Expanding the clinical and genetic spectrum of ALPK3 variants: Phenotypes identified in pediatric cardiomyopathy patients and adults with heterozygous variants

Introduction: Biallelic damaging variants in ALPK3, encoding alpha-protein kinase 3, cause pediatric-onset cardiomyopathy with manifestations that are incompletely defined. Methods and Results: We analyzed clinical manifestations of damaging biallelic ALPK3 variants in 19 pediatric patients, including nine previously published cases. Among these, 11 loss-of-function (LoF) variants, seven compound LoF and deleterious missense variants, and one homozygous deleterious missense variant were identified. Among 18 live-born patients, 8 exhibited neonatal dilated cardiomyopathy (44.4%; 95% CI: 21.5%-69.2%) that subsequently transitioned into ventricular hypertrophy. The majority of patients had extracardiac phenotypes, including contractures, scoliosis, cleft palate, and facial dysmorphisms. We observed no association between variant type or location, disease severity, and/or extracardiac manifestations. Myocardial histopathology showed focal cardiomyocyte hypertrophy, subendocardial fibroelastosis in patients under 4 years of age, and myofibrillar disarray in adults. Rare heterozygous ALPK3 variants were also assessed in adult-onset cardiomyopathy patients. Among 1548 Dutch patients referred for initial genetic analyses, we identified 39 individuals with rare heterozygous ALPK3 variants (2.5%; 95% CI: 1.8%-3.4%), including 26 missense and 10 LoF variants. Among 149 U.S. patients without pathogenic variants in 83 cardiomyopathy-related genes, we identified six missense and nine LoF ALPK3 variants (10.1%; 95% CI: 5.7%-16.1%). LoF ALPK3 variants were increased in comparison to matched controls (Dutch cohort, P = 1.6×10−5; U.S. cohort, P = 2.2×10−13). Conclusion: Biallelic damaging ALPK3 variants cause pediatric cardiomyopathy manifested by DCM transitioning to hypertrophy, often with poor contractile function. Additional extracardiac features occur in most patients, including musculoskeletal abnormalities and cleft palate. Heterozygous LoF ALPK3 variants are enriched in adults with cardiomyopathy and may contribute to their cardiomyopathy. Adults with ALPK3 LoF variants therefore warrant evaluations for cardiomyopathy

A prospective study of the psychological impact, understanding and disclosure of gene test results for hypertrophic cardiomyopathy and long QT syndrome.

© 2010 Ivan MaccioccaHypertrophic cardiomyopathy (HCM) and Long QT syndrome (LQTS) are inherited cardiovascular conditions for which genetic testing has become more common in clinical practice. The most concerning feature of these conditions is sudden death which can be prevented if those at risk are identified. Research into the clinical and molecular aspects of these conditions has advanced rapidly but research on the psychosocial implications of genetic testing for these conditions has lagged behind. The present study aimed to add to the limited body of research about the impact of genetic testing for HCM and LQTS to guide genetic health professionals working with families who are considering genetic testing. A multi-centre prospective questionnaire-based study was conducted to examine the impact of diagnostic and predictive testing for HCM and LQTS. Understanding of test results, risk perception, motivations for and concerns about testing and psychological impact of result disclosure were examined as well as disclosure of gene test result to relatives. Participants were recruited from four Australian and one British site. Questionnaires were completed before testing and at two weeks and three months post-disclosure. Data from participants who underwent diagnostic testing (n=46, 15-76 years old, 40 (80%) tested positive) were analysed separately to those who had predictive testing (n=77, 14-67 years old, 29 (38%) tested positive). A high proportion of participants from both the diagnostic and predictive gene testing groups were pleased they had testing, recalled their result accurately and in the diagnostic group, understood the implications of their result for their own health and their relatives. In those who had predictive testing, perceptions of the likelihood of developing disease, level of worry, and the number of concerns about LQTS and HCM reported were consistent with gene test result. More than 90% of participants in both groups disclosed their gene test results to first‐degree relatives. Concerns about sudden death were evident in participants from both the diagnostic and predictive group, confirming anecdotal reports from clinical practice. Concerns about the possibility of at-risk relatives inheriting either LQTS or HCM and the unpredictable natural history of both conditions were also common concerns. For the predictive testing group, multivariable linear regression analysis adjusting for baseline psychological scores and potential confounders, and accounting for family clusters demonstrated a higher mean anxiety (p=0.005) and distress (p=0.003) score in gene positive compared to gene negative participants at 2 weeks, but these differences were less apparent at 3 months. There was no difference in depression scores at any time point in those who underwent predictive testing. The same analysis was performed in the diagnostic testing group and there were no statistically significant differences in adjusted mean anxiety, distress and depression scores when comparing participants with gene positive and gene negative results at any time point. Overall, high proportions of participants who underwent diagnostic and predictive testing were pleased to have undergone testing, understood the implications of their result and disclosed their result to relatives. There was no evidence for significant negative psychological sequelae three months after receipt of test result in participants who had either diagnostic or predictive testing. Implications for practice are presented

Genetic counseling for Indigenous Australians: an exploratory study from the perspective of genetic health professionals

Indigenous populations are thought to have particularly low levels of access to genetic health services, and cultural issues may be a contributing factor. This article presents the findings of the first study of genetic health service provision to Indigenous Australians. This qualitative study aimed to identify elements of culturally-competent genetic health service provision in Indigenous Australian contexts. Twelve semi-structured interviews were conducted with genetic counselors and clinical geneticists from around Australia who had delivered services to Indigenous Australians. Participants were asked to describe their experiences and identify any collective cultural needs of Indigenous clients, as well as comment on specific training and resources they had received or used. Interviews were audio-recorded and transcribed with thematic analysis conducted on the data. The findings show that participants were reluctant to generalize the needs of Indigenous peoples. Some participants asserted that Indigenous peoples have needs that differ from the general population, while others felt that there were no collective cultural needs, instead advocating an individualized approach. Being flexible and practical, taking time to build rapport, recognizing different family structures and decision-making processes, as well as socio-economic disadvantage were all identified as important factors in participants\u27 interactions with Indigenous clients. Indigenous support workers and hospital liaison officers were seen as valuable resources for effective service provision. The implications of this study for training and practice are discussed

Genetic basis of childhood cardiomyopathy

Background: The causes of cardiomyopathy in children are less well described than in adults. We evaluated the clinical diagnoses and genetic causes of childhood cardiomyopathy and outcomes of cascade genetic testing in family members. Methods: We recruited children from a pediatric cardiology service or genetic heart diseases clinic. We performed Sanger, gene panel, exome or genome sequencing and classified variants for pathogenicity using American College of Molecular Genetics and Genomics guidelines. Results: Cardiomyopathy was diagnosed in 221 unrelated children aged ≤18 years. Children mostly had hypertrophic cardiomyopathy (n=98, 44%) or dilated cardiomyopathy (n=89, 40%). The highest genetic testing diagnostic yields were in restrictive cardiomyopathy (n=16, 80%) and hypertrophic cardiomyopathy (n=65, 66%), and lowest in dilated cardiomyopathy (n=26, 29%) and left ventricular noncompaction (n=3, 25%). Pathogenic variants were primarily found in genes encoding sarcomere proteins, withTNNT2andTNNI3variants associated with more severe clinical outcomes. Ten children (4.5%) had multiple pathogenic variants. Genetic test results prompted review of clinical diagnosis in 14 families with syndromic, mitochondrial or metabolic gene variants. Cascade genetic testing in 127 families confirmed 24 de novo variants, recessive inheritance in 8 families, and supported reclassification of 12 variants. Conclusions: Genetic testing of children with cardiomyopathy supports a precise clinical diagnosis, which may inform prognosis.</p

Cpipe: a shared variant detection pipeline designed for diagnostic settings

The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical genomics in mind. Here we present Cpipe, a pipeline designed specifically for clinical genetic disease diagnostics. Cpipe was developed by the Melbourne Genomics Health Alliance, an Australian initiative to promote common approaches to genomics across healthcare institutions. As such, Cpipe has been designed to provide fast, effective and reproducible analysis, while also being highly flexible and customisable to meet the individual needs of diverse clinical settings. Cpipe is being shared with the clinical sequencing community as an open source project and is available at http://cpipeline.org

Two-step offer and return of multiple types of additional genomic findings to families after ultrarapid trio genomic testing in the acute care setting: a study protocol

Introduction As routine genomic testing expands, so too does the opportunity to look for additional health information unrelated to the original reason for testing, termed additional findings (AF). Analysis for many different types of AF may be available, particularly to families undergoing trio genomic testing. The optimal model for service delivery remains to be determined, especially when the original test occurs in the acute care setting.Methods and analysis Families enrolled in a national study providing ultrarapid genomic testing to critically ill children will be offered analysis for three types of AF on their stored genomic data: paediatric-onset conditions in the child, adult-onset conditions in each parent and reproductive carrier screening for the parents as a couple. The offer will be made 3–6 months after diagnostic testing. Parents will have access to a modified version of the Genetics Adviser web-based decision support tool before attending a genetic counselling appointment to discuss consent for AF. Parental experiences will be evaluated using qualitative and quantitative methods on data collected through surveys, appointment recordings and interviews at multiple time points. Evaluation will focus on parental preferences, uptake, decision support use and understanding of AF. Genetic health professionals’ perspectives on acceptability and feasibility of AF will also be captured through surveys and interviews.Ethics and dissemination This project received ethics approval from the Melbourne Health Human Research Ethics Committee as part of the Australian Genomics Health Alliance protocol: HREC/16/MH/251. Findings will be disseminated through peer-review journal articles and at conferences nationally and internationally

Investigation of current models of care for genetic heart disease in Australia: A national clinical audit

Background: This sub-study of the Australian Genomics Cardiovascular Genetic Disorders Flagship sought to conduct the first nation-wide audit in Australia to establish the current practices across cardiac genetics clinics. Method: An audit of records of patients with a suspected genetic heart disease (cardiomyopathy, primary arrhythmia, autosomal dominant congenital heart disease) who had a cardiac genetics consultation between 1st January 2016 and 31 July 2018 and were offered a diagnostic genetic test. Results: This audit included 536 records at multidisciplinary cardiac genetics clinics from 11 public tertiary hospitals across five Australian states. Most genetic consultations occurred in a clinic setting (90%), followed by inpatient (6%) and Telehealth (4%). Queensland had the highest proportion of Telehealth consultations (9% of state total). Sixty-six percent of patients had a clinical diagnosis of a cardiomyopathy, 28% a primary arrhythmia, and 0.7% congenital heart disease. The reason for diagnosis was most commonly as a result of investigations of symptoms (73%). Most patients were referred by a cardiologist (85%), followed by a general practitioner (9%) and most genetic tests were funded by the state Genetic Health Service (73%). Nationally, 29% of genetic tests identified a pathogenic or likely pathogenic gene variant; 32% of cardiomyopathies, 26% of primary arrhythmia syndromes, and 25% of congenital heart disease. Conclusion: We provide important information describing the current models of care for genetic heart diseases throughout Australia. These baseline data will inform the implementation and impact of whole genome sequencing in the Australian healthcare landscape

Unique cardiac phenotype in ALPK3-related disease: Progression from dilated cardiomyopathy to hypertrophic cardiomyopathy

Introduction: Biallelic truncating variants in ALPK3 have recently been described to cause pediatric cardiomyopathy (CMP). Functional studies have found disorganized intercalated discs and sarcomeres and calcium mishandling in both patients and mutant stemcellderived cardiomyocytes. Objectives: To delineate the clinical and genetic spectrum of ALPK3related disease and study genotypephenotype correlations. Methods: We collected clinical and genetic data on ALPK3related CMP patients, and performed ALPK3 staining in heart and skeletal muscle of 3 individuals carrying biallelic truncating variants. Results: We report biallelic ALPK3 mutations for a total of 18 patients: 9 previously reported cases and 9 novel patients from 6 families. Nine patients had biallelic truncating variants, 7 had a truncating and a missense variant, and 1 had a homozygous missense variant in ALPK3. Nine of 16 liveborn patients showed (biventricular) DCM during neonatal life that transitioned to predominantly HCM with surveillance. Several patients showed extracardiac features, including short stature (8/13), contractures (6/15), severe scoliosis (5/12), cleft palate (CP) or velopharyngeal insufficiency (5/15), and dysmorphic (Noonanlike) facies (8/14). Biopsy of 4 patients showed focal cardiomyocyte hypertrophy, subendocardial fibroelastosis <4 years of age, and myofibrillar disarray at adult age. ALPK3 staining confirmed its nuclear expression in heart and skeletal muscle, but no differences were observed between patients and controls. Mutations predominantly cluster in exon 6 and the alphakinase domain. No association between mutation type or location and disease severity was observed. Conclusion: Although it has been previously shown that HCM may progress to DCM, we describe a unique cardiac phenotype of DCM transitioning to predominantly HCM. We extend the ALPK3 phenotype to include CP and contractures, however no genotypephenotype correlation could be established. Alpk3 mice displayed a similar cardiac phenotype, but did not show fibrosis or extracardiac features. Expression of a truncated ALPK3 protein in humans may explain the differences in clinical manifestation between the patients and Alpk3 mice that do not produce ALPK3 protein