Bridging clinical care and research in Ontario, Canada: Maximizing diagnoses from reanalysis of clinical exome sequencing data.

We examined the utility of clinical and research processes in the reanalysis of publicly-funded clinical exome sequencing data in Ontario, Canada. In partnership with eight sites, we recruited 287 families with suspected rare genetic diseases tested between 2014 and 2020. Data from seven laboratories was reanalyzed with the referring clinicians. Reanalysis of clinically relevant genes identified diagnoses in 4% (13/287); four were missed by clinical testing. Translational research methods, including analysis of novel candidate genes, identified candidates in 21% (61/287). Of these, 24 families have additional evidence through data sharing to support likely diagnoses (8% of cohort). This study indicates few diagnoses are missed by clinical laboratories, the incremental gain from reanalysis of clinically-relevant genes is modest, and the highest yield comes from validation of novel disease-gene associations. Future implementation of translational research methods, including continued reporting of compelling genes of uncertain significance by clinical laboratories, should be considered to maximize diagnoses.

Best practices for the interpretation and reporting of clinical whole genome sequencing.

Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.

Hyperimmunoglobulinemia E syndrome associated with coronary artery aneurysms: deficiency of central memory CD4+ T cells and expansion of effector memory CD4+ T cells.

BACKGROUND: Hyperimmunoglobulinemia E syndrome is a primary immunodeficiency disorder characterized by elevated IgE levels, recurrent infections, pruritic rash, and skeletal and dental abnormalities. Autosomal dominant, autosomal recessive, and sporadic forms have been described. Coronary artery aneurysms and analysis of central (TCMs) and effector (TEMs) memory T cells have not been previously reported with this syndrome. OBJECTIVE: To describe a 30-year-old woman with hyperimmunoglobulinemia E syndrome who was found to have coronary artery aneurysms, deficiency in CD4+ TCMs, and expansion of CD4+ TEMs expressing CD45RA antigen (TEMRAs). METHODS: The patient presented to the clinic after hospitalization for chest pain. Coronary angiogram performed during the hospitalization revealed aneurysms in multiple coronary arteries with thrombus formation. In addition, she had a history of recurrent pneumonia, staphylococcal skin abscesses, and a pruritic facial rash. An extensive immunologic evaluation was performed. RESULTS: Immunologic studies revealed increased serum IgE levels (13,434 IU/dL), decreased proliferative responses to the soluble recall antigens tetanus toxoid and Candida albicans, and normal responses to mitogens. Analysis of lymphocyte subsets showed a deficiency of CD4+ TEMs and an increase in CD4+ TEMRAs. In addition, a decreased proportion and number of memory B cells and a deficiency in antibody response to pneumococcal antigens were observed. CONCLUSION: Hyperimmunoglobulinemia E syndrome may be associated with coronary artery aneurysms and with deficiency in CD4+ TEMs and expansion of CD4+ TEMRAs. Comprehensive immunologic evaluation should be performed in patients with this syndrome.

Children's street connections in a Canadian community.

Preteen children's street activities in a small southern Ontario city were examined for understandings about how children on the street affiliate with one another and with adults after school. The everyday connections between children, shopkeepers, and municipal workers demonstrate that the municipal workers and merchants can offer caring, support, and sanctions to children when parents or teachers are not accompanying them. This provides children on the street with a form of guidance from extrafamilial mentors. The findings point to community-based potentials for naturally occurring crime prevention strategies, a significant aspect of Canada's new law: Youth Criminal Justice Act. 2003.