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.

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.

Genome Sequencing for Diagnosing Rare Diseases.

BACKGROUND: Genetic variants that cause rare disorders may remain elusive even after expansive testing, such as exome sequencing. The diagnostic yield of genome sequencing, particularly after a negative evaluation, remains poorly defined. METHODS: We sequenced and analyzed the genomes of families with diverse phenotypes who were suspected to have a rare monogenic disease and for whom genetic testing had not revealed a diagnosis, as well as the genomes of a replication cohort at an independent clinical center. RESULTS: We sequenced the genomes of 822 families (744 in the initial cohort and 78 in the replication cohort) and made a molecular diagnosis in 218 of 744 families (29.3%). Of the 218 families, 61 (28.0%) - 8.2% of families in the initial cohort - had variants that required genome sequencing for identification, including coding variants, intronic variants, small structural variants, copy-neutral inversions, complex rearrangements, and tandem repeat expansions. Most families in which a molecular diagnosis was made after previous nondiagnostic exome sequencing (63.5%) had variants that could be detected by reanalysis of the exome-sequence data (53.4%) or by additional analytic methods, such as copy-number variant calling, to exome-sequence data (10.8%). We obtained similar results in the replication cohort: in 33% of the families in which a molecular diagnosis was made, or 8% of the cohort, genome sequencing was required, which showed the applicability of these findings to both research and clinical environments. CONCLUSIONS: The diagnostic yield of genome sequencing in a large, diverse research cohort and in a small clinical cohort of persons who had previously undergone genetic testing was approximately 8% and included several types of pathogenic variation that had not previously been detected by means of exome sequencing or other techniques. (Funded by the National Human Genome Research Institute and others.).

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.

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.

What affects implementation of the UK major trauma rehabilitation prescription? A survey informed by the behaviour change wheel.

OBJECTIVE: Major trauma 'Rehabilitation Prescriptions' aim to facilitate continuity of care and describe patient needs following discharge from UK Major Trauma Centre (MTCs), however research suggests rehabilitation prescriptions are not being implemented as intended. We aimed to identify factors influencing completion and use of rehabilitation prescriptions using the Behaviour Change Wheel (BCW) and Theoretical Domains Framework (TDF). DESIGN: Online survey informed by the TDF and BCW. SETTING: UK trauma rehabilitation pathway. POPULATION: Rehabilitation and trauma service providers involved in completing and/or using rehabilitation prescriptions (n = 78). ANALYSIS: Mean scores were calculated for TDF behavioural domains, identifying facilitators (score ≥5) and barriers (≤3.5) to rehabilitation prescription implementation. Thematic analysis of free text data informed by the BCW/TDF identified further facilitators and barriers, plus potential behaviour change strategies. RESULTS: Most respondents worked in UK MTCs (n = 63) and were physiotherapists (n = 34), trauma rehabilitation coordinators (n = 16) or occupational therapists (n = 15). 'Social/professional role and identity', 'knowledge' and 'emotion' (the highest-scoring TDF domains) were facilitators to implementing rehabilitation prescriptions. Qualitative data identified barriers to rehabilitation prescription completion, including 'seen as tick-box exercise','not a priority', lack of resources (IT and workforce), poor inter-service communication, limited knowledge/training. Facilitators included therapist buy-in, standardised training, easy inter-service rehabilitation prescription transfer, usefulness for sharing patient needs. CONCLUSIONS: Although rehabilitation prescriptions are valued by some service providers, their effectiveness is hindered by negative attitudes, limited knowledge and poor communication. Uncertainties exist about whether rehabilitation prescriptions achieve their goals, particularly in documenting patient needs, engaging patients in rehabilitation, and informing onward referrals following MTC discharge. Improving IT systems, empowering patients, redirecting funding, and providing training might improve their usage. Further research should explore service provider and patient perspectives, and prospective long-term follow-up on outcomes of rehabilitation prescription recommendations.

A Randomized Trial Utilizing EEG Brain Computer Interface to Improve Facial Emotion Recognition in Autistic Adults.

PURPOSE: Many individuals with autism spectrum disorder (ASD) experience challenges with facial emotion recognition (FER), which may exacerbate social difficulties in ASD. Few studies have examined whether FER can be experimentally manipulated and improved for autistic people. This study utilized a randomized controlled trial design to examine acceptability and preliminary clinical impact of a novel mixed reality-based neurofeedback program, FER Assistant, using EEG brain computer interface (BCI)-assisted technology to improve FER for autistic adolescents and adults. METHODS: Twenty-seven autistic male participants (M age: 21.12 years; M IQ: 105.78; 85% white) were randomized to the active condition to receive FER Assistant (n = 17) or waitlist control (n = 10). FER Assistant participants received ten sessions utilizing BCI-assisted neurofeedback training in FER. All participants, regardless of randomization, completed a computerized FER task at baseline and endpoint. RESULTS: Results partially indicated that FER Assistant was acceptable to participants. Regression analyses demonstrated that participation in FER Assistant led to group differences in FER at endpoint, compared to a waitlist control. However, analyses examining reliable change in FER indicated no reliable improvement or decline for FER Assistant participants, whereas two waitlist participants demonstrated reliable decline. CONCLUSION: Given the preliminary nature of this work, results collectively suggest that FER Assistant may be an acceptable intervention. Results also suggest that FER may be a potential mechanism that is amenable to intervention for autistic individuals, although additional trials using larger sample sizes are warranted.

Experience of the first adult-focussed undiagnosed disease program in Australia (AHA-UDP): solving rare and puzzling genetic disorders is ageless.

BACKGROUND: Significant recent efforts have facilitated increased access to clinical genetics assessment and genomic sequencing for children with rare diseases in many centres, but there remains a service gap for adults. The Austin Health Adult Undiagnosed Disease Program (AHA-UDP) was designed to complement existing UDP programs that focus on paediatric rare diseases and address an area of unmet diagnostic need for adults with undiagnosed rare conditions in Victoria, Australia. It was conducted at a large Victorian hospital to demonstrate the benefits of bringing genomic techniques currently used predominantly in a research setting into hospital clinical practice, and identify the benefits of enrolling adults with undiagnosed rare diseases into a UDP program. The main objectives were to identify the causal mutation for a variety of diseases of individuals and families enrolled, and to discover novel disease genes. METHODS: Unsolved patients in whom standard genomic diagnostic techniques such as targeted gene panel, exome-wide next generation sequencing, and/or chromosomal microarray, had already been performed were recruited. Genome sequencing and enhanced genomic analysis from the research setting were applied to aid novel gene discovery. RESULTS: In total, 16/50 (32%) families/cases were solved. One or more candidate variants of uncertain significance were detected in 18/50 (36%) families. No candidate variants were identified in 16/50 (32%) families. Two novel disease genes (TOP3B, PRKACB) and two novel genotype-phenotype correlations (NARS, and KMT2C genes) were identified. Three out of eight patients with suspected mosaic tuberous sclerosis complex had their diagnosis confirmed which provided reproductive options for two patients. The utility of confirming diagnoses for patients with mosaic conditions (using high read depth sequencing and ddPCR) was not specifically envisaged at the onset of the project, but the flexibility to offer recruitment and analyses on an as-needed basis proved to be a strength of the AHA-UDP. CONCLUSION: AHA-UDP demonstrates the utility of a UDP approach applying genome sequencing approaches in diagnosing adults with rare diseases who have had uninformative conventional genetic analysis, informing clinical management, recurrence risk, and recommendations for relatives.

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.