Next generation of free? Points to consider when navigating sponsored genetic testing

Genetics has been integrated into patient care across many subspecialties. However, genetic and genomic testing (GT) remain expensive with disparities in access both within Canada and internationally. It is, therefore, not surprising that sponsored GT has emerged as one alternative. Sponsored GT, for the purpose of this document, refers to clinical-grade GT partially or fully subsidised by industry. In return, industry sponsors-usually pharmaceutical or biotechnology companies-may have access to patients' genetic data, practitioner information, DNA and/or other information. The availability of sponsored GT options in the Canadian healthcare landscape has appeared to simplify patient and practitioner access to GT, but the potential ethical and legal considerations, as well as the nuances of a publicly funded healthcare system, must also be considered. This document offers preliminary guidance for Canadian healthcare practitioners encountering sponsored GT in practice. Further research and dialogue is urgently needed to explore this issue to provide fulsome considerations that one must be aware of when availing such options.

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.

Spliceosome malfunction causes neurodevelopmental disorders with overlapping features

Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50-deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function.

Assessing the Performance of the Clinician-reported Genetic Testing Utility InDEx (C-GUIDE): Further Evidence of Inter-rater Reliability

PURPOSE

Advanced genomic and genetic testing technologies are quickly diffusing into clinical practice, but standardized approaches to assessing their clinical utility are limited. Previous work developed and generated preliminary evidence of validity for a novel outcome measure, the Clinician-reported Genetic testing Utility InDEx (C-GUIDE). C-GUIDE is a 17-item measure that captures the utility of genetic testing from the providers' perspective. Preliminary evidence of its inter-rater reliability was obtained through a clinical vignette study. The purpose of this study was to further assess its inter-rater reliability using actual clinical cases.

METHODS

One genetic counselor and one medical geneticist independently completed C-GUIDE Version 1.1 after genetic test results were disclosed to a shared set of 42 patients. Raters also completed a case description questionnaire, including information about the patient's age, indication for testing, and type of test performed. Inter-rater reliability was assessed by comparing the raters' C-GUIDE scores using ANOVA to generate intra-class correlation coefficients (ICCs), absolute agreement, and mixed repeated measures ANOVA.

FINDINGS

Of the 42 patients studied, the most common indications for testing were hearing loss (n = 18) and craniosynostosis (n = 11), and the most common tests ordered were gene panels (n = 20) and microarrays (n = 10). Test results were diagnostic or partially diagnostic for 11 patients, potentially diagnostic for 14 patients, or nondiagnostic for 17 patients. The overall ICC was 0.95 (95% CI, 0.89-0.97) and absolute agreement was acceptable (>70%) for 15 individual items. Inter-rater agreement was excellent (ICC > 0.90) for 8 items, good (ICC = 0.75-0.89) for 3 items, moderate (ICC = 0.50-0.74) for 4 items and poor (ICC < 0.50) for 2 items. Absolute agreement was unacceptable (<70%), and rater agreement was fair (ICC = 0.40-0.59) for 2 items. For the global rating, the ICC was 0.62 (95% CI, 0.39-0.77), and the absolute agreement was 61.9%.

IMPLICATIONS

Rater instructions for item completion have been modified to improve consistency of item interpretation. Although further assessments of reliability are warranted after modifications, these findings provide additional tentative evidence of C-GUIDE's inter-rater reliability and suggest that it may be useful as a strategy for measuring the value of genetic testing, as perceived by genetics providers.

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.

Applying the Clinician-reported Genetic testing Utility InDEx (C-GUIDE) to genome sequencing: further evidence of validity

Genome sequencing (GS) outperforms other rare disease diagnostics, but standardized approaches to assessing its clinical utility are limited. This study assessed the validity of the Clinician-reported Genetic testing Utility InDEx (C-GUIDE), a novel tool for assessing the utility of genetic testing from a clinician's perspective, for GS. C-GUIDE ratings were completed for patients who received GS results. For each patient, total C-GUIDE and single item global scores were calculated. Construct validity was assessed using linear regression to determine the association between C-GUIDE total and global item scores and measure the effects of potential explanatory variables. Ratings were completed for 67 pediatric and 36 adult patients. GS indications were neurological for 70.9% and results were diagnostic for 28.2%. When the C-GUIDE assessed primary (PV), secondary (SV), and pharmacogenomic (PGx) variants, on average, a one unit increase in the global item score was associated with an increase of 7.3 in the C-GUIDE score (p < 0.05). Diagnostic results were associated with an increase in C-GUIDE score of 5.0 compared to non-diagnostic results (p < 0.05) and an increase of one SV was associated with an increase of 2.5 (p < 0.05). For children, decreased age of one year was associated with an increase in C-GUIDE score of 0.3 (p < 0.05). Findings provide evidence that C-GUIDE measures the construct of clinical utility in pediatric and adult rare disease populations and is sensitive to changes in utility related to variant type. Quantifying the clinical utility of GS using C-GUIDE can inform efforts to optimize its use in patient care.

Rapid Genetic Testing in Pediatric and Neonatal Critical Care: A Scoping Review of Emerging Ethical Issues

BACKGROUND

Rapid genome-wide sequencing (rGWS) is being increasingly used to aid in prognostication and decision-making for critically ill newborns and children. Although its feasibility in this fast-paced setting has been described, this new paradigm of inpatient genetic care raises new ethical challenges.

OBJECTIVE

A scoping review was performed to (1) identify salient ethical issues in this area of practice; and (2) bring attention to gaps and ethical tensions that warrant more deliberate exploration.

METHODS

Data sources, Ovid Medline and Cochrane Central Register of Controlled Trials, were searched up to November 2021. Articles included were those in English relating to rGWS deployed rapidly in a critical care setting. Publications were examined for ethical themes and were further characterized as including a superficial or in-depth discussion of that theme. New themes were inductively identified as they emerged.

RESULTS

Ninety-nine studies, published in 2012 or thereafter, met inclusion criteria. Themes identified elaborated upon established ethical principles related to beneficence and nonmaleficence (ie, clinical utility, medical uncertainty, impact on family, and data security) autonomy (ie, informed consent), and justice (ie, resource allocation and disability rights). Many themes were only narrowly discussed.

CONCLUSIONS

The application of rGWS in neonatal and pediatric acute care is inherently tied to ethically charged issues, some of which are reported here. Attention to the ethical costs and benefits of rGWS is not always discussed, with important gaps and unanswered questions that call for ongoing focus on these ethical considerations in this next application of acute care genomics.

The utility of DNA methylation signatures in directing genome sequencing workflow: Kabuki syndrome and CDK13-related disorder

Kabuki syndrome (KS) is a neurodevelopmental disorder characterized by hypotonia, intellectual disability, skeletal anomalies, and postnatal growth restriction. The characteristic facial appearance is not pathognomonic for KS as several other conditions demonstrate overlapping features. For 20‐30% of children with a clinical diagnosis of KS, no causal variant is identified by conventional genetic testing of the two associated genes, KMT2D and KDM6A. Here, we describe two cases of suspected KS that met clinical diagnostic criteria and had a high gestalt match on the artificial intelligence platform Face2Gene. Although initial KS testing was negative, genome‐wide DNA methylation (DNAm) was instrumental in guiding genome sequencing workflow to establish definitive molecular diagnoses. In one case, a positive DNAm signature for KMT2D led to the identification of a cryptic variant in KDM6A by genome sequencing; for the other case, a DNAm signature different from KS led to the detection of another diagnosis in the KS differential, CDK13‐related disorder. This approach illustrates the clinical utility of DNAm signatures in the diagnostic workflow for the genome analyst or clinical geneticist—especially for disorders with overlapping clinical phenotypes.

Canadian College of Medical Geneticists (CCMG) points to consider: resuming genetic services in a pandemic-a summary

The COVID-19 pandemic has disrupted the provision of genetic care in Canada. With the public health effort to flatten the curve, many clinics have moved to virtual care for select populations of patients while triaging and postponing others. As genetic services are asked to gradually resume, a roadmap is needed to ensure clinical care decisions for at-risk patients are transparent and equitable, that postponed care is resumed and that patients with or waiting for a genetic diagnosis are not disproportionately affected or abandoned.The purpose of this document is to highlight the guiding ethical principles and stakeholder considerations in resuming genetic services to help guide the competing needs going forward of both limiting exposures while maintaining high-quality care. Considerations highlighted are (1) environment of practice, (2) nature of consult, (3) patient factors, (4) provider factors, and (5) laboratory factors. The intended users are those providing genetic care in a Canadian context with the recognition that there are clinic-specific and regional variations that will influence decision-making. While specific to the Canadian context, the ethical principles used to guide these decisions would be relevant for consideration in other jurisdictions.

Please give me a copy of my child's raw genomic data

In this work, we explore whether raw genetic data generated during sequencing ought to be returned to a pediatric patient and/or their parents/guardians. We identify the principles used by various professional societies in their guidelines on the return of secondary findings and apply them to this new context. We conclude that since each situation is unique, decisions should be made on a case-by-case basis according to the best interests of the child.

The point-of-care use of a facial phenotyping tool in the genetics clinic: Enhancing diagnosis and education with machine learning

Computer-assisted pattern recognition platforms, such as Face2Gene® (F2G), can facilitate the diagnosis of children with rare genetic syndromes by comparing a patient's features to known genetic diagnoses. Our work designed, implemented, and evaluated an innovative model of care in clinical genetics in a heterogeneous and multicultural patient population that utilized this facial phenotyping software at the point-of-care. We assessed the performance of F2G by comparing the suggested diagnoses to the patient's confirmed molecular diagnosis. Providers' overall experiences with the technology and trainees' educational experiences were assessed with questionnaires. We achieved an overall diagnostic yield of 57%. This increased to 82% when cases diagnosed with syndromes not recognized by F2G were removed. The mean rank of a confirmed diagnosis in the top 10 was 2.3 (CI 1.5-3.2) and the mean gestalt score 37.6%. The most commonly suggested diagnoses were Noonan syndrome, mucopolysaccharidosis, and 22q11.2 deletion syndrome. Our qualitative assessment revealed that clinicians and trainees saw value using the tool in practice. Overall, this work helped to implement an innovative patient care delivery model in clinical genetics that utilizes a facial phenotyping tool at the point-of-care. Our data suggest that F2G has utility in the genetics clinic as a clinical decision support tool in diverse populations, with a majority of patients having their eventual diagnosis listed in the top 10 suggested syndromes based on a photograph alone. It shows promise for further integration into clinical care and medical education, and we advocate for its continued use, adoption and refinement along with transparent and accountable industrial partnerships.

Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine

The standard of care for first-tier clinical investigation of the etiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion-deletions (indels) and single nucleotide variant (SNV) mutations. Whole genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilized WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a 4-fold increase in diagnostic rate over CMA (8%) (p-value = 1.42e-05) alone and >2-fold increase in CMA plus targeted gene sequencing (13%) (p-value = 0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harboring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counseling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis.

A majority of parents of children with peanut allergy fear using the epinephrine auto-injector

Prompt epinephrine administration is crucial in managing anaphylaxis, but epinephrine auto-injectors (EAIs) are underutilized by patients and their families. Children with peanut allergy were recruited from the Allergy Clinics at the Montreal Children's Hospital, food allergy advocacy organizations and organizations providing products to allergic individuals. Parents of children who had been prescribed an EAI were queried on whether they were fearful of using it and on factors that may contribute to fear. A majority of parents (672/1209 = 56%) expressed fear regarding the use of the EAI. Parents attributed the fear to hurting the child, using the EAI incorrectly or a bad outcome. Parents whose child had longer disease duration or a severe reaction and parents who were satisfied with the EAI training or found it easy to use were less likely to be afraid. Families may benefit from simulation training and more education on the recognition and management of anaphylaxis.

Update on antidepressant use during breastfeeding

QUESTION

Many of my patients who are diagnosed with postpartum depression want to continue breastfeeding. How safe are the newer antidepressant medications during breastfeeding?

ANSWER

The newer antidepressants transfer into breast milk in low amounts and have not been associated with serious adverse events. Therefore, the antidepressant most effective for the woman should be considered.

Postmortem vascular pathology in PHACES syndrome: a case report

This case describes the clinical course and autopsy findings of a 5-year-old girl with PHACES syndrome. While the etiopathogenesis of this condition is not yet understood, the pathological changes documented support the concept that the primary defect in PHACES syndrome is an arteriopathy.

Germline EPHB2 receptor variants in familial colorectal cancer

Familial clustering of colorectal cancer occurs in 15-20% of cases, however recognized cancer syndromes explain only a small fraction of this disease. Thus, the genetic basis for the majority of hereditary colorectal cancer remains unknown. EPHB2 has recently been implicated as a candidate tumor suppressor gene in colorectal cancer. The aim of this study was to evaluate the contribution of EPHB2 to hereditary colorectal cancer. We screened for germline EPHB2 sequence variants in 116 population-based familial colorectal cancer cases by DNA sequencing. We then estimated the population frequencies and characterized the biological activities of the EPHB2 variants identified. Three novel nonsynonymous missense alterations were detected. Two of these variants (A438T and G787R) result in significant residue changes, while the third leads to a conservative substitution in the carboxy-terminal SAM domain (V945I). The former two variants were found once in the 116 cases, while the V945I variant was present in 2 cases. Genotyping of additional patients with colorectal cancer and control subjects revealed that A438T and G787R represent rare EPHB2 alleles. In vitro functional studies show that the G787R substitution, located in the kinase domain, causes impaired receptor kinase activity and is therefore pathogenic, whereas the A438T variant retains its receptor function and likely represents a neutral polymorphism. Tumor tissue from the G787R variant case manifested loss of heterozygosity, with loss of the wild-type allele, supporting a tumor suppressor role for EPHB2 in rare colorectal cancer cases. Rare germline EPHB2 variants may contribute to a small fraction of hereditary colorectal cancer.