Genetic counselors outside of the genetics clinic: Roles, practices, and ethico-legal implications in light of lagging legal recognition across Canada.

Advances in medical genetics have led to a significant increase in demand for genetic services and expertise across almost all medical specialties. Genetic counselors (GCs) in Canada play key roles in genetic services both within and outside of the Genetics Clinic, while not being regulated or legally recognized as healthcare professionals (HCPs) in most provinces. Understanding whether GCs outside of the "traditional" Genetics Clinic influence patient care, their level of professional autonomy and supervisory structure is, therefore, important. In this study, we explore the current landscape of GC practice outside of the Genetics Clinic by describing positions, determining the professional scope of practice, as defined by the Canadian Association of Genetic Counselors (CAGC) and Canadian Board of Genetic Counseling (CBGC) core competencies, and by elucidating associated ethico-legal implications. An online survey was developed and distributed to GCs working with patient-related data in Canada in positions outside of the Genetics Clinic through the CAGC ListServ and accessed between March 5 and April 9, 2021. Thirty GCs were included in the study, with 16/30 in public healthcare system positions. Most respondents held roles with direct (11/30) and indirect (14/30) impact on patient care and management, and the majority reported performing their primary roles with minimal supervision (56%) or complete independence (36%). Most roles (22/25) elicited by respondents were considered to be within the GC scope of practice, except for administrative tasks and special projects. GCs were the only genetics-trained professional(s) in 8/30 of respondents' workplaces. The results of the current study support the value of GCs translatable skillset in positions beyond the Genetics Clinic, and outline ethico-legal implications for GCs, regulated HCPs, patients, and health institutions in the absence of legal recognition, including medical-legal liability and title protection. This study provides evidence in support of regulation of GCs as HCPs.

Persistent chylothorax associated with lymphatic malformation type 6 due to biallelic pathogenic variants in PIEZO1.

PIEZO1 is required for lymphatic valve formation, and several lymphatic abnormalities have been reported to be associated with autosomal recessive PIEZO1 pathogenic variants including neonatal hydrops, lymphedema involving various body regions, and chylothorax. Persistent or recurrent chylothorax has been infrequently described in association with pathogenic variants in the PIEZO1 gene. We present a 4-year-old female with bilateral pleural effusions detected prenatally, who was diagnosed with bilateral chylothoraces post-partum. She subsequently had recurrent pleural effusions involving both pleural cavities, which tended to improve with restriction of her fat intake, and, one occasion, subcutaneous octreotide. She also had bilateral calf, and intermittent cheek swelling. Genetic testing revealed two deleterious variants in PIEZO1: c.2330-2_2330-1del and c.3860G > A (p.Trp1287*), both of which were classified as likely pathogenic. This supported a diagnosis of Lymphatic Malformation Type 6 (OMIM 616843), also known as Hereditary Lymphedema Type III. Hereditary Lymphedema type III can be associated with persistent chylothorax that can vary in size over time.

The implementation of an enhanced clinical model to improve the diagnostic yield of exome sequencing for patients with a rare genetic disease: A Canadian experience.

The introduction of clinical exome sequencing (ES) has provided a unique opportunity to decrease the diagnostic odyssey for patients living with a rare genetic disease (RGD). ES has been shown to provide a diagnosis in 29%-57% of patients with a suspected RGD, with as many as 70% remaining undiagnosed. There is a need to advance the clinical model of care by more formally integrating approaches that were previously considered research into an enhanced diagnostic workflow. We developed an Exome Clinic, which set out to evaluate a workflow for improving the diagnostic yield of ES for patients with an undiagnosed RGD. Here, we report the outcomes of 47 families who underwent clinical ES in the first year of the clinic. The diagnostic yield from clinical ES was 40% (19/47). Families who remained undiagnosed after ES had the opportunity for follow-up studies that included phenotyping and candidate variant segregation in relatives, genomic matchmaking, and ES reanalysis. This enhanced diagnostic workflow increased the diagnostic yield to 55% (26/47), predominantly through the resolution of variants and genes of uncertain significance. We advocate that this approach be integrated into mainstream clinical practice and highlight the importance of a coordinated translational approach for patients with RGD.

p21 protein-activated kinase 1 is associated with severe regressive autism, and epilepsy.

The p21-activated kinase (PAK) family of proteins function as key effectors of RHO family GTPases in mammalian cells to regulate many pathways including Ras/Raf/MEK/ERK and Wnt/ß-catenin, amongst others. Here we report an individual with a novel autosomal dominant disorder characterized by severe regressive autism, intellectual disability, and epilepsy. Exome sequencing of the proband and her parents revealed a de novo variant in the PAK1 gene ([NM_001128620] c.362C>T/p.Pro121Leu). Studies in patient cells showed a clear effect on PAK1 protein function, including altered phosphorylation of targets (JNK and ERK), decreased abundance of ß-catenin, and concomitant altered expression downstream of these key regulators. Our findings add PAK1 to the list of PAK proteins and kinases which when mutated cause rare genetic diseases.

The unsolved rare genetic disease atlas? An analysis of the unexplained phenotypic descriptions in OMIM®.

For years, the genetics community has estimated the number of individual rare genetic diseases to be approximately 6,000-8,000. A commonly quoted derivation of this estimate is based on the simple addition of the number of phenotypic entries with and without confirmed molecular etiologies in the Online Mendelian Inheritance in Man (OMIM®). Here, we examine the validity of this estimation by mining the phenotypic entries in OMIM that are of likely or suspected Mendelian inheritance without a molecular cause (MIM number prefix "%" or "null"). Of the 3,204 unsolved phenotypic entries in OMIM, only two-thirds (2,034 entries) represented rare diseases. Of these, 8% were considered "well-established" based on their description in commonly used reference textbooks. We hypothesize based on the large proportion of entries that represent single families reported prior to 2011, that a number of the unsolved entries represent pathogenic variants in known genes. The novel gene discovery potential of these entries is therefore likely lower than originally thought. Given that the majority of the ~300 new disease-gene associations curated each year by OMIM were never associated with a "%" or "null" sign, the true scope of the rare disease atlas is likely much larger than previously anticipated.

Phenotype and mutation expansion of the PTPN23 associated disorder characterized by neurodevelopmental delay and structural brain abnormalities.

PTPN23 is a His-domain protein-tyrosine phosphatase implicated in ciliogenesis, the endosomal sorting complex required for transport (ESCRT) pathway, and RNA splicing. Until recently, no defined human phenotype had been associated with alterations in this gene. We identified and report a cohort of seven patients with either homozygous or compound heterozygous rare deleterious variants in PTPN23. Combined with four patients previously reported, a total of 11 patients with this disorder have now been identified. We expand the phenotypic and variation spectrum associated with defects in this gene. Patients have strong phenotypic overlap, suggesting a defined autosomal recessive syndrome caused by reduced function of PTPN23. Shared characteristics of affected individuals include developmental delay, brain abnormalities (mainly ventriculomegaly and/or brain atrophy), intellectual disability, spasticity, language disorder, microcephaly, optic atrophy, and seizures. We observe a broad range of variants across patients that are likely strongly reducing the expression or disrupting the function of the protein. However, we do not observe any patients with an allele combination predicted to result in complete loss of function of PTPN23, as this is likely incompatible with life, consistent with reported embryonic lethality in the mouse. None of the observed or reported variants are recurrent, although some have been identified in homozygosis in patients from consanguineous populations. This study expands the phenotypic and molecular spectrum of PTPN23 associated disease and identifies major shared features among patients affected with this disorder, while providing additional support to the important role of PTPN23 in human nervous and visual system development and function.