Clinical interpretation of KCNH2 variants using a robust PS3/BS3 functional patch-clamp assay.

Long QT syndrome (LQTS), caused by the dysfunction of cardiac ion channels, increases the risk of sudden death in otherwise healthy young people. For many variants in LQTS genes, there is insufficient evidence to make a definitive genetic diagnosis. We have established a robust functional patch-clamp assay to facilitate classification of missense variants in KCNH2, one of the key LQTS genes. A curated set of 30 benign and 30 pathogenic missense variants were used to establish the range of normal and abnormal function. The extent to which variants reduced protein function was quantified using Z scores, the number of standard deviations from the mean of the normalized current density of the set of benign variant controls. A Z score of -2 defined the threshold for abnormal loss of function, which corresponds to 55% wild-type function. More extreme Z scores were observed for variants with a greater loss-of-function effect. We propose that the Z score for each variant can be used to inform the application and weighting of abnormal and normal functional evidence criteria (PS3 and BS3) within the American College of Medical Genetics and Genomics variant classification framework. The validity of this approach was demonstrated using a series of 18 KCNH2 missense variants detected in a childhood onset LQTS cohort, where the level of function assessed using our assay correlated to the Schwartz score (a scoring system used to quantify the probability of a clinical diagnosis of LQTS) and the length of the corrected QT (QTc) interval.

Defining core outcomes of reproductive genetic carrier screening: A Delphi survey of Australian and New Zealand stakeholders.

OBJECTIVE: Understanding the value, benefits and harms of health interventions is needed to inform best practice and ensure responsible implementation of new approaches to patient care. Such value is demonstrated through the assessment of outcomes; however, which outcomes are assessed is often highly varied across studies and can hinder the ability to draw robust conclusions. The Core Outcome Development for Carrier Screening study aims to understand the outcomes that can meaningfully capture the value of reproductive genetic carrier screening (RGCS). METHOD: The authors report an iterative, two-round online Delphi survey of Australian and New Zealand stakeholders to determine the degree of consensus regarding the core outcomes of RGCS. Panellists ranked 83 outcomes according to their perceived importance on a nine-point Likert scale. Using the distribution of rankings, outcomes were grouped into tiers representative of their perceived level of importance and agreement between groups. RESULTS: The top tier outcomes represent those agreed to be critically important for all future studies of RGCS to assess and were used to define a preliminary core outcome set encompassing the domains (1) primary laboratory outcomes, (2) pregnancy outcomes, (3) resource use and, (4) perceived utility of RGCS. CONCLUSION: These findings can guide the selection of meaningful outcomes in studies aiming to demonstrate the value of RGCS. A future international consensus process will expand on these findings and guide the inclusion of diverse perspectives across the range of settings in which RGCS is offered.

Multi-site validation of a functional assay to adjudicate SCN5A Brugada Syndrome-associated variants.

Brugada Syndrome (BrS) is an inheritable arrhythmia condition that is associated with rare, loss-of-function variants in the cardiac sodium channel gene, SCN5A. Interpreting the pathogenicity of SCN5A missense variants is challenging and ~79% of SCN5A missense variants in ClinVar are currently classified as Variants of Uncertain Significance (VUS). An in vitro SCN5A-BrS automated patch clamp assay was generated for high-throughput functional studies of NaV1.5. The assay was independently studied at two separate research sites - Vanderbilt University Medical Center and Victor Chang Cardiac Research Institute - revealing strong correlations, including peak INa density (R2=0.86). The assay was calibrated according to ClinGen Sequence Variant Interpretation recommendations using high-confidence variant controls (n=49). Normal and abnormal ranges of function were established based on the distribution of benign variant assay results. The assay accurately distinguished benign controls (24/25) from pathogenic controls (23/24). Odds of Pathogenicity values derived from the experimental results yielded 0.042 for normal function (BS3 criterion) and 24.0 for abnormal function (PS3 criterion), resulting in up to strong evidence for both ACMG criteria. The calibrated assay was then used to study SCN5A VUS observed in four families with BrS and other arrhythmia phenotypes associated with SCN5A loss-of-function. The assay revealed loss-of-function for three of four variants, enabling reclassification to likely pathogenic. This validated APC assay provides clinical-grade functional evidence for the reclassification of current VUS and will aid future SCN5A-BrS variant classification.

The role of genetic testing in diagnosis and care of inherited cardiac conditions in a specialised multidisciplinary clinic.

BACKGROUND: The diagnostic yield of genetic testing for inherited cardiac diseases is up to 40% and is primarily indicated for screening of at-risk relatives. Here, we evaluate the role of genomics in diagnosis and management among consecutive individuals attending a specialised clinic and identify those with the highest likelihood of having a monogenic disease. METHODS: A retrospective audit of 1697 consecutive, unrelated probands referred to a specialised, multidisciplinary clinic between 2002 and 2020 was performed. A concordant clinical and genetic diagnosis was considered solved. Cases were classified as likely monogenic based on a score comprising a positive family history, young age at onset, and severe phenotype, whereas low-scoring cases were considered to have a likely complex aetiology. The impact of a genetic diagnosis was evaluated. RESULTS: A total of 888 probands fulfilled the inclusion criteria, and genetic testing identified likely pathogenic or pathogenic (LP/P) variants in 330 individuals (37%) and suspicious variants of uncertain significance (VUS) in 73 (8%). Research-focused efforts identified 46 (5%) variants, missed by conventional genetic testing. Where a variant was identified, this changed or clarified the final diagnosis in a clinically useful way for 51 (13%). The yield of suspicious VUS across ancestry groups ranged from 15 to 20%, compared to only 10% among Europeans. Even when the clinical diagnosis was uncertain, those with the most monogenic disease features had the greatest diagnostic yield from genetic testing. CONCLUSIONS: Research-focused efforts can increase the diagnostic yield by up to 5%. Where a variant is identified, this will have clinical utility beyond family screening in 13%. We demonstrate the value of genomics in reaching an overall diagnosis and highlight inequities based on ancestry. Acknowledging our incomplete understanding of disease phenotypes, we propose a framework for prioritising likely monogenic cases to solve their underlying cause of disease.

Outcomes of Importance to Patients in Reproductive Genetic Carrier Screening: A Qualitative Study to Inform a Core Outcome Set.

There is significant heterogeneity in the outcomes assessed across studies of reproductive genetic carrier screening (RGCS). Only a small number of studies have measured patient-reported outcomes or included patients in the selection of outcomes that are meaningful to them. This study was a cross-sectional, qualitative study of 15 patient participants conducted to inform a core outcome set. A core outcome set is an approach to facilitate standardisation in outcome reporting, allowing direct comparison of outcomes across studies to enhance understanding of impacts and potential harms. The aim of this study was to incorporate the patient perspective in the development of a core outcome set by eliciting a detailed understanding of outcomes of importance to patients. Data were collected via online, semi-structured interviews using a novel method informed by co-design and the nominal group technique. Data were analysed using reflexive thematic analysis. Outcomes elicited from patient stakeholder interviews highlighted several under-explored areas for future research. This includes the role of grief and loss in increased risk couples, the role of empowerment in conceptualising the utility of RGCS, the impact of societal context and barriers that contribute to negative experiences, and the role of genetic counselling in ensuring that information needs are met and informed choice facilitated as RGCS becomes increasingly routine. Future research should focus on incorporating outcomes that accurately reflect patient needs and experience.

Recommendations for clinical interpretation of variants found in non-coding regions of the genome.

BACKGROUND: The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. METHODS: We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. RESULTS: We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. CONCLUSIONS: These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.

A calibrated functional patch-clamp assay to enhance clinical variant interpretation in KCNH2-related long QT syndrome.

Modern sequencing technologies have revolutionized our detection of gene variants. However, in most genes, including KCNH2, the majority of missense variants are currently classified as variants of uncertain significance (VUSs). The aim of this study was to investigate the utility of an automated patch-clamp assay for aiding clinical variant classification in KCNH2. The assay was designed according to recommendations proposed by the Clinical Genome Sequence Variant Interpretation Working Group. Thirty-one variants (17 pathogenic/likely pathogenic, 14 benign/likely benign) were classified internally as variant controls. They were heterozygously expressed in Flp-In HEK293 cells for assessing the effects of variants on current density and channel gating in order to determine the sensitivity and specificity of the assay. All 17 pathogenic variant controls had reduced current density, and 13 of 14 benign variant controls had normal current density, which enabled determination of normal and abnormal ranges for applying evidence of moderate or supporting strength for VUS reclassification. Inclusion of functional assay evidence enabled us to reclassify 6 out of 44 KCNH2 VUSs as likely pathogenic. The high-throughput patch-clamp assay can provide moderate-strength evidence for clinical interpretation of clinical KCNH2 variants and demonstrates the value of developing automated patch-clamp assays for functional characterization of ion channel gene variants.

Incorporating patient perspectives in the development of a core outcome set for reproductive genetic carrier screening: a sequential systematic review.

There is currently no consensus on the key outcomes of reproductive genetic carrier screening (RGCS). This has led to a large amount of variability in approaches to research, limiting direct comparison and synthesis of findings. In a recently published systematic review of quantitative studies on RGCS, we found that few studies incorporated patient-reported outcomes. In response to this gap, we conducted a sequential systematic review of qualitative studies to identify outcomes exploring the patient experience of RGCS. In conjunction with the review of quantitative studies, these outcomes will be used to inform the development of a core outcome set. Text excerpts relevant to outcomes, including quotes and themes, were extracted verbatim and deductively coded as outcomes. We conducted a narrative synthesis to group outcomes within domains previously defined in our review of quantitative studies, and identify any new domains that were unique to qualitative studies. Seventy-eight outcomes were derived from qualitative studies and grouped into 19 outcome domains. Three new outcome domains were identified; 'goals of pre- and post-test genetic counselling', 'acceptability of further testing and alternative reproductive options', and 'perceived utility of RGCS'. The identification of outcome domains that were not identified in quantitative studies indicates that outcomes reflecting the patient perspective may be under-represented in the quantitative literature on this topic. Further work should focus on ensuring that outcomes reflect the real world needs and concerns of patients in order to maximise translation of research findings into clinical practice.

Decision-making about genetic health information among family dyads: a systematic literature review.

Decisions involving two individuals (i.e., dyadic decision-making) have been increasingly studied in healthcare research. There is evidence of bi-directional influences in decision-making processes among spousal, provider-patient and parent-child dyads. Genetic information can directly impact biologically related individuals. Thus, it is important to understand dyadic decision-making about genetic health information among family members. This systematic literature review aimed to identify literature examining decision-making among family dyads. Peer-reviewed publications were included if they reported quantitative empirical research on dyadic decision-making about genetic information, published between January 1998 and August 2020 and written in English. The search was conducted in 6 databases and returned 3167 articles, of which 15 met the inclusion criteria. Most studies were in the context of cancer genetic testing (n = 8) or reproductive testing or screening (n = 5). Studies reported two broad categories of decisions with dyadic influence: undergoing screening or testing (n = 10) and sharing information with family (n = 5). Factors were correlated between dyads such as attitudes, knowledge, behaviors and psychological wellbeing. Emerging evidence shows that dyad members influence each other when making decisions about receiving or sharing genetic information. Our findings emphasize the importance of considering both members of a dyad in intervention design and clinical interactions.

Systematic review of outcomes in studies of reproductive genetic carrier screening: Towards development of a core outcome set.

PURPOSE: Current practice recommendations support the widespread implementation of reproductive genetic carrier screening (RGCS). These consensus-based recommendations highlight a research gap, with findings from current studies being insufficient to meet the standard required for more rigorous evidence-based recommendations. This systematic review assessed methodological aspects of studies on RGCS to inform the need for a core outcome set. METHODS: We conducted a systematic search to identify peer-reviewed published studies offering population-based RGCS. Study designs, outcomes, and measurement methods were extracted. A narrative synthesis was conducting using an existing outcome taxonomy and criteria used in the evaluation of genetic screening programs as frameworks. RESULTS: Sixty-five publications were included. We extracted 120 outcomes representing 24 outcome domains. Heterogeneity in outcome selection, measurement methods and time points of assessment was extensive. Quality appraisal raised concerns for bias. We found that reported outcomes had limited applicability to criteria used to evaluate genetic screening programs. CONCLUSION: Despite a large body of literature, diverse approaches to research have limited the conclusions that can be cumulatively drawn from this body of evidence. Consensus regarding meaningful outcomes for evaluation of RGCS would be a valuable first step in working towards evidence-based practice recommendations, supporting the development of a core outcome set.

The Core Outcome DEvelopment for Carrier Screening (CODECS) study: protocol for development of a core outcome set.

BACKGROUND: Reproductive genetic carrier screening is a type of genetic testing available to those planning a pregnancy, or during their first trimester, to understand their risk of having a child with a severe genetic condition. There is a lack of consensus for 'what to measure' in studies on this intervention, leading to heterogeneity in choice of outcomes and methods of measurement. Such outcome heterogeneity has implications for the quality and comparability of these studies and has led to a lack of robust research evidence in the literature to inform policy and decision-making around the offer of this screening. As reproductive genetic carrier screening becomes increasingly accessible within the general population, it is timely to investigate the outcomes of this intervention. OBJECTIVES: The development of a core outcome set is an established methodology to address issues with outcome heterogeneity in research. We aim to develop a core outcome set for reproductive genetic carrier screening to clarify and standardise outcomes for research and practice. METHODS: In accordance with guidance from the COMET (Core Outcome Measures in Effectiveness Trials) Initiative, this study will consist of five steps: (i) a systematic review of quantitative studies, using narrative synthesis to identify previously reported outcomes, their definitions, and methods of measurement; (ii) a systematic review of qualitative studies using content analysis to identify excerpts related to patient experience and perspectives that can be interpreted as outcomes; (iii) semi-structured focus groups and interviews with patients who have undertaken reproductive genetic carrier screening to identify outcomes of importance to them; (iv) Delphi survey of key stakeholders, including patients, clinicians, and researchers, to refine and prioritise the list of outcomes generated from the previous steps; and (v) a virtual consensus meeting with a purposive sample of key stakeholders to finalise the core outcome set for reporting. DISCUSSION: This protocol outlines the core outcome set development process and its novel application in the setting of genetic testing. This core outcome set will support the standardisation of outcome reporting in reproductive carrier screening research and contribute to an evolving literature on outcomes to evaluate genetic testing and genetic counselling as health interventions. COMET CORE OUTCOME SET REGISTRATION: http://www.comet-initiative.org/Studies/Details/1381 .

Patient and Relative Experiences and Decision-making About Genetic Testing and Counseling for Familial ALS and FTD: A Systematic Scoping Review.

Genetic testing and counseling is an emerging part of care for patients with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) and their families. This scoping review aimed to map patients' and relatives' experiences of genetic testing and counseling for familial ALS and FTD and the factors influencing their decision to proceed with testing or counseling. Informed by the Joanna Briggs Institute methodology, 5 databases were systematically searched. Thirty studies from 39 references were included. A descriptive numerical summary analysis and narrative synthesis was conducted. Mostly positive diagnostic testing experiences were reported, but issues arose due to progressive disease and discordant results. Predictive testing impacted at-risk relatives, regardless of the result received, and psychosocial sequelae ranged from relief to guilt, worry or contemplating suicide. Four reproductive testing experiences were reported. Personal, familial and practical factors, and the lived experience of disease, informed decision-making. Greater uncertainty and complexity may be faced in familial ALS/FTD than in other late-onset neurodegenerative diseases due to clinical and genetic heterogeneity, and testing limitations. Genetic counseling models of care should consider this difference to ensure that individuals with, or at risk of, ALS/FTD are effectively managed. Implications for research and practice are discussed.

Psychosocial Implications of Living with Catecholaminergic Polymorphic Ventricular Tachycardia in Adulthood.

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a rare inherited arrhythmogenic disease with a high risk of sudden cardiac death. The impact on health-related quality of life (HR-QoL) and psychosocial outcomes is not known. We sought to provide the first description of HR-QoL and psychosocial wellbeing of adults with CPVT, parents of affected children and at-risk relatives. Participants were recruited through the Australian Genetic Heart Disease Registry and invited to complete a cross-sectional survey comprising a number of validated scales and open-ended questions. Thirty-five participants completed surveys (response rate 65%), including 19 with CPVT, 10 unaffected parents of a child with CPVT, and 7 at-risk relatives (one participant considered patient and parent). Young patients <40 years were significantly more likely to report anxiety (p = 0.04), depression (p = 0.03) and posttraumatic stress symptoms (p = 0.02) compared to older CPVT patients. Further, young patients with an implantable cardioverter defibrillator (ICD) reported significantly worse device-related distress (p = 0.04) and shock anxiety (p = 0.003). Patients with a genetic diagnosis had worse psychological adaptation than those patients without a gene result. Parents perceived their affected children to have poor quality of life across all subdomains compared to healthy age-matched children, however quality of life of parents and at-risk relatives was comparable to population norms. Ongoing psychosocial care is required for young people with CPVT. Those with an ICD and/or undergoing genetic testing may require additional support. The challenges of CPVT management should extend beyond the clinical and genetic aspects of care to incorporate greater psychosocial support, and further reinforces the need for a multidisciplinary approach to care.

Sex discordance identification following non-invasive prenatal testing.

OBJECTIVE: The objectives of this study were to characterise genotype-phenotype discordance identified in the routine clinical setting and to explore the associated diagnostic and counselling challenges. METHOD: Cases were derived from a cohort of pregnant women who attended a multisite specialist prenatal screening and ultrasound service for non-invasive prenatal testing by cell-free DNA analysis and midtrimester fetal morphology assessment. RESULTS: Seven cases of genotype-phenotype discordance were identified from a cohort of 12 919 women between June 2013 and March 2017 (incidence 1/1845 pregnancies). A variety of disorders of sexual differentiation were subsequently diagnosed. CONCLUSION: Sex chromosomes are the basis of sexual differentiation during embryonic development. Variations of the traditional XX or XY karyotype may result in conditions where the genotype is discordant with the phenotype. Detection of these conditions in the past typically occurred during adolescence, due to delayed puberty, or during adulthood, due to infertility. With the increasing availability of non-invasive prenatal testing and high-resolution ultrasound, more cases of genotype-phenotype sex discordance are being identified in routine clinical practice during early pregnancy. These discordant results present significant diagnostic and counselling challenges, and their potential should be included in increasingly complex pre-NIPT counselling.

Activity of etv5a and etv5b genes in the hypothalamus of fasted zebrafish is influenced by serotonin.

Serotonin has been implicated in the inhibition of food intake in vertebrates. However, the mechanisms through which serotonin acts has yet to be elucidated. Recently, ETV5 (ets variant gene 5) has been associated with obesity and food intake control mechanisms in mammals. We have analyzed a putative physiological function of the two etv5 paralogous genes (etv5a and etv5b) in neuronal food intake control in adult zebrafish that have been exposed to different nutritional conditions. A feeding assay was established and fluoxetine, a selective serotonin re-uptake inhibitor (SSRI), was applied. Gene expression changes in the hypothalamus were determined using real-time PCR. Fasting induced an up-regulation of etv5a and etv5b in the hypothalamus, whereas increased serotonin levels in the fasted fish counteracted the increase in expression. To investigate potential mechanisms the expression of further food intake control genes was determined. The results show that an increase of serotonin in fasting fish causes a reduction in the activity of genes stimulating food intake. This is in line with a previously demonstrated anorexigenic function of serotonin. Our results suggest that obesity-associated ETV5 has a food intake stimulating function and that this function is modulated through serotonin.

Confirmation of childhood acute lymphoblastic leukemia variants, ARID5B and IKZF1, and interaction with parental environmental exposures.

Genome wide association studies (GWAS) have established association of ARID5B and IKZF1 variants with childhood acute lymphoblastic leukemia (ALL). Epidemiological studies suggest that environmental factors alone appear to make a relatively minor contribution to disease risk. The polygenic nature of childhood ALL predisposition together with the timing of environmental triggers may hold vital clues for disease etiology. This study presents results from an Australian GWAS of childhood ALL cases (n = 358) and population controls (n = 1192). Furthermore, we utilised family trio (n = 204) genotypes to extend our investigation to gene-environment interaction of significant loci with parental exposures before conception, and child's sex and age. Thirteen SNPs achieved genome wide significance in the population based case/control analysis; ten annotated to ARID5B and three to IKZF1. The most significant SNPs in these regions were ARID5B rs4245595 (OR 1.63, CI 1.38-1.93, P = 2.13×10(-9)), and IKZF1 rs1110701 (OR 1.69, CI 1.42-2.02, p = 7.26×10(-9)). There was evidence of gene-environment interaction for risk genotype at IKZF1, whereby an apparently stronger genetic effect was observed if the mother took folic acid or if the father did not smoke prior to pregnancy (respective interaction P-values: 0.04, 0.05). There were no interactions of risk genotypes with age or sex (P-values >0.2). Our results evidence that interaction of genetic variants and environmental exposures may further alter risk of childhood ALL however, investigation in a larger population is required. If interaction of folic acid supplementation and IKZF1 variants holds, it may be useful to quantify folate levels prior to initiating use of folic acid supplements.