describing 46 frameworks were selected for inclusion and classified into categories based on their scope: (1) criteria frameworks, which provide an overview of eHTA; (2) process frameworks, which offer stepwise guidance for conducting eHTA, including preferred methods; and (3) methods frameworks, which provide detailed descriptions of specific eHTA methods. Most of the frameworks did not specify their target users or the specific stage of technology development.

CONCLUSIONS

Despite some variability and gaps found across existing frameworks, the structure provided by this review helps inform eHTA applications. Remaining challenges are the frameworks' limited accessibility to users without a background in health economics, poor distinctions being made among early lifecycle stages and technology types, and the inconsistent terminology used to describe eHTA in different contexts.

The effect of rapid exome sequencing on downstream health care utilization for infants with suspected genetic disorders in an intensive care unit

PURPOSE

This study aimed to compare downstream utilization of medical services among critically ill infants admitted to intensive care units who received rapid exome sequencing (ES) and those who followed alternative diagnostic testing pathways.

METHODS

Using propensity score-weighted regression models including sex, age at admission, and severity indicators, we compared a group of 47 infants who underwent rapid ES with a group of 211 infants who did not receive rapid ES. Utilization and cost indicators were compared between cohorts using negative binomial models for utilization and two-part models for costs.

RESULTS

After controlling for patients' sociodemographic and clinical characteristics, we found no statistically significant difference in outpatient visits, hospitalizations, intensive care unit or total length of stay, or length of stay-associated costs between the cohorts at 12- or 26-month follow-up. Similarly, there was no evidence of higher utilization or costs by the ES group when infants who died were removed from the analysis.

CONCLUSION

When examining utilization during and beyond the diagnostic trajectory, there is no evidence that ES changes frequency of outpatient visits or use of in-hospital resources in critically ill infants with suspected genetic disorders.

Where is genetic medicine headed? Exploring the perspectives of Canadian genetic professionals on future trends using the Delphi method

Driven by technological and scientific advances, the landscape of genetic medicine is rapidly changing, which complicates strategic planning and decision-making in this area. To address this uncertainty, we sought to understand genetic professionals' opinions about the future of clinical genetic and genomic services in Canada. We used the Delphi method to survey Canadian genetic professionals about their perspectives on whether scenarios about changes in service delivery and the use of genomic testing would be broadly implemented in their jurisdiction by 2030. We conducted two survey rounds; the response rates were 32% (27/84) and 67% (18/27), respectively. The most likely scenario was the universal use of noninvasive prenatal screening. The least likely scenarios involved population-based genome-wide sequencing for unaffected individuals. Overall, the scenarios perceived as most likely were those that have existing evidence about their benefit and potential medical necessity, whereas scenarios were seen as unlikely if they involved emerging technologies. Participants expected that the need for genetic healthcare services would increase by 2030 owing to changes in clinical guidelines and increased use of genome-wide sequencing. This study highlights the uncertainty in the future of genetic and genomic service provision and contributes evidence that could be used to inform strategic planning in clinical genetics.

Toward the diagnosis of rare childhood genetic diseases: what do parents value most?

Genomic testing is becoming routine for diagnosing rare childhood genetic disease. Evidence underlying sustainable implementation is limited, focusing on short-term endpoints such as diagnostic yield, unable to fully characterize patient and family valued outcomes. Although genomic testing is becoming widely available, evidentiary and outcomes uncertainty persist as key challenges for implementation. We examine whether the current evidence base reflects public tolerance for uncertainty for genomics to diagnose rare childhood genetic disease. We conducted focus groups with general population parents in Vancouver, Canada, and Oxford, United Kingdom, to discuss expectations and concerns related to genomic testing to diagnose rare childhood genetic disease. Applying a purposive sampling technique, recruitment continued until thematic saturation was reached. Transcripts were analysed using thematic analysis. Thirty-three parents participated across four focus groups. Participants valued causal diagnoses alongside management strategies to improve patient health and wellbeing. Further, participants valued expanding the evidence base to reduce evidentiary uncertainty while ensuring security of information. Willingness to pay out of pocket for testing reflected perceived familial health benefit. Diagnostic yield fails to fully capture valued outcomes, and efforts to resolve uncertainty better reflect public priorities. Evaluations of genomic testing that fully integrate valued endpoints are necessary to ensure consistency with best practices and public willingness to accept the uncertain familial benefit.

Far and wide: Exploring provider utilization of remote service provision for genome-wide sequencing in Canada

Background

In Canada, funding for genome‐wide sequencing (GWS; exome and whole genome) is provincially regulated. We characterized the uptake of GWS by genetics health professionals (GHPs) across Canada and describe how they use remote technologies for patient access to GWS and genomic counseling.

Methods

We distributed a survey to 574 Canadian GHPs addressing: GWS use, remote technologies (e.g., telephone, videoconferencing) for GWS and provider opinions regarding these technologies. Data were summarized using descriptive statistics. Associations between variables were evaluated using Chi‐square and Fisher's Exact tests for categorical data, and t‐tests or Mann–Whitney U tests for continuous data.

Results

Of 116 GHPs, 50% reported using GWS in the last year and 57% of GWS users reported using remote technologies. Clinical geneticists who did not use GWS reported lack of provincial funding as the principal reason. Remote technologies were most commonly used for informed consent and results, and rarely used for initial consultations. Average wait times for a GWS appointment were shorter for remote appointments (mean 44.2 (SD 40.2) weeks) than for in‐person (mean 58.2 (SD 42.9), p = 0.036).

Conclusion

The use of GWS varied across Canada, professional designation, and discipline. Funding remains a barrier to GWS access. Remote technologies increase patient access with reduced wait times.

Economic Evidence on Potentially Curative Gene Therapy Products: A Systematic Literature Review

OBJECTIVE

The aim of this review was to summarize all available evidence on the cost effectiveness of potentially curative gene therapies and identify challenges that economic evaluations face in this area.

METHODS

We conducted a systematic review of four databases (PubMed/MEDLINE, Embase, CINAHL, EconLit) and grey literature sources. We conducted the search on August 23, 2019 and updated it on November 26, 2020. We included all English, French and Spanish language studies that addressed a gene therapy that had received regulatory approval or had entered a phase III trial, and also reported on costs related to the therapy. Critical appraisal was conducted to assess quality of reporting in included studies.

RESULTS

Fifty-six studies were identified. Of the 42 full economic evaluations, 71% (n = 30) evaluated chimeric antigen receptor T-cell therapies, most used either a Markov model (n = 17, 40%) and/or a partitioned survival model (n = 17, 40%), and 76% (n = 32) adopted a public or private payer perspective. The model characteristics with the greatest impact on cost effectiveness included assumptions about the efficacy of the treatment and the comparators used.

CONCLUSION

All gene therapies in this review were shown to be more effective than their comparators, although due to high costs not all were considered cost effective at standard cost-effectiveness thresholds. Despite their high cost, some gene therapies have the potential to dominate the alternatives in conditions with high mortality/disability. The choice of comparator and assumptions regarding long-term effectiveness had substantial impacts on cost-effectiveness estimates and need to be carefully considered. Both the quality of inputs and the quality of reporting were highly variable.

Utilization and uptake of clinical genetics services in high-income countries: A scoping review

Ongoing rapid growth in the need for genetic services has the potential to severely strain the capacity of the clinical genetics workforce to deliver this care. Unfortunately, assessments of the scale of this health policy challenge and potential solutions are hampered by the lack of a consolidated evidence base on the growth in genetic service utilization. To enable health policy research and strategic planning by health systems in this area, we conducted a scoping review of the literature on the utilization and uptake of clinical genetics services in high-income countries published between 2010 and 2018. One-hundred-and-ninety-five unique studies were included in the review. Most focused on cancer (85/195; 44%) and prenatal care (50/195; 26%), which are consistently the two areas with the greatest volume of genetic service utilization in both the United States and other high-income countries. Utilization and uptake rates varied considerably and were influenced by contextual factors including health system characteristics, provider knowledge, and patient preferences. Moreover, growth in genetic service utilization appears to be driven to a significant degree by technological advances and the integration of new tests into clinical care. Our review highlights both the policy challenge posed by the rapid growth in the utilization of genetic services and the variability in this trend across clinical indications and health systems.

Utilization of telehealth in paediatric genome-wide sequencing: Health services implementation issues in the CAUSES Study

INTRODUCTION

Genome-wide sequencing (exome or whole genome) is transforming the care and management of paediatric patients with a rare disease because of its diagnostic capabilities. Genome-wide sequencing is most effective when both parents and the child are sequenced as a trio. Genetic counselling is recommended for all families considering genome-wide sequencing. Although telehealth is well established in genetic counselling for hereditary cancer and prenatal genetics, its use with genome-wide sequencing has not been well studied. The CAUSES Clinic at BC Children's and Women's Hospitals was a translational paediatric trio-based genome-wide sequencing initiative. Pre-test genetic counselling via telehealth (at a clinical site near the family's residence) was offered to families who had been previously evaluated by a clinical geneticist. We report on the first 300 families seen in the CAUSES clinic and compare health services implementation issues of families seen via telehealth versus on-site.

METHODS

Demographics, cost to families (travel and time), time to first appointment, complete trio sample accrual and diagnostic rates were studied.

RESULTS

Of the 300 patients, 58 (19%) were seen via telehealth and 242 (81%) were seen on-site for pre-test counselling. The mean time to completion of accrual of trio samples in the telehealth group was 56.3 (standard deviation ±87.3) days versus 18.9 (standard deviation ±62.4) days in the onsite group (p < 2.2 × 10^-16). The mean per-family estimated actual or potential travel/time cost savings were greater in the telehealth group (Can$987; standard deviation = Can$1151) than for those seen on-site (Can$305; standard deviation = Can$589) (p = 0.0004).

CONCLUSIONS

Telehealth allowed for access to genome-wide sequencing for families in remote communities and for them to avoid significant travel and time costs; however, there was a significant delay to accrual of the complete trio samples in the telehealth group, impacting on time of result reporting and delaying diagnoses for families for whom genome-wide sequencing was diagnostic.

Evaluating New Zealanders' Values for Drug Coverage Decision Making: Trade-Offs between Treatments for Rare and Common Conditions

BACKGROUND

New Zealand's near static healthcare budget limits access to expensive medications including those for rare conditions. As such, it is necessary to know the public's priority for values in the drug funding decision-making process.

OBJECTIVES

The objectives of this study were to measure the relative societal importance of values of New Zealanders in informing drug funding decisions and to determine how New Zealanders trade off funding in various scenarios between common and rare diseases.

METHODS

An online survey was conducted between 17 April and 17 May, 2019 on a sample of 500 New Zealanders aged ≥ 18 years. Participants ranked 13 values using an analytical hierarchy process. Participants were then presented with different trade-off scenarios to measure their attitudes towards funding drugs for common and rare diseases.

RESULTS

The values ranked in the top five by most were potential effect on quality of life (71.8%), ability of the drug to work (57.6%), severity (57.6%), safety (57%), and potential to extend life (56%). Adherence and rarity held the lowest and second lowest ranking. Most believe that resources should be allocated towards drugs that have been proven to work and have the greatest health benefits. In trade-offs between access to an expensive drug therapy for a rare disease with uncertain benefits or receive a fixed cash payment, the overwhelming consensus was to receive the cash payment.

CONCLUSIONS

New Zealanders ultimately value drug-related factors (e.g. quality of life and efficacy) and disease-related factors (e.g. severity of disease and equity) the most but did not value disease rarity.

The composition and capacity of the clinical genetics workforce in high-income countries: a scoping review

As genetics becomes increasingly integrated into all areas of health care and the use of complex genetic tests continues to grow, the clinical genetics workforce will likely face greatly increased demand for its services. To inform strategic planning by health-care systems to prepare to meet this future demand, we performed a scoping review of the genetics workforce in high-income countries, summarizing all available evidence on its composition and capacity published between 2010 and 2019. Five databases (MEDLINE, Embase, PAIS, CINAHL, and Web of Science) and gray literature sources were searched, resulting in 162 unique studies being included in the review. The evidence presented includes the composition and size of the workforce, the scope of practice for genetics and nongenetics specialists, the time required to perform genetics-related tasks, case loads of genetics providers, and opportunities to increase efficiency and capacity. Our results indicate that there is currently a shortage of genetics providers and that there is a lack of consensus about the appropriate boundaries between the scopes of practice for genetics and nongenetics providers. Moreover, the results point to strategies that may be used to increase productivity and efficiency, including alternative service delivery models, streamlining processes, and the automation of tasks.

Evaluating Canadians' Values for Drug Coverage Decision Making

BACKGROUND

Decision makers are facing growing challenges in prioritizing drugs for reimbursement because of soaring drug costs and increasing pressures on financial resources. In addition to cost and effectiveness, payers are using other values to dictate which drugs are prioritized for funding, yet there are limited data on the Canadian public's priorities.

OBJECTIVES

To measure the relative societal importance of values considered most relevant in informing drug reimbursement decisions in a representative sample of Canadians.

METHODS

An online survey of 2539 Canadians aged 19 years and older was performed in which 13 values used in drug funding prioritization were ranked and then weighted using an analytic hierarchy process.

RESULTS

Canadians value safe and efficacious drugs that have certainty of evidence. The values ranked in the top 5 by most of our subjects were potential effect on quality of life (65.4%), severity of the disease (62.6%), ability of drug to work (61.1%), safety (60.5%), and potential to extend life (49.4%). Values related to patient or disease characteristics such as rarity, socioeconomic status, and health and lifestyle choices held the lowest rankings and weights.

CONCLUSIONS

Canadians value, above all, treatment-related factors (eg, efficacy and safety) and disease-related factors (eg, severity and equity). Decision makers are currently using additional justifications to prioritize drugs for reimbursement, such as rarity and unmet need, which were not found to be highly valued by Canadians. Decision makers should integrate the public's values into a Canadian reimbursement framework for prioritization of drugs competing for limited funds.

The Genomic Consultation Service: A clinical service designed to improve patient selection for genome-wide sequencing in British Columbia

BACKGROUND

Access to clinical diagnostic genome-wide sequencing (GWS; exome or whole genome sequencing) is limited in British Columbia. The establishment of a translational research initiative (CAUSES) to provide diagnostic genome-wide sequencing for 500 children necessitated the development of a genomic consultation service, a clinical service established to provide consultation for physicians considering GWS for their pediatric patients throughout British Columbia. The Genomic Consultation Service provides patient-specific genomic advice that may include: GWS, multi-gene panel, single gene test, referral to medical genetics for clinical evaluation, or no genetic testing. Here, we describe and evaluate this service.

METHODS

We analyzed referral patterns, patient demographics, clinical indications, and genomic advice provided during the first year of this service. Comparison of outcomes from the first 6 months versus the last 6 months was performed.

RESULTS

A total of 407 referrals (238 males and 169 females [p = .0006]) were processed in the first year. Only children were eligible for referral and average patient age was 8 years. Medical genetics was the most frequent referring discipline, followed by biochemical disease and pediatric neurology, respectively. Most patients (68%) had syndromic intellectual disability. There was a significant difference in the frequency of referrals not appropriate for GWS in the first versus the second 6 months of the service (75/220 vs. 42/187; p = .01) suggesting increasing awareness of testing criteria by referring physicians.

CONCLUSION

This triage service is utilized throughout the province and appears to be an important factor in the high diagnostic rate (>40%) achieved in our GWS program.

Evaluating the use of parental reports to estimate health care resource utilization in children with suspected genetic disorders

OBJECTIVE

A key step in evaluating the cost-effectiveness of diagnostic genome-wide sequencing (GWS) services is to measure the cost of prior and subsequent diagnosis-related health care resource utilization by patients. The majority of patients using diagnostic GWS services are children, and parental surveys are often used to complement utilization data abstracted from medical records. The objective of this study was to evaluate the validity of parental reports for children with very high levels of resource utilization.

METHOD

Primary caregivers of children enrolled in the CAUSES Research Clinic, a diagnostic GWS programme at B.C. Children's Hospital, completed an online survey. Parent-reported health care encounters for the 6-month period prior to survey completion were compared to utilization data abstracted from electronic medical records (EMR). The association between demographic characteristics and the probability of survey completion was tested using logistic regression. Agreement between parent-reported and EMR data was evaluated using Cohen's kappa, prevalence- and bias-adjusted kappa (PABAK), and the intraclass correlation coefficient (ICC).

RESULTS

There were no major differences in demographic characteristics or resource utilization levels between families that completed the survey and those who did not. Agreement between parental reports and EMR data was high for hospitalizations (κ = 0.71; PABAK = 0.89; ICC = 0.77) but lower for outpatient physician visits (κ = 0.21; PABAK = 0.48; ICC = 0.27).

CONCLUSIONS

Parental surveys are a valuable tool for estimating health care resource utilization during a 6-month recall period for children with suspected genetic disorders but are best used to complement utilization data collected from other sources.

The cost and diagnostic yield of exome sequencing for children with suspected genetic disorders: a benchmarking study

PURPOSE

This study aimed to generate benchmark estimates for the cost, diagnostic yield, and cost per positive diagnosis of diagnostic exome sequencing (ES) in heterogeneous pediatric patient populations and to illustrate how the design of an ES service can influence its cost and yield.

METHODS

A literature review and Monte Carlo simulations were used to generate benchmark estimates for singleton and trio ES. A cost model for the Clinical Assessment of the Utility of Sequencing and Evaluation as a Service (CAUSES) study, which is testing a proposed delivery model for diagnostic ES in British Columbia, is used to illustrate the potential effects of changing the service design.

RESULTS

The benchmark diagnostic yield was 34.3% (95% confidence interval (CI): 23.2-46.5) for trio ES and 26.5% (95% CI: 12.9-42.9) for singleton ES. The benchmark cost of delivery was C$6,437 (95% CI: $5,305-$7,704) in 2016 Canadian dollars (US$4,859; 4,391€) for trio ES and C$2,576 (95% CI: $1,993-$3,270) (US$1,944; 1,757€) for singleton ES. Scenario models for CAUSES suggest that alternative service designs could reduce costs but might lead to a higher cost per diagnosis due to lower yields.

CONCLUSION

Broad conclusions about the cost-effectiveness of ES should be drawn with caution when relying on studies that use cost or yield assumptions that lie at the extremes of the benchmark ranges.

What will the crowd fund? Preferences of prospective donors for drug development fundraising campaigns

Biomedical researchers are increasingly turning to project-based online fundraising (i.e., crowdfunding) as a complementary source of research funding. To help inform the fundraising strategies adopted by researchers who take this approach, we conducted an online survey of prospective donors in North America. Respondents indicated not only an overwhelming preference for donating to projects conducted by nonprofit research organizations, but also an openness to donating to companies that have a 'for-benefit' corporate structure. They also showed a strong preference for projects that have alternate sources of funding, that have the potential to yield a curative therapy, and that focus on common and pediatric diseases.