Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease.

Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and, with new innovative methods, can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the Genomics Research to Elucidate the Genetics of Rare Diseases consortium and analyzed using the seqr platform. The addition of CNV detection to exome analysis identified causal CNVs for 171 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb. The causal CNVs consisted of 140 deletions, 15 duplications, 3 suspected complex structural variants (SVs), 3 insertions, and 10 complex SVs, the latter two groups being identified by orthogonal confirmation methods. To classify CNV variant pathogenicity, we used the 2020 American College of Medical Genetics and Genomics/ClinGen CNV interpretation standards and developed additional criteria to evaluate allelic and functional data as well as variants on the X chromosome to further advance the framework. We interpreted 151 CNVs as likely pathogenic/pathogenic and 20 CNVs as high-interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher-resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.

A Near-Peer Interprofessional Educational Fellowship Program for Training Pre-Clinical Medical Students in the Best Practices of Teaching and Learning.

Medical school often has opportunities for students to engage in peer or near-peer teaching, however structured teacher training is rarely conducted. We present an Educational Fellowship for rising M2 students as teaching assistants for first year Physician Assistant students. In this near-peer interprofessional teaching model, the M2 students learn pedagogical theory and best practices for teaching and learning. The curriculum and experience may be used by any healthcare profession. Since many healthcare professions have classes during the summer, we present our program as a conceptual model for other institutions.

Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt.

Pathogenic variants in multiple genes on the X chromosome have been implicated in syndromic and non-syndromic intellectual disability disorders. ZFX on Xp22.11 encodes a transcription factor that has been linked to diverse processes including oncogenesis and development, but germline variants have not been characterized in association with disease. Here, we present clinical and molecular characterization of 18 individuals with germline ZFX variants. Exome or genome sequencing revealed 11 variants in 18 subjects (14 males and 4 females) from 16 unrelated families. Four missense variants were identified in 11 subjects, with seven truncation variants in the remaining individuals. Clinical findings included developmental delay/intellectual disability, behavioral abnormalities, hypotonia, and congenital anomalies. Overlapping and recurrent facial features were identified in all subjects, including thickening and medial broadening of eyebrows, variations in the shape of the face, external eye abnormalities, smooth and/or long philtrum, and ear abnormalities. Hyperparathyroidism was found in four families with missense variants, and enrichment of different tumor types was observed. In molecular studies, DNA-binding domain variants elicited differential expression of a small set of target genes relative to wild-type ZFX in cultured cells, suggesting a gain or loss of transcriptional activity. Additionally, a zebrafish model of ZFX loss displayed an altered behavioral phenotype, providing additional evidence for the functional significance of ZFX. Our clinical and experimental data support that variants in ZFX are associated with an X-linked intellectual disability syndrome characterized by a recurrent facial gestalt, neurocognitive and behavioral abnormalities, and an increased risk for congenital anomalies and hyperparathyroidism.

Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort.

PURPOSE: Genome sequencing (GS)-specific diagnostic rates in prospective tightly ascertained exome sequencing (ES)-negative intellectual disability (ID) cohorts have not been reported extensively. METHODS: ES, GS, epigenetic signatures, and long-read sequencing diagnoses were assessed in 74 trios with at least moderate ID. RESULTS: The ES diagnostic yield was 42 of 74 (57%). GS diagnoses were made in 9 of 32 (28%) ES-unresolved families. Repeated ES with a contemporary pipeline on the GS-diagnosed families identified 8 of 9 single-nucleotide variations/copy-number variations undetected in older ES, confirming a GS-unique diagnostic rate of 1 in 32 (3%). Episignatures contributed diagnostic information in 9% with GS corroboration in 1 of 32 (3%) and diagnostic clues in 2 of 32 (6%). A genetic etiology for ID was detected in 51 of 74 (69%) families. Twelve candidate disease genes were identified. Contemporary ES followed by GS cost US$4976 (95% CI: $3704; $6969) per diagnosis and first-line GS at a cost of $7062 (95% CI: $6210; $8475) per diagnosis. CONCLUSION: Performing GS only in ID trios would be cost equivalent to ES if GS were available at $2435, about a 60% reduction from current prices. This study demonstrates that first-line GS achieves higher diagnostic rate than contemporary ES but at a higher cost.

Erythromelalgia caused by the missense mutation p.Arg220Pro in an alternatively spliced exon of SCN9A (NaV1.7).

Erythromelalgia (EM), is a familial pain syndrome characterized by episodic 'burning' pain, warmth, and erythema. EM is caused by monoallelic variants in SCN9A, which encodes the voltage-gated sodium channel (NaV) NaV1.7. Over 25 different SCN9A mutations attributed to EM have been described to date, all identified in the SCN9A transcript utilizing exon 6N. Here we report a novel SCN9A missense variant identified in seven related individuals with stereotypic episodes of bilateral lower limb pain presenting in childhood. The variant, XM_011511617.3:c.659G>C;p.(Arg220Pro), resides in the exon 6A of SCN9A, an exon previously shown to be selectively incorporated by developmentally regulated alternative splicing. The mutation is located in the voltage-sensing S4 segment of domain I, which is important for regulating channel activation. Functional analysis showed the p.Arg220Pro mutation altered voltage-dependent activation and delayed channel inactivation, consistent with a NaV1.7 gain-of-function molecular phenotype. These results demonstrate that alternatively spliced isoforms of SCN9A should be included in all genomic testing of EM.

Promoting Quality of Life: Suggestions for Mental Health Care Providers Working with Young Autistic Adults.

There is a growing population of autistic adults in need of supports from a service delivery system that, at present, fails to accommodate their needs adequately and equitably. Unfortunately, there is a shortage of trained behavioral health service providers to meet the needs of young autistic adults. Quality of life (QoL), or one's perception of, and satisfaction with, life in relation to held goals and expectations, has been identified as a key outcome of interest by autistic self-advocates. By supporting autistic clients to hone their strengths and interests, integrate various aspects of their identity, identify goals, and connect to appropriate resources, providers can promote clients' self-knowledge and self-determination, in the service of improving QoL. In this Perspectives article, we offer concrete recommendations to mental health providers, including those who do not specialize in autism, with the goal of supporting implementation of evidence-based strategies that improve QoL and promote self-determination among young autistic clients.

Why is this topic important?: Mental health care providers who are not autism specialists often feel unable to help autistic adult clients. However, relying on specialists to provide treatment for autistic adults can delay access to needed care. There is a need for well-trained clinicians and other service providers who can effectively work with autistic adults. What is the purpose of this article?: Young autistic adults face many challenges related to transition into adulthood, including greater independence desires and external expectations. The early adult years are also a period of heightened risk for emerging mental health problems. The goal of this article is to offer guidance to mental health service providers on how to effectively support autistic adults, while respecting autonomy, identity, and diversity. The guidance we offer is drawn from research, clinical practice, and lived experience. What personal or professional perspectives do the authors bring to this topic?: In addition to an autistic adult and self-advocate, the authors are clinical researchers and clinicians with expertise in working with adolescents and adults as service providers. What is already known about this topic?: Although a wider range of effective intervention practices is needed, there are a growing number of scientifically based and respectful treatments now available to address mental health concerns and promote quality of life (QoL). Unfortunately, it is widely recognized that there is a shortage of providers who work with autistic clients. One reason for the shortage is that some highly capable and well-trained providers do not treat autistic clients. What do the authors recommend?: We recommend that providers focus on strengths, abilities, and potential rather than focus on perceived deficits when working with autistic clients, so that we as a society can better meet the service needs of the autistic community. Specifically, we encourage a focus on improving QoL, structuring services to focus on self-determination and empowerment, emphasizing intersectionality or existence of multiple identities with personal meaning, and helping clients and their families navigate service systems and supports that are available. How will these recommendations help autistic adults now or in the future?: By increasing the number of providers who can work effectively work with adult autistic clients, we can hopefully minimize delays in service delivery and increase availability of high-quality services.

Psychometric Properties of the Dutch Contextual Assessment of Social Skills (CASS): An Independent Observational Outcome Measure of Social Skills in Autistic Adolescents.

The goal of this study was to translate and adapt the original 9-item of the Contextual Assessment of Social Skills (CASS) to a Dutch version and assess its psychometric qualities. Autistic adolescents aged 12 to 18 years (n = 99) took part in a randomized controlled trial. In this study, pre-intervention data were utilized. The original CASS was adapted to ensure cultural relevance and the content validity was assessed. Data was used to assess reliability and structural validity, using confirmatory factor analysis. 4-item were added to the CASS during the adaptation to better align with the objectives of the experimental intervention. The original 9-item had inter-item correlations between .01 and .70. The Cronbach's alpha for the original 4-item total score was moderate (α = .69), while for a 7-item total score, it was high (α = .86). This 7-item total score had a sufficient model fit (Comparative Fit Index = .90). This total score had a significant correlation with the Assertion subscale of the Social Skills Improvement System-Adolescent (SSIS-A) (r = 0.26, p < .01), and the Social Responsiveness Scale-2 (SRS-2) total score (r = - .21, p = .04) indicating sufficient convergent validity. The CASS total score was not correlated with the Repetitive and Restricted Behavior scale of the SRS-2 (r = - .08, p = .43), indicating sufficient divergent validity. The Dutch CASS can be considered a conceptually sound and reliable observational instrument for assessing social conversational skills in Dutch autistic youth. Further evaluation of its feasibility when implemented in practice, outside of clinical research, is needed.Trial registration: Dutch trail register NTR6255 (NL6117) 08/02/2017 https://www.trialregister.nl/trial/6117.

Clinical features, treatments, their impact, and quality of life for Myasthenia Gravis patients in Australia.

This survey provides an update on the experience of Myasthenia Gravis (MG) patients in Australia. Items were drawn from the 2011 Australian Survey and a 2019 US survey allowing for comparative discussion of survey findings. Patients were recruited through the Myasthenia Alliance Australia. Following consent, patients completed an online survey using REDCap software. Questions included demographics, clinical features, treatment side-effects and quality of life (QOL) scales. Samples for completion of survey sections ranged from N = 242-280 representing a power level of over 80%. Female and seronegative patients reported a significantly greater symptom load, earlier disease onset, longer time to diagnosis, more MG exacerbations, treatment side-effects, and poorer QOL. For exacerbation management there was a higher rate of oral corticosteroid use (66%), a lower use of Intravenous Immunoglobulin (IVIg, 47%) and particularly, Therapeutic Plasma Exchange (TPE, 4.5%) within this sample. Although steroid induced side-effects were rarer (9-34%), a comparatively high use of corticosteroids was reported for current and overall treatments including those for MG crises (52-83%). Common treatment side-effects reported by 57-85% of patients, included fatigue, weight gain, a decrease in the ability to fight infections, gastrointestinal symptoms, and muscle weakness. The impact of MG on daily activities and QOL was considerable, but those who had a thymectomy reported better QOL. The survey identified areas for potential practice improvement in MG treatments (corticosteroids, IVIg, TPE), particularly for exacerbation management, and review is recommended. Further research on gender and antibody status differentials regarding clinical features is required.

Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease.

Copy number variants (CNVs) are significant contributors to the pathogenicity of rare genetic diseases and with new innovative methods can now reliably be identified from exome sequencing. Challenges still remain in accurate classification of CNV pathogenicity. CNV calling using GATK-gCNV was performed on exomes from a cohort of 6,633 families (15,759 individuals) with heterogeneous phenotypes and variable prior genetic testing collected at the Broad Institute Center for Mendelian Genomics of the GREGoR consortium. Each family's CNV data was analyzed using the seqr platform and candidate CNVs classified using the 2020 ACMG/ClinGen CNV interpretation standards. We developed additional evidence criteria to address situations not covered by the current standards. The addition of CNV calling to exome analysis identified causal CNVs for 173 families (2.6%). The estimated sizes of CNVs ranged from 293 bp to 80 Mb with estimates that 44% would not have been detected by standard chromosomal microarrays. The causal CNVs consisted of 141 deletions, 15 duplications, 4 suspected complex structural variants (SVs), 3 insertions and 10 complex SVs, the latter two groups being identified by orthogonal validation methods. We interpreted 153 CNVs as likely pathogenic/pathogenic and 20 CNVs as high interest variants of uncertain significance. Calling CNVs from existing exome data increases the diagnostic yield for individuals undiagnosed after standard testing approaches, providing a higher resolution alternative to arrays at a fraction of the cost of genome sequencing. Our improvements to the classification approach advances the systematic framework to assess the pathogenicity of CNVs.

Evaluation of the feasibility, diagnostic yield, and clinical utility of rapid genome sequencing in infantile epilepsy (Gene-STEPS): an international, multicentre, pilot cohort study.

BACKGROUND: Most neonatal and infantile-onset epilepsies have presumed genetic aetiologies, and early genetic diagnoses have the potential to inform clinical management and improve outcomes. We therefore aimed to determine the feasibility, diagnostic yield, and clinical utility of rapid genome sequencing in this population. METHODS: We conducted an international, multicentre, cohort study (Gene-STEPS), which is a pilot study of the International Precision Child Health Partnership (IPCHiP). IPCHiP is a consortium of four paediatric centres with tertiary-level subspecialty services in Australia, Canada, the UK, and the USA. We recruited infants with new-onset epilepsy or complex febrile seizures from IPCHiP centres, who were younger than 12 months at seizure onset. We excluded infants with simple febrile seizures, acute provoked seizures, known acquired cause, or known genetic cause. Blood samples were collected from probands and available biological parents. Clinical data were collected from medical records, treating clinicians, and parents. Trio genome sequencing was done when both parents were available, and duo or singleton genome sequencing was done when one or neither parent was available. Site-specific protocols were used for DNA extraction and library preparation. Rapid genome sequencing and analysis was done at clinically accredited laboratories, and results were returned to families. We analysed summary statistics for cohort demographic and clinical characteristics and the timing, diagnostic yield, and clinical impact of rapid genome sequencing. FINDINGS: Between Sept 1, 2021, and Aug 31, 2022, we enrolled 100 infants with new-onset epilepsy, of whom 41 (41%) were girls and 59 (59%) were boys. Median age of seizure onset was 128 days (IQR 46-192). For 43 (43% [binomial distribution 95% CI 33-53]) of 100 infants, we identified genetic diagnoses, with a median time from seizure onset to rapid genome sequencing result of 37 days (IQR 25-59). Genetic diagnosis was associated with neonatal seizure onset versus infantile seizure onset (14 [74%] of 19 vs 29 [36%] of 81; p=0·0027), referral setting (12 [71%] of 17 for intensive care, 19 [44%] of 43 non-intensive care inpatient, and 12 [28%] of 40 outpatient; p=0·0178), and epilepsy syndrome (13 [87%] of 15 for self-limited epilepsies, 18 [35%] of 51 for developmental and epileptic encephalopathies, 12 [35%] of 34 for other syndromes; p=0·001). Rapid genome sequencing revealed genetic heterogeneity, with 34 unique genes or genomic regions implicated. Genetic diagnoses had immediate clinical utility, informing treatment (24 [56%] of 43), additional evaluation (28 [65%]), prognosis (37 [86%]), and recurrence risk counselling (all cases). INTERPRETATION: Our findings support the feasibility of implementation of rapid genome sequencing in the clinical care of infants with new-onset epilepsy. Longitudinal follow-up is needed to further assess the role of rapid genetic diagnosis in improving clinical, quality-of-life, and economic outcomes. FUNDING: American Academy of Pediatrics, Boston Children's Hospital Children's Rare Disease Cohorts Initiative, Canadian Institutes of Health Research, Epilepsy Canada, Feiga Bresver Academic Foundation, Great Ormond Street Hospital Charity, Medical Research Council, Murdoch Children's Research Institute, National Institute of Child Health and Human Development, National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre, One8 Foundation, Ontario Brain Institute, Robinson Family Initiative for Transformational Research, The Royal Children's Hospital Foundation, University of Toronto McLaughlin Centre.

Feedback Related Negativity Amplitude is Greatest Following Deceptive Feedback in Autistic Adolescents.

The purpose of this study is to investigate if feedback related negativity (FRN) can capture instantaneous elevated emotional reactivity in autistic adolescents. A measurement of elevated reactivity could allow clinicians to better support autistic individuals without the need for self-reporting or verbal conveyance. The study investigated reactivity in 46 autistic adolescents (ages 12-21 years) completing the Affective Posner Task which utilizes deceptive feedback to elicit distress presented as frustration. The FRN event-related potential (ERP) served as an instantaneous quantitative neural measurement of emotional reactivity. We compared deceptive and distressing feedback to both truthful but distressing feedback and truthful and non-distressing feedback using the FRN, response times in the successive trial, and Emotion Dysregulation Inventory (EDI) reactivity scores. Results revealed that FRN values were most negative to deceptive feedback as compared to truthful non-distressing feedback. Furthermore, distressing feedback led to faster response times in the successive trial on average. Lastly, participants with higher EDI reactivity scores had more negative FRN values for non-distressing truthful feedback compared to participants with lower reactivity scores. The FRN amplitude showed changes based on both frustration and reactivity. The findings of this investigation support using the FRN to better understand emotion regulation processes for autistic adolescents in future work. Furthermore, the change in FRN based on reactivity suggests the possible need to subgroup autistic adolescents based on reactivity and adjust interventions accordingly.

Heterozygous rare variants in NR2F2 cause a recognizable multiple congenital anomaly syndrome with developmental delays.

Nuclear receptor subfamily 2 group F member 2 (NR2F2 or COUP-TF2) encodes a transcription factor which is expressed at high levels during mammalian development. Rare heterozygous Mendelian variants in NR2F2 were initially identified in individuals with congenital heart disease (CHD), then subsequently in cohorts of congenital diaphragmatic hernia (CDH) and 46,XX ovotesticular disorders/differences of sexual development (DSD); however, the phenotypic spectrum associated with pathogenic variants in NR2F2 remains poorly characterized. Currently, less than 40 individuals with heterozygous pathogenic variants in NR2F2 have been reported. Here, we review the clinical and molecular details of 17 previously unreported individuals with rare heterozygous NR2F2 variants, the majority of which were de novo. Clinical features were variable, including intrauterine growth restriction (IUGR), CHD, CDH, genital anomalies, DSD, developmental delays, hypotonia, feeding difficulties, failure to thrive, congenital and acquired microcephaly, dysmorphic facial features, renal failure, hearing loss, strabismus, asplenia, and vascular malformations, thus expanding the phenotypic spectrum associated with NR2F2 variants. The variants seen were predicted loss of function, including a nonsense variant inherited from a mildly affected mosaic mother, missense and a large deletion including the NR2F2 gene. Our study presents evidence for rare, heterozygous NR2F2 variants causing a highly variable syndrome of congenital anomalies, commonly associated with heart defects, developmental delays/intellectual disability, dysmorphic features, feeding difficulties, hypotonia, and genital anomalies. Based on the new and previous cases, we provide clinical recommendations for evaluating individuals diagnosed with an NR2F2-associated disorder.

De novo PHF5A variants are associated with craniofacial abnormalities, developmental delay, and hypospadias.

PURPOSE: The SF3B splicing complex is composed of SF3B1-6 and PHF5A. We report a developmental disorder caused by de novo variants in PHF5A. METHODS: Clinical, genomic, and functional studies using subject-derived fibroblasts and a heterologous cellular system were performed. RESULTS: We studied 9 subjects with congenital malformations, including preauricular tags and hypospadias, growth abnormalities, and developmental delay who had de novo heterozygous PHF5A variants, including 4 loss-of-function (LOF), 3 missense, 1 splice, and 1 start-loss variant. In subject-derived fibroblasts with PHF5A LOF variants, wild-type and variant PHF5A mRNAs had a 1:1 ratio, and PHF5A mRNA levels were normal. Transcriptome sequencing revealed alternative promoter use and downregulated genes involved in cell-cycle regulation. Subject and control fibroblasts had similar amounts of PHF5A with the predicted wild-type molecular weight and of SF3B1-3 and SF3B6. SF3B complex formation was unaffected in 2 subject cell lines. CONCLUSION: Our data suggest the existence of feedback mechanisms in fibroblasts with PHF5A LOF variants to maintain normal levels of SF3B components. These compensatory mechanisms in subject fibroblasts with PHF5A or SF3B4 LOF variants suggest disturbed autoregulation of mutated splicing factor genes in specific cell types, that is, neural crest cells, during embryonic development rather than haploinsufficiency as pathomechanism.

De-implementation of Low-Value Practices for Autism Spectrum Disorder.

Due to a variety of factors, Autism Spectrum Disorder (ASD) has long been tethered to use of low-value practice (LVP), arguably moreso than any other psychiatric or neurodevelopmental condition. Although dissemination of empirically supported treatments (EST) for autistic individuals has expanded markedly over the past decade, there has not been concomitant reduction in the use of LVP. It is critical that clinicians and scientists not only promote the implementation of EST, but also facilitate the de-implementation (abandonment and/or divestment) of ineffective or harmful practices. In this review, we describe a data-driven approach that can be used to identify LVP, drawing from established criteria for identification of evidence-based treatments (e.g., APA Division 12, National Clearinghouse on Autism Evidence and Practice; SAMHSA), as well as broader considerations such as social validity, cost, and parsimony. Herein, a data-based approach to LVP identification is proposed with a goal of improving quality of service access. Within an implementation science framework, we identify specific facilitators that sustain LVP use, and recommendations for subsequent de-implementation strategies are offered.

Pathways to Psychopathology Among Autistic Adults.

PURPOSE OF REVIEW: Autistic adults frequently require treatment of mental health problems. Increased rates of suicidality and diminished quality of life among autistic people may be partially attributable to psychiatric symptoms. Some risk factors for mental health problems in autistic people are likely the same as risk factors present in neurotypical individuals, but unique factors that are specific to neurodivergent individuals, and some even more specific to autistic people, may exist. Understanding pathways from autism to mental health problems could inform intervention efforts at the individual and societal levels. RECENT FINDINGS: We review a growing body of research identifying risk processes across the affective, cognitive, and social domains. Consistent with the principle of equifinality, different processes appear to independently and jointly lead to heightened risk for the onset of mental health problems. Autistic adults frequently utilize mental healthcare services, and experience heightened risk for chronic impairment as a result of mental health problems. Understanding causal and developmental risk processes in autism should inform personalized treatment. We synthesize extant research on these processes and offer suggestions for addressing them therapeutically and societally.