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Angelman syndrome (AS) is a genetic neurodevelopmental disorder caused by loss or deficient expression of UBE3A on the maternally inherited allele. In 10-15% of individuals with a clinical diagnosis of AS, a molecular diagnosis cannot be established with conventional testing. We describe a 13-year-old male with an atypical presentation of AS, who was found to have a novel, maternally inherited, intronic variant in UBE3A (c.3-12T>A) using genome sequencing (GS). Targeted sequencing of RNA isolated from blood confirmed the creation of a new acceptor splice site. These GS results ended a six-year diagnostic odyssey and revealed a 50% recurrence risk for the unaffected parents. This case illustrates a previously unreported splicing variant causing AS. Intronic variants identifiable by GS may account for a proportion of individuals who are suspected of having well-known genetic disorders despite negative prior genetic testing.

Purpose: RAC3 is an underexamined member of the Rho GTPase gene family that is expressed in the developing brain and linked to key cellular functions. De novo missense variants in the homolog RAC1 were recently associated with developmental disorders. In the RAC subfamily, transforming missense changes at certain shared residues have been observed in human cancers and previously characterized in experimental studies. The purpose of this study was to determine whether constitutional dysregulation of RAC3 is associated with human disease. Methods: We discovered a RAC3 variant in the index case using genome sequencing, and searched for additional variants using international data-sharing initiatives. Functional effects of the variants were assessed using a multifaceted approach generalizable to most clinical laboratory settings. Results: We rapidly identified five individuals with de novo monoallelic missense variants in RAC3, including one recurrent change. Every participant had severe intellectual disability and brain malformations. In silico protein modeling, and prior in vivo and in situ experiments, supported a transforming effect for each of the three different RAC3 variants. All variants were observed in databases of somatic variation in cancer. Conclusions: Missense variants in RAC3 cause a novel brain disorder, likely through a mechanism of constitutive protein activation.

BACKGROUND Genetic testing is often pursued in children with medical complexity (CMC), in an attempt to establish a unifying diagnosis, understand pathogenicity and disease progression, guide care and inform reproductive planning. CMC are defined by at least one chronic condition, technology dependence, multiple subspecialist involvement, and high healthcare utilization. Despite multiple efforts to confirm clinical suspicion of an underlying genetic condition, many remain undiagnosed. Whole genome sequencing (WGS) is becoming increasingly available as an informative diagnostic tool. The application of genomic technology to this population has the potential to increase the proportion of CMC for whom diagnoses are established, in an effort to reduce time and emotional burden of the diagnostic process, and reduce health care system costs. OBJECTIVES The main purpose of this study was to optimize the clinical implementation of state-of-the-art genome diagnostics for CMC, in terms of diagnostic yield. DESIGN/METHODS We conducted a prospective study using patients followed by the Complex Care program at a large urban tertiary care center. Research ethics board approval was obtained. Of 435 patients screened, 114 were eligible for inclusion as an underlying genetic condition was clinically suspected but not established to date by conventional genetic testing. To date, 21 participants were evaluated through a clinical genetic assessment, previous genetic testing review and peripheral blood-derived DNA sequence. A laboratory team identified candidate genetic variants associated with patients’ clinical symptoms, as well as other paediatric medically actionable variants. When found, these variants were validated as clinically significant by comparing the child’s DNA to his parents’. WGS diagnostic yield was then determined by calculating the proportion of cases for which a genetic diagnosis was established. RESULTS Of the 21 patients recruited, nine WGS analysis were completed thus far. Among these, four participants were diagnosed with established diseases, two of which were considered as novel diseases. One case was identified with a possible diagnosis, however, the interpretation of this clinical phenotype remains of unknown significance. The other four patients of the study remained undiagnosed. Given these preliminary results, the diagnostic yield of WGS was predicted at 44% in CMC. This can be compared to a previous study performed at our center in which the diagnostic rate for chromosomal microarray alone was reported to be 8% and microarray plus targeted gene sequencing 13%. CONCLUSION This study has shown WGS to be feasible and achieve a higher diagnostic yield in our complex care population. As detection rates improve and laboratory costs decrease overtime, WGS will undoubtedly become a more informative diagnostic tool, particularly in this population. Optimizing the application of this increasingly sophisticated genomic technology warrants further consideration.