Evaluation of the diagnostic accuracy of exome sequencing and its impact on diagnostic thinking for patients with rare disease in a publicly funded health care system: A prospective cohort study

PURPOSE

To evaluate the diagnostic utility of publicly funded clinical exome sequencing (ES) for patients with suspected rare genetic diseases.

METHODS

We prospectively enrolled 297 probands who met eligibility criteria and received ES across 5 sites in Ontario, Canada, and extracted data from medical records and clinician surveys. Using the Fryback and Thornbury Efficacy Framework, we assessed diagnostic accuracy by examining laboratory interpretation of results and assessed diagnostic thinking by examining the clinical interpretation of results and whether clinical-molecular diagnoses would have been achieved via alternative hypothetical molecular tests.

RESULTS

Laboratories reported 105 molecular diagnoses and 165 uncertain results in known and novel genes. Of these, clinicians interpreted 102 of 105 (97%) molecular diagnoses and 6 of 165 (4%) uncertain results as clinical-molecular diagnoses. The 108 clinical-molecular diagnoses were in 104 families (35% diagnostic yield). Each eligibility criteria resulted in diagnostic yields of 30% to 40%, and higher yields were achieved when >2 eligibility criteria were met (up to 45%). Hypothetical tests would have identified 61% of clinical-molecular diagnoses.

CONCLUSION

We demonstrate robustness in eligibility criteria and high clinical validity of laboratory results from ES testing. The importance of ES was highlighted by the potential 40% of patients that would have gone undiagnosed without this test.

Exome and genome sequencing for rare genetic disease diagnosis: A scoping review and critical appraisal of clinical guidance documents produced by genetics professional organizations

PURPOSE

Exome and genome sequencing have rapidly transitioned from research methods to widely used clinical tests for diagnosing rare genetic diseases. We sought to synthesize the topics covered and appraise the development processes of clinical guidance documents generated by genetics professional organizations.

METHODS

We conducted a scoping review of guidance documents published since 2010, systematically identified in peer-reviewed and gray literature, using established methods and reporting guidelines. We coded verbatim recommendations by topic using content analysis and critically appraised documents using the Appraisal of Guidelines Research and Evaluation (AGREE) II tool.

RESULTS

We identified 30 guidance documents produced by 8 organizations (2012-2022), yielding 611 recommendations covering 21 topics. The most common topic related to findings beyond the primary testing indication. Mean AGREE II scores were low across all 6 quality domains; scores for items related to rigor of development were among the lowest. More recently published documents generally received higher scores.

CONCLUSION

Guidance documents included a broad range of recommendations but were of low quality, particularly in their rigor of development. Developers should consider using tools such as AGREE II and basing recommendations on living knowledge syntheses to improve guidance development in this evolving space.

Protocol for a Prospective, Observational Cost-effectiveness Analysis of Returning Secondary Findings of Genome Sequencing for Unexplained Suspected Genetic Conditions

PURPOSE

Although costly, genome-wide sequencing (GWS) detects an extensive range of variants, enhancing our ability to diagnose and assess risk for an increasing number of diseases. In addition to detecting variants related to the indication for testing, GWS can detect secondary variants in BRCA1, BRCA2, and other genes for which early intervention may improve health. As the list of secondary findings grows, there is increased demand for surveillance and management by multiple specialists, adding pressure to constrained health care budgets. Secondary finding testing is actively debated because some consider it opportunistic screening for future health risks that may not manifest. Given the economic implications of secondary finding testing and follow-up and its unproven clinical utility, the objective is to assess the incremental cost-effectiveness of secondary finding ascertainment per case detected and per unit of improved clinical utility in families of children with unexplained suspected genetic conditions undergoing clinical GWS.

METHODS

Those undergoing trio genome or exome sequencing are eligible for the study. Positive secondary finding index cases will be matched to negative controls (1:2) based on age group, primary result(s) type, and clinical indication. During the 2-year study, 71 cases and 142 matched controls are expected. Health service use will be collected in patients and 1 adult family member every 6 months. The per-child and per-dyad total cost will be determined by multiplying use of each resource by a corresponding unit price and summing all cost items. Costs will be estimated from the public and societal payer perspectives. The mean cost per child and per dyad for secondary finding-positive and secondary finding-negative groups will be compared statistically. If important demographic differences are observed between groups, ordinary least-squares regression, log transformation, or other nonparametric technique will be used to compare adjusted mean costs. The ratio of the difference in mean cost to the secondary finding yield will be used to estimate incremental cost-effectiveness. In secondary analyses, effectiveness will be estimated using the number of clinical management changes due to secondary findings or the Clinician-Reported Genetic Testing Utility Index (C-GUIDE) score, a validated measure of clinical utility. Sensitivity analysis will be undertaken to assess the robustness of the findings to variation in key parameters.

IMPLICATIONS

This study generates key evidence to inform clinical practice and funding allocation related to secondary finding testing. The inclusion of family members and a new measure of clinical utility represent important advancements in economic evaluation in genomics.

Bridging clinical care and research in Ontario, Canada: Maximizing diagnoses from reanalysis of clinical exome sequencing data

We examined the utility of clinical and research processes in the reanalysis of publicly-funded clinical exome sequencing data in Ontario, Canada. In partnership with eight sites, we recruited 287 families with suspected rare genetic diseases tested between 2014 and 2020. Data from seven laboratories was reanalyzed with the referring clinicians. Reanalysis of clinically relevant genes identified diagnoses in 4% (13/287); four were missed by clinical testing. Translational research methods, including analysis of novel candidate genes, identified candidates in 21% (61/287). Of these, 24 families have additional evidence through data sharing to support likely diagnoses (8% of cohort). This study indicates few diagnoses are missed by clinical laboratories, the incremental gain from reanalysis of clinically-relevant genes is modest, and the highest yield comes from validation of novel disease-gene associations. Future implementation of translational research methods, including continued reporting of compelling genes of uncertain significance by clinical laboratories, should be considered to maximize diagnoses.

Comparing genome sequencing technologies to improve rare disease diagnostics: a protocol for the evaluation of a pilot project, Genome-wide Sequencing Ontario

BACKGROUND

Genome-wide sequencing has emerged as a promising strategy for the timely diagnosis of rare diseases, but it is not yet available as a clinical test performed in Canadian diagnostic laboratories. We describe the protocol for evaluating a 2-year pilot project, Genome-wide Sequencing Ontario, to offer high-quality clinical genome-wide sequencing in Ontario, Canada.

METHODS

The Genome-wide Sequencing Ontario protocol was codesigned by the Ontario Ministry of Health, the Hospital for Sick Children in Toronto and the Children's Hospital of Eastern Ontario in Ottawa. Enrolment of a prospective cohort of patients began on Apr. 1, 2021. Eligible cases with blood samples available for the index case and both parents (i.e., trios) are randomized to receive exome sequencing or genome sequencing. We will collect patient-level data and ascertain costs associated with the laboratory workflow for exome sequencing and genome sequencing. We will compare point estimates for the diagnostic utility and timeliness of exome sequencing and genome sequencing, and we will determine an incremental cost-effectiveness ratio (expressed as the incremental cost of genome sequencing versus exome sequencing per additional patient with a causal variant detected).

INTERPRETATION

Findings from this work will provide robust evidence for the diagnostic utility, cost-effectiveness and timeliness of exome sequencing and genome sequencing, and will be disseminated via academic publications and policy briefs. Findings will inform provincial and cross-provincial policy related to the long-term organization, delivery and reimbursement of clinical-grade genome diagnostics for rare disease.

Neurophysiological Characteristics of Allgrove (Triple A) Syndrome: Case Report and Literature Review

Allgrove or “Triple A” syndrome is characterized by alacrima, achalasia, and adrenocorticotropic hormone-resistant adrenal insufficiency, as well as central and peripheral nervous system involvement. Patients demonstrate heterogeneity with regard to their age of symptom onset, disease severity, and nature of clinical symptoms. Neurophysiological testing has also shown variability ranging from: motor neuron disease with prominent bulbar involvement, motor-predominant neuropathy, or sensorimotor polyneuropathy with axonal or mixed axonal and demyelinating features. We report an 11-year-old boy who presented with neurological symptoms of progressive spasticity and peripheral neuropathy. His neurophysiological testing confirmed a sensorimotor polyneuropathy with axonal and demyelinating features. Exome sequencing identified compound heterozygote variants in the AAAS gene. We summarize the neurophysiological findings in him and 29 other patients with Allgrove syndrome where nerve conduction study findings were available thereby providing a review of the heterogeneity in neurophysiological findings that have been reported in this rare disorder.

A Novel Mutation in MARS in a Patient with Charcot-Marie-Tooth Disease, Axonal, Type 2U with Congenital Onset

Charcot-Marie-Tooth disease is a phenotypically and genetically heterogeneous group of disorders affecting both motor and sensory neurons. Exome sequencing has driven discovery of genes responsible for Charcot-Marie-Tooth disease with more than 70 genes now associated with this neuromuscular disease. The MARS gene was recently reported as the cause of Charcot-Marie-Tooth 2U, a slowly progressive axonal sensorimotor polyneuropathy with adult-onset reported in six patients. We report here a patient with a progressive, early childhood-onset, motor-predominant form of Charcot-Marie-Tooth disease. Exome sequencing identified a novel MARS variant (c.1189G>A; p.Ala397Thr) that was not present in her unaffected mother; her unaffected father was unavailable. Further studies using structural modeling and a yeast humanization assay support pathogenicity of the variant. Our study expands the phenotype of Charcot-Marie-Tooth 2U, while highlighting the utility of functional assays to evaluate variant pathogenicity.

Severe neurocognitive and growth disorders due to variation in THOC2, an essential component of nuclear mRNA export machinery

Highly conserved TREX-mediated mRNA export is emerging as a key pathway in neuronal development and differentiation. TREX subunit variants cause neurodevelopmental disorders (NDDs) by interfering with mRNA export from the cell nucleus to the cytoplasm. Previously we implicated four missense variants in the X-linked THOC2 gene in intellectual disability (ID). We now report an additional six affected individuals from five unrelated families with two de novo and three maternally inherited pathogenic or likely pathogenic variants in THOC2 extending the genotypic and phenotypic spectrum. These comprise three rare missense THOC2 variants that affect evolutionarily conserved amino acid residues and reduce protein stability and two with canonical splice-site THOC2 variants that result in C-terminally truncated THOC2 proteins. We present detailed clinical assessment and functional studies on a de novo variant in a female with an epileptic encephalopathy and discuss an additional four families with rare variants in THOC2 with supportive evidence for pathogenicity. Severe neurocognitive features, including movement and seizure disorders, were observed in this cohort. Taken together our data show that even subtle alterations to the canonical molecular pathways such as mRNA export, otherwise essential for cellular life, can be compatible with life, but lead to NDDs in humans.

Association of Early-Onset Spasticity and Risk for Cognitive Impairment With Mutations at Amino Acid 499 in SPAST

Hereditary spastic paraplegia is a phenotypically and genetically heterogeneous group of neurodegenerative disorders characterized by lower extremity weakness and spasticity. Spastic paraplegia 4 (SPG4), caused by heterozygous mutations in the gene SPAST, typically causes a late-onset, uncomplicated form of hereditary spastic paraplegia in affected individuals. Additional clinical features in SPG4 have been reported on occasion, but no genotype-phenotype correlation has been established. Through targeted clinical testing, we identified 2 unrelated female patients with the same de novo p.Arg499His mutation in SPAST. Both patients presented with early-onset spasticity resulting in delayed motor milestones, which led to a diagnosis of cerebral palsy in one child and tethered cord in the other. Review of the literature identified several patients with mutations at amino acid 499 and early-onset symptoms associated with a risk of cognitive impairment. Early and accurate diagnosis of children with early-onset spasticity is important for informed prognosis and genetic counselling.

Field boundaries in Great Britain: stock and change between 1984, 1990 and 1998

Field boundaries are man-made features found worldwide and their multiple functions in agricultural landscapes are now widely recognised. These landscape features have declined drastically in many developed countries as a result of agricultural intensification. In Great Britain, field boundaries are regarded as elements of particular significance in the countryside, both in term of extent and value, whether ecological, cultural, or aesthetic. The Countryside Surveys of Great Britain, a national ecological, surveillance programme initiated in the late 1970s, provides information about the change in extent and ecological condition of field boundaries. In this paper, we present the main results on field boundaries derived from the latest survey, Countryside Survey 2000. These include stock and change of boundaries for the 1990-1998 period as well as an update of the previously published 1984-1990 data. Special attention is given to the evolution of the length of hedges. Applicability of the Countryside Survey methodology to other monitoring programmes and further use of the data is discussed together with the potential ecological consequences of the changes described in the paper.

Endothelial cell activity varies in patients at risk for the adult respiratory distress syndrome

OBJECTIVE

The endothelial cell produces many bioactive compounds that are presumed to play important roles in the pathogenesis of the adult respiratory distress syndrome (ARDS). We postulated that individuals with sepsis and trauma-two at-risk diagnoses for the development of ARDS--might demonstrate differences in the degree of endothelial cell activity.

DESIGN

Prospective cohort study.

SETTING

Intensive care unit patients in a tertiary, university-affiliated, city hospital.

PATIENTS

Fifty-five intensive care unit patients (19 with sepsis and 36 trauma patients).

INTERVENTIONS

Plasma measurements of three endothelial cell products--von Willebrand factor antigen, soluble intercellular adhesion molecule-1 (ICAM-1), and soluble E-selectin-were performed within 8 hrs of patients meeting our inclusion criteria, and at the clinical onset of ARDS.

MEASUREMENTS AND MAIN RESULTS

Twenty-six percent of the septic patients and 25% of the trauma patients developed ARDS. The median (and 25% to 75% quartiles) concentrations of all three mediators measured in the sepsis patients (von Willebrand factor antigen 399% [375% to 452%], ICAM-1 573 ng/mL [470 to 980], and soluble E-selectin 180 ng/mL [81 to 340]) were significantly higher (p < .001 for each individual analysis) than in the trauma patients (von Willebrand factor antigen 256% [217% to 310%], ICAM-1 148 ng/mL [113 to 210], and soluble E-selectin 42 ng/mL [31 to 65 ng/ mL]). In addition, neither the ICAM-1 nor soluble E-selectin concentrations measured in the trauma patients were different (p = .17 and p = .24, respectively) from normal controls. In those patients who developed ARDS, the differences in the concentrations of all three endothelial cell mediators between the sepsis and trauma patients persisted (p = .008 for von Willebrand factor antigen, p = .003 for ICAM-1, and p = .003 for E-selectin).

CONCLUSION

These findings suggest that differences in endothelial cell activity exist between sepsis and trauma patients who are at risk for the development of ARDS.

The ITE Land classification: Providing an environmental stratification of Great Britain

The surface of Great Britain (GB) varies continuously in land cover from one area to another. The objective of any environmentally based land classification is to produce classes that match the patterns that are present by helping to define clear boundaries. The more appropriate the analysis and data used, the better the classes will fit the natural patterns. The observation of inter-correlations between ecological factors is the basis for interpreting ecological patterns in the field, and the Institute of Terrestrial Ecology (ITE) Land Classification formalises such subjective ideas. The data inevitably comprise a large number of factors in order to describe the environment adequately. Single factors, such as altitude, would only be useful on a national basis if they were the only dominant causative agent of ecological variation.The ITE Land Classification has defined 32 environmental categories called 'land classes', initially based on a sample of 1-km squares in Great Britain but subsequently extended to all 240 000 1-km squares. The original classification was produced using multivariate analysis of 75 environmental variables. The extension to all squares in GB was performed using a combination of logistic discrimination and discriminant functions. The classes have provided a stratification for successive ecological surveys, the results of which have characterised the classes in terms of botanical, zoological and landscape features.The classification has also been applied to integrate diverse datasets including satellite imagery, soils and socio-economic information. A variety of models have used the structure of the classification, for example to show potential land use change under different economic conditions. The principal data sets relevant for planning purposes have been incorporated into a user-friendly computer package, called the 'Countryside Information System'.

Linking satellite and field survey data, through the use of gis, as implemented in Great Britain in the Countryside Survey 1990 project

The Institute of Terrestrial Ecology (ITE) has been studying land use and the effects of land use on ecology for two decades. A series of national field surveys have been undertaken by the Land Use Section of ITE since 1978, the most recent being Countryside Survey 1990 (CS1990). The three-year project brought together field survey and remote sensing data which were analyzed using Geographical Information Systems (GIS). National and regional land-cover patterns were described and changes estimated.The data collected by the field survey part of CS1990 recorded stratified samples based on a land classification. Thematic maps for surveyed 1-km squares covered physiography, agriculture and semi-natural vegetation, forestry, structures and boundaries. The same sites were surveyed in 1984 and 1990 with 14 000 digital maps produced describing both years. GIS was used to generate stock figures for each year, and overlay allowed change between survey dates to be estimated.GIS was used to compare data collected from both field survey and satellite imagery so that both sets of information could be qualified when expressed as national figures.This paper describes the historical development of the ITE Land Classification, examines the way in which data were collected for surveys, with particular reference to Countryside Survey 1990, and shows how satellite and field survey data can be linked through GIS.

von Willebrand factor antigen levels are not predictive for the adult respiratory distress syndrome

In patients with nonpulmonary sepsis, von Willebrand factor antigen (vWF:Ag or Factor VIIR:Ag) levels have been reported to be predictive for the development of the adult respiratory distress syndrome (ARDS). We addressed the ability to generalize these results by measuring serial Factor vWF:Ag levels in 96 patients at risk for the development of ARDS. Patients with sepsis, pancreatitis, hypertransfusion, witnessed aspiration of gastric contents, abdominal trauma, chest trauma, and multiple fractures were studied. Sequential measurements were obtained at enrollment into the study (T = 0), and T = 6, 12, 24, and 48 h. Subjects were grouped into sepsis and nonsepsis categories and analyzed according to the following outcome definitions: ARDS and non-ARDS. The mean values for the sepsis and nonsepsis groups were elevated above normal at all time points. A statistically significant difference occurred in the mean vWF:Ag level for the ARDS and non-ARDS patients in the nonsepsis group at T = 0 (p = 0.05). To assess the clinical utility of these results, ROC (receiver operating characteristics) curves were plotted at T = 0, and optimal cutoff values of vWF:Ag were determined. In the sepsis group, the best value for vWF:Ag above which patients would actually develop ARDS was 399%, resulting in a 70% sensitivity and a 47% specificity. For the non-sepsis patients, the optimal value was 273%, yielding a sensitivity of 64% and a specificity of 52%. We conclude that measuring vWF:Ag levels are not helpful in predicting the progression to ARDS in multiple at-risk patients.