Australian Genomics: Outcomes of a 5-year national program to accelerate the integration of genomics in healthcare

Enhancing diagnostic outcomes in kidney genetic disorders: the KidGen national kidney genomics study protocol

BACKGROUND

Genetic kidney disease (GKD) significantly affects the community and is responsible for a notable portion of adult kidney disease cases and about half of cases in paediatric patients. It substantially impacts the quality of life and life expectancy for affected children and adults across all stages of kidney disease. Precise genetic diagnosis in GKD promises to improve patient outcomes, provide access to targeted treatments, and reduce the disease burden for individuals, families, and healthcare systems. Genetic investigations are increasingly used in nephrology practice; however, many patients who undergo testing still lack a definitive diagnosis.

METHODS

The KidGen National Kidney Genomics Study aims to increase diagnostic yield for those with suspected monogenic kidney disease without a diagnosis after standard diagnostic genetic testing. The program will seek to enrol up to 200 families from KidGen Collaborative kidney genetics clinics across Australia who have yet to receive conclusive diagnoses despite prior testing. Participants will undergo a personalised pathway of research genomic investigations. These include re-analysing existing data and/or undergoing advanced genomic testing methods, including short and long-read whole-genome sequencing, RNA sequencing, and functional genomics strategies using mouse modelling or kidney organoids.

DISCUSSION

The KidGen National Kidney Genomics Study is a coordinated, multidisciplinary extension of previous research projects that aims to assess the diagnostic yield of advanced genomic approaches. The study's evidence will drive changes to current diagnostic pathways, including identifying which chronic kidney disease patients are most likely to benefit from a more comprehensive genomic approach to diagnosis.

A call to action to scale up research and clinical genomic data sharing

Genomic data from millions of individuals have been generated worldwide to drive discovery and clinical impact in precision medicine. Lowering the barriers to using these data collectively is needed to equitably realize the benefits of the diversity and scale of population data. We examine the current landscape of global genomic data sharing, including the evolution of data sharing models from data aggregation through to data visiting, and for certain use cases, cross-cohort analysis using federated approaches across multiple environments. We highlight emerging examples of best practice relating to participant, patient and community engagement; evolution of technical standards, tools and infrastructure; and impact of research and health-care policy. We outline 12 actions we can all take together to scale up efforts to enable safe global data sharing and move beyond projects demonstrating feasibility to routinely cross-analysing research and clinical data sets, optimizing benefit.

Genomic sequencing: the case for equity of care in the era of personalized medicine

Over the past two decades, genomic sequencing (exome and genome) has proven to be critical in providing a faster and more accurate diagnosis as well as tailored treatment plans for a variety of populations. Despite its potential, disparities in access to genomic sequencing persist, predominantly among underrepresented and socioeconomically disadvantaged groups and populations. This inequity stems from factors such as: 1) high costs of sequencing, 2) significant gaps in insurance coverage, 3) limited availability of genetic services in many healthcare institutions and geographic areas, and 4) lack of diversity in genetic research and databases. Addressing these barriers is essential to realizing the full benefits of personalized treatment approaches for all individuals. By doing so, healthcare systems can move towards a more inclusive model that delivers optimal care for everyone. This manuscript emphasizes these issues by considering diverse perspectives from various ethnic groups, summarizing findings across different patient populations (adults, pediatrics, critical/non-critical care), and highlighting the importance of collaboration and workforce training in genomic sequencing and interpretation. IMPACT: Presentation of exemplary studies demonstrating the advantages of genomic sequencing in various clinical settings and a variety of high-risk populations. Review of obstacles in providing equitable genomic medical care and the importance of national and international collaborations An overview of the ethical aspects of genomic sequencing is provided.

Hospital-wide access to genomic data advanced pediatric rare disease research and clinical outcomes

Boston Children's Hospital has established a genomic sequencing and analysis research initiative to improve clinical care for pediatric rare disease patients. Through the Children's Rare Disease Collaborative (CRDC), the hospital offers CLIA-grade exome and genome sequencing, along with other sequencing types, to patients enrolled in specialized rare disease research studies. The data, consented for broad research use, are harmonized and analyzed with CRDC-supported variant interpretation tools. Since its launch, 66 investigators representing 26 divisions and 45 phenotype-based cohorts have joined the CRDC. These studies enrolled 4653 families, with 35% of analyzed cases having a finding either confirmed or under further investigation. This accessible and harmonized genomics platform also supports additional institutional data collections, research and clinical, and now encompasses 13,800+ patients and their families. This has fostered new research projects and collaborations, increased genetic diagnoses and accelerated innovative research via integration of genomics research with clinical care.

Assessing the unmet needs of genomic testing in Australia: a geospatial exploration

The role of genomic testing in rare disease clinical management is growing. However, geographical and socioeconomic factors contribute to inequitable uptake of testing. Geographical investigations of genomic testing across Australia have not been undertaken. Therefore, we aimed to investigate the geospatial distribution of genomic testing nationally between remoteness areas, and areas of varying socioeconomic advantage and disadvantage. We requested patient postcodes, age, and test type from genomic testing records from seven Australian laboratories for a 6-month period between August 2019 and June 2022. Postcode data were aggregated to Local Government Areas (LGAs) and visualised geospatially. Data were further aggregated to Remoteness Areas and Socio-Economic Index for Areas (SEIFA) quintiles for exploratory analysis. 11,706 records were eligible for analysis. Most tests recorded were paediatric (n = 8358, 71.4%). Microarray was the most common test captured (n = 8186, 69.9%). The median number of tests per LGA was 5.4 (IQR 1.0-21.0). Fifty-seven (10.4%) LGAs had zero tests recorded. Remoteness level was negatively correlated with number of tests across LGAs (rho = -0.781, p < 0.001). However, remote areas recorded the highest rate of testing per 100,000 populations. SEIFA score positively correlated with number of tests across LGAs (rho = 0.386, p < 0.001). The third SEIFA quintile showed the highest rate of testing per 100,000 populations. Our study establishes a foundation for ongoing assessment of genomic testing accessibility and equity and highlights the need to improve access to genomic testing for patients who are disadvantaged geographically or socioeconomically. Future research should include additional laboratories to achieve a larger representation of genomic testing rates nationally.

Rare disease genomic testing in the UK and Ireland: promoting timely and equitable access

PURPOSE AND SCOPE

The aim of this position statement is to provide recommendations regarding the delivery of genomic testing to patients with rare disease in the UK and Ireland. The statement has been developed to facilitate timely and equitable access to genomic testing with reporting of results within commissioned turnaround times.

METHODS OF STATEMENT DEVELOPMENT

A 1-day workshop was convened by the UK Association for Clinical Genomic Science and attended by key stakeholders within the NHS Genomic Medicine Service, including clinical scientists, clinical geneticists and patient support group representatives. The aim was to identify best practice and innovations for streamlined, geographically consistent services delivering timely results. Attendees and senior responsible officers for genomic testing services in the UK nations and Ireland were invited to contribute.

RESULTS AND CONCLUSIONS

We identified eight fundamental requirements and describe these together with key enablers in the form of specific recommendations. These relate to laboratory practice (proportionate variant analysis, bioinformatics pipelines, multidisciplinary team working model and test request monitoring), compliance with national guidance (variant classification, incidental findings, reporting and reanalysis), service development and improvement (multimodal testing and innovation through research, informed by patient experience), service demand, capacity management, workforce (recruitment, retention and development), and education and training for service users. This position statement was developed to provide best practice guidance for the specialist genomics workforce within the UK and Ireland but is relevant to any publicly funded healthcare system seeking to deliver timely rare disease genomic testing in the context of high demand and limited resources.

Nationwide, Couple-Based Genetic Carrier Screening

BACKGROUND

Genomic sequencing technology allows for identification of reproductive couples with an increased chance, as compared with that in the general population, of having a child with an autosomal recessive or X-linked genetic condition.

METHODS

We investigated the feasibility, acceptability, and outcomes of a nationwide, couple-based genetic carrier screening program in Australia as part of the Mackenzie's Mission project. Health care providers offered screening to persons before pregnancy or early in pregnancy. The results obtained from testing at least 1281 genes were provided to the reproductive couples. We aimed to ascertain the psychosocial effects on participants, the acceptability of screening to all participants, and the reproductive choices of persons identified as having an increased chance of having a child with a condition for which we screened.

RESULTS

Among 10,038 reproductive couples enrolled in the study, 9107 (90.7%) completed screening, and 175 (1.9%) were newly identified as having an increased chance of having a child with a genetic condition for which we screened. These conditions involved pathogenic variants in 90 different genes; 74.3% of the conditions were autosomal recessive. Three months after receiving the results, 76.6% of the couples with a newly identified increased chance had used or planned to use reproductive interventions to avoid having an affected child. Those newly identified as having an increased chance had greater anxiety than those with a low chance. The median level of decisional regret was low in all result groups, and 98.9% of participants perceived screening to be acceptable.

CONCLUSIONS

Couple-based reproductive genetic carrier screening was largely acceptable to participants and was used to inform reproductive decision making. The delivery of screening to a diverse and geographically dispersed population was feasible. (Funded by the Medical Research Future Fund of the Australian government; ClinicalTrials.gov number, NCT04157595.).

Variation Exists in Service Delivery: Similarities and Differences in the Provision of a Whole Genome Sequencing Service for Paediatric Rare Disease Patients in the National Health Service in England

INTRODUCTION

The National Health Service (NHS) in England is the first to offer whole genome sequencing (WGS) as part of standard care. As a high-income country with a universal healthcare system, England contributes a valuable perspective to global developments in WGS.

METHODS

We used an implementation science approach with mixed methods to characterise delivery of WGS for paediatric rare diseases: observations and field notes of consent appointments in clinical genetics and mainstream settings and follow-up qualitative semi-structured interviews with the clinical team. Process maps were developed for each department to identify similarities and variations between sites and thematic analysis of interview data to understand barriers and facilitators.

RESULTS

Data collection occurred in 12 departments (7 genetic, 3 neurology, 1 cardiology, and 1 general paediatric) across 7 NHS Trusts. 26 observations of 21 healthcare professionals were conducted, alongside 19 follow-up interviews. Two master maps were developed - one for clinical genetics and one for the mainstream. We identified 11 steps involved in delivering WGS, including 9 variations and 9 similarities. We identified most variation in the processes related to the "who," "when," "how," and "where" as these were aspects that could be adapted to fit into the specific set-up of the department. Barriers included reluctance to uptake in the mainstream and difficulties tracking samples.

CONCLUSION

Recommendations include developing standard operating procedures and hiring healthcare professionals responsible for facilitating consent alongside administrative aspects. These would reduce the burden on clinical geneticists and improve turnaround times as well as contribute to streamlining and standardisation of the service.

Shaping the future of kidney genetics in Australia: proceedings from the KidGen policy implementation workshop 2023

The KidGen Collaborative's Policy Implementation Workshop 2023 celebrated the 10th anniversary of Australia's first kidney genetics clinic in Brisbane. This event marked the establishment of a national network now comprising 19 kidney genetics clinics across Australia, all dedicated to providing equitable access to genomic testing for families affected by genetic kidney diseases. The workshop reflected on past progress and outlined future objectives for kidney genetics in Australia, recognising the collaborative efforts of clinical teams, researchers, and patients. Key insights from the workshop are documented in the proceedings.

Implementation and Evaluation of a National Multidisciplinary Kidney Genetics Clinic Network Over 10 Years

Introduction

Diagnostic genomic sequencing is the emerging standard of care in nephrology. There is a growing need to scale up the implementation of genomic diagnostics nationally to improve patient outcomes.

Methods

This pragmatic study provided genomic or genetic testing to patients with suspected monogenic kidney disease through a national network of kidney genetics clinics (KGCs). We sought to evaluate the experiences of implementing genomic diagnostics across Australia and associated diagnostic outcomes between 2013 and 2022.

Results

We successfully established and expanded a nationwide network of 20 clinics as of 2022; concurrently developing laboratory, research, and education programs to scale the clinical application of genomics in nephrology. We report on an Australian cohort of 1506 kidney patients, of whom 1322 received their test results. We assessed barriers to implementation in the nephrology context, and where possible, applied real-time solutions to improve clinical processes over 10 years.

Conclusion

Developing a multidisciplinary kidney genetics model across multiple health services nationally was highly successful. This model supported optimal care of individuals with monogenic kidney disease in an economically responsible way. It has continued to evolve with technological and service developments and is now set to scale further as genomic testing for kidney patients transitions to health care system funding.

Determining priority indicators of utility for genomic testing in rare disease: A Delphi study

PURPOSE

Determining the value of genomic tests in rare disease necessitates a broader conceptualization of genomic utility beyond diagnostic yield. Despite widespread discussion, consensus toward which aspects of value to consider is lacking. This study aimed to use expert opinion to identify and refine priority indicators of utility in rare disease genomic testing.

METHODS

We used 2 survey rounds following Delphi methodology to obtain consensus on indicators of utility among experts involved in policy, clinical, research, and consumer advocacy leadership in Australia. We analyzed quantitative and qualitative data to identify, define, and determine priority indicators.

RESULTS

Twenty-five experts completed round 1 and 18 completed both rounds. Twenty indicators reached consensus as a priority in value assessment, including those relating to prognostic information, timeliness of results, practical and health care outcomes, clinical accreditation, and diagnostic yield. Whereas indicators pertaining to discovery research, disutility, and factors secondary to primary reason for testing were considered less of a priority and were removed.

CONCLUSION

This study obtained expert consensus on different utility indicators that are considered a priority in determining the value of genomic testing in rare disease in Australia. Indicators may inform a standardized approach to evidence generation and assessment to guide future research, decision making, and implementation efforts.

The cost of proband and trio exome and genome analysis in rare disease: A micro-costing study

PURPOSE

Rare disease genomic testing is a complex process involving various resources. Accurate resource estimation is required for informed prioritization and reimbursement decisions. This study aims to analyze the costs and cost drivers of clinical genomic testing.

METHODS

Based on genomic sequencing workflows we microcosted limited virtual panel analysis on exome sequencing backbone, proband and trio exome, and genome testing for proband and trio analysis in 2023 Australian Dollars ($). Deterministic and probabilistic sensitivity analyses were undertaken.

RESULTS

Panel testing costs AUD $2373 ($733-$6166), and exome sequencing costs $2823 ($802-$7206) and $5670 ($2006-$11,539) for proband and trio analysis, respectively. Genome sequencing costs $4840 ($2153-$9890) and $11,589 ($5842-$16,562) for proband and trio analysis. The most expensive cost component of genomic testing was sequencing (36.9%-69.4% of total cost), with labor accounting for 27.1%-63.2% of total cost.

CONCLUSION

We provide a comprehensive analysis of rare disease genomic testing costs, for a range of clinical testing types and contexts. This information will accurately inform economic evaluations of rare disease genomic testing and decision making on policy settings that assist with implementation, such as genomic testing reimbursement.

Challenges and solutions to system-wide use of precision oncology as the standard of care paradigm

The personalised oncology paradigm remains challenging to deliver despite technological advances in genomics-based identification of actionable variants combined with the increasing focus of drug development on these specific targets. To ensure we continue to build concerted momentum to improve outcomes across all cancer types, financial, technological and operational barriers need to be addressed. For example, complete integration and certification of the 'molecular tumour board' into 'standard of care' ensures a unified clinical decision pathway that both counteracts fragmentation and is the cornerstone of evidence-based delivery inside and outside of a research setting. Generally, integrated delivery has been restricted to specific (common) cancer types either within major cancer centres or small regional networks. Here, we focus on solutions in real-world integration of genomics, pathology, surgery, oncological treatments, data from clinical source systems and analysis of whole-body imaging as digital data that can facilitate cost-effectiveness analysis, clinical trial recruitment, and outcome assessment. This urgent imperative for cancer also extends across the early diagnosis and adjuvant treatment interventions, individualised cancer vaccines, immune cell therapies, personalised synthetic lethal therapeutics and cancer screening and prevention. Oncology care systems worldwide require proactive step-changes in solutions that include inter-operative digital working that can solve patient centred challenges to ensure inclusive, quality, sustainable, fair and cost-effective adoption and efficient delivery. Here we highlight workforce, technical, clinical, regulatory and economic challenges that prevent the implementation of precision oncology at scale, and offer a systematic roadmap of integrated solutions for standard of care based on minimal essential digital tools. These include unified decision support tools, quality control, data flows within an ethical and legal data framework, training and certification, monitoring and feedback. Bridging the technical, operational, regulatory and economic gaps demands the joint actions from public and industry stakeholders across national and global boundaries.

A multitiered analysis platform for genome sequencing: Design and initial findings of the Australian Genomics Cardiovascular Disorders Flagship

Purpose

The Australian Genomics Cardiovascular Disorders Flagship was a national multidisciplinary collaboration. It aimed to investigate the feasibility of genome sequencing (GS) and functional genomics to resolve variants of uncertain significance (VUS) in the clinical management of patients and families with cardiomyopathies, primary arrhythmias, and congenital heart disease (CHD).

Methods

Between April 2019 and December 2021, 600 probands meeting cardiovascular disorder criteria from 17 cardiology and genetics clinics across Australia were enrolled in the Flagship and underwent GS. The Flagship adopted a tiered approach to GS analysis. Tier 1 analysis assessed genes with established clinical validity for each cardiovascular condition. Tier 2 analysis assessed lesser-evidenced research-based genes. Tier 3 analysis assessed the functional impact of VUS that remained after tier 1 and tier 2 analysis.

Results

Overall, a pathogenic or likely pathogenic variant was identified in 41% of participants with a cardiomyopathy, 40% with an arrhythmia syndrome, and 15% with a familial CHD/CHD+Extra Cardiac Anomalies. A VUS outcome ranged from 13% for arrhythmias to 34% for CHD/CHD+Extra Cardiac Anomalies participants. Tier 2 research analysis identified a likely pathogenic/pathogenic variant for a further 15 participants and a VUS for an additional 15 participants.

Conclusion

The Flagship successfully facilitated a model of care that harnesses clinical GS and functional genomics for the resolution of VUS in the clinical setting. This valuable data set can be used to inform clinical practice and facilitate research into the future.

'Integrating Ethics and Equity with Economics and Effectiveness for newborn screening in the genomic age: A qualitative study protocol of stakeholder perspectives

BACKGROUND

Newborn bloodspot screening is a well-established population health initiative that detects serious, childhood-onset, treatable conditions to improve health outcomes. With genomic technologies advancing rapidly, many countries are actively discussing the introduction of genomic assays into newborn screening programs. While adding genomic testing to Australia's newborn screening program could improve outcomes for infants and families, it must be considered against potential harms, ethical, legal, equity and social implications, and economic and health system impacts. We must ask not only 'can' we use genomics to screen newborns?' but 'should we'?' and 'how much should health systems invest in genomic newborn screening?'.

METHODS

This study will use qualitative methods to explore understanding, priorities, concerns and expectations of genomic newborn screening among parents/carers, health professionals/scientists, and health policy makers across Australia. In-depth, semi-structured interviews will be held with 30-40 parents/carers recruited via hospital and community settings, 15-20 health professionals/scientists, and 10-15 health policy makers. Data will be analysed using inductive content analysis. The Sydney Children's Hospital Network Human Research Ethics Committee approved this study protocol [2023/ETH02371]. The Standards for Reporting Qualitative Research will guide study planning, conduct and reporting.

DISCUSSION

Few studies have engaged a diverse range of stakeholders to explore the implications of genomics in newborn screening in a culturally and genetically diverse population, nor in a health system underpinned by universal health care. As the first study within a multi-part research program, findings will be used to generate new knowledge on the risks and benefits and importance of ethical, legal, social and equity implications of genomic newborn screening from the perspective of key stakeholders. As such it will be the foundation on which child and family centered criteria can be developed to inform health technology assessments and drive efficient and effective policy decision-making on the implementation of genomics in newborn screening.

Diagnostic utility of exome sequencing followed by research reanalysis in human brain malformations

This study aimed to determine the diagnostic yield of singleton exome sequencing and subsequent research-based trio exome analysis in children with a spectrum of brain malformations seen commonly in clinical practice. We recruited children ≤ 18 years old with a brain malformation diagnosed by magnetic resonance imaging and consistent with an established list of known genetic causes. Patients were ascertained nationally from eight tertiary paediatric centres as part of the Australian Genomics Brain Malformation Flagship. Chromosome microarray was required for all children, and those with pathogenic copy number changes were excluded. Cytomegalovirus polymerase chain reaction on neonatal blood spots was performed on all children with polymicrogyria with positive patients excluded. Singleton exome sequencing was performed through a diagnostic laboratory and analysed using a clinical exome sequencing pipeline. Undiagnosed patients were followed up in a research setting, including reanalysis of the singleton exome data and subsequent trio exome sequencing. A total of 102 children were recruited. Ten malformation subtypes were identified with the commonest being polymicrogyria (36%), pontocerebellar hypoplasia (14%), periventricular nodular heterotopia (11%), tubulinopathy (10%), lissencephaly (10%) and cortical dysplasia (9%). The overall diagnostic yield for the clinical singleton exome sequencing was 36%, which increased to 43% after research follow-up. The main source of increased diagnostic yield was the reanalysis of the singleton exome data to include newly discovered gene-disease associations. One additional diagnosis was made by trio exome sequencing. The highest phenotype-based diagnostic yields were for cobblestone malformation, tubulinopathy and lissencephaly and the lowest for cortical dysplasia and polymicrogyria. Pathogenic variants were identified in 32 genes, with variants in 6/32 genes occurring in more than one patient. The most frequent genetic diagnosis was pathogenic variants in TUBA1A. This study shows that over 40% of patients with common brain malformations have a genetic aetiology identified by exome sequencing. Periodic reanalysis of exome data to include newly identified genes was of greater value in increasing diagnostic yield than the expansion to trio exome. This study highlights the genetic and phenotypic heterogeneity of brain malformations, the importance of a multidisciplinary approach to diagnosis and the large number of patients that remain without a genetic diagnosis despite clinical exome sequencing and research reanalysis.

Eliciting parental preferences and values for the return of additional findings from genomic sequencing

Health economic evidence is needed to inform the design of high-value and cost-effective processes for returning genomic results from analyses for additional findings (AF). This study reports the results of a discrete-choice experiment designed to elicit preferences for the process of returning AF results from the perspective of parents of children with rare conditions and to estimate the value placed on AF analysis. Overall, 94 parents recruited within the Australian Genomics and Melbourne Genomics programmes participated in the survey, providing preferences in a total of 1128 choice scenarios. Statistically significant preferences were identified for the opportunity to change the choices made about AF; receiving positive AF in person from a genetic counsellor; timely access to a medical specialist and high-quality online resources; receiving automatic updates through a secure online portal if new information becomes available; and lower costs. For AF uptake rates ranging between 50-95%, the mean per person value from AF analysis was estimated at AU$450-$1700 (US$300-$1140). The findings enable the design of a value-maximising process of analysis for AF in rare-disease genomic sequencing.

Development of a microcosting protocol to determine the economic cost of diagnostic genomic testing for rare diseases in Australia

INTRODUCTION

Genomic testing is a relatively new, disruptive and complex health technology with multiple clinical applications in rare diseases, cancer and infection control. Genomic testing is increasingly being implemented into clinical practice, following regulatory approval, funding and adoption in models of care, particularly in the area of rare disease diagnosis. A significant barrier to the adoption and implementation of genomic testing is funding. What remains unclear is what the cost of genomic testing is, what the underlying drivers of cost are and whether policy differences contribute to cost variance in different jurisdictions, such as the requirement to have staff with a medical license involved in testing. This costing study will be useful in future economic evaluations and health technology assessments to inform optimal levels of reimbursement and to support comprehensive and comparable assessment of healthcare resource utilisation in the delivery of genomic testing globally.

METHODS

A framework is presented that focuses on uncovering the process of genomic testing for any given laboratory, evaluating its utilisation and unit costs, and modelling the cost drivers and overall expenses associated with delivering genomic testing. The goal is to aid in refining and implementing policies regarding both the regulation and funding of genomic testing. A process-focused (activity-based) methodology is outlined, which encompasses resources, assesses individual cost components through a combination of bottom-up and top-down microcosting techniques and allows disaggregation of resource type and process step.

ETHICS AND DISSEMINATION

The outputs of the study will be reported at relevant regional genetics and health economics conferences, as well as submitted to a peer-reviewed journal focusing on genomics. Human research ethics committee approval is not required for this microcosting study. This study does not involve research on human subjects, and all data used in the analysis are either publicly available.

Genomic newborn screening for rare diseases

Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.

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.

Evolution of virtual gene panels over time and implications for genomic data re-analysis

Purpose

Re-analyzing genomic information from patients without a molecular diagnosis is known to improve diagnostic yields. There are different mechanisms responsible for this increase, but the discovery of new, and refinement of existing, gene-disease relationships are one of the most prominent drivers of new diagnoses. This study examines the incorporation of new knowledge into virtual diagnostic gene panels and how this affects the potential for re-analysis.

Methods

We used PanelApp Australia to explore how the gene content of 112 rare-disease panels evolved between 2019 and 2022. By dividing these panels into groups that examined Specific and Broad rare-diseases clinical testing indications, we determined the granular changes in panel composition.

Results

Characterizing how the panels present at the launch of PanelApp Australia changed, revealed that the diagnostic genes available for analysis increased in 82% of the Specific rare-disease panels and in 97% of the Broad rare-disease panels. Examining how the panels had evolved showed that different panels were changing at different rates and in different ways. The median number of diagnostic grade genes in the Specific rare-disease panel increased by 4 (0-63), whereas the median number of gene gains in the Broad rare-disease panels was 27 (0-432). Monthly snapshots demonstrated that these changes were highly variable among different panels.

Conclusion

Knowledge about gene-disease associations is changing dynamically. Using fixed time periods may not be the best strategy to guide re-analysis frequency, as a result, some conditions may benefit from an approach based on the availability of new information rather than the passage of time.