Exome Sequencing and the Management of Neurometabolic Disorders.

BACKGROUND: Whole-exome sequencing has transformed gene discovery and diagnosis in rare diseases. Translation into disease-modifying treatments is challenging, particularly for intellectual developmental disorder. However, the exception is inborn errors of metabolism, since many of these disorders are responsive to therapy that targets pathophysiological features at the molecular or cellular level. METHODS: To uncover the genetic basis of potentially treatable inborn errors of metabolism, we combined deep clinical phenotyping (the comprehensive characterization of the discrete components of a patient's clinical and biochemical phenotype) with whole-exome sequencing analysis through a semiautomated bioinformatics pipeline in consecutively enrolled patients with intellectual developmental disorder and unexplained metabolic phenotypes. RESULTS: We performed whole-exome sequencing on samples obtained from 47 probands. Of these patients, 6 were excluded, including 1 who withdrew from the study. The remaining 41 probands had been born to predominantly nonconsanguineous parents of European descent. In 37 probands, we identified variants in 2 genes newly implicated in disease, 9 candidate genes, 22 known genes with newly identified phenotypes, and 9 genes with expected phenotypes; in most of the genes, the variants were classified as either pathogenic or probably pathogenic. Complex phenotypes of patients in five families were explained by coexisting monogenic conditions. We obtained a diagnosis in 28 of 41 probands (68%) who were evaluated. A test of a targeted intervention was performed in 18 patients (44%). CONCLUSIONS: Deep phenotyping and whole-exome sequencing in 41 probands with intellectual developmental disorder and unexplained metabolic abnormalities led to a diagnosis in 68%, the identification of 11 candidate genes newly implicated in neurometabolic disease, and a change in treatment beyond genetic counseling in 44%. (Funded by BC Children's Hospital Foundation and others.).

The genotypic and phenotypic spectrum of MTO1 deficiency.

BACKGROUND: Mitochondrial diseases, a group of multi-systemic disorders often characterized by tissue-specific phenotypes, are usually progressive and fatal disorders resulting from defects in oxidative phosphorylation. MTO1 (Mitochondrial tRNA Translation Optimization 1), an evolutionarily conserved protein expressed in high-energy demand tissues has been linked to human early-onset combined oxidative phosphorylation deficiency associated with hypertrophic cardiomyopathy, often referred to as combined oxidative phosphorylation deficiency-10 (COXPD10). MATERIAL AND METHODS: Thirty five cases of MTO1 deficiency were identified and reviewed through international collaboration. The cases of two female siblings, who presented at 1 and 2years of life with seizures, global developmental delay, hypotonia, elevated lactate and complex I and IV deficiency on muscle biopsy but without cardiomyopathy, are presented in detail. RESULTS: For the description of phenotypic features, the denominator varies as the literature was insufficient to allow for complete ascertainment of all data for the 35 cases. An extensive review of all known MTO1 deficiency cases revealed the most common features at presentation to be lactic acidosis (LA) (21/34; 62% cases) and hypertrophic cardiomyopathy (15/34; 44% cases). Eventually lactic acidosis and hypertrophic cardiomyopathy are described in 35/35 (100%) and 27/34 (79%) of patients with MTO1 deficiency, respectively; with global developmental delay/intellectual disability present in 28/29 (97%), feeding difficulties in 17/35 (49%), failure to thrive in 12/35 (34%), seizures in 12/35 (34%), optic atrophy in 11/21 (52%) and ataxia in 7/34 (21%). There are 19 different pathogenic MTO1 variants identified in these 35 cases: one splice-site, 3 frameshift and 15 missense variants. None have bi-allelic variants that completely inactivate MTO1; however, patients where one variant is truncating (i.e. frameshift) while the second one is a missense appear to have a more severe, even fatal, phenotype. These data suggest that complete loss of MTO1 is not viable. A ketogenic diet may have exerted a favourable effect on seizures in 2/5 patients. CONCLUSION: MTO1 deficiency is lethal in some but not all cases, and a genotype-phenotype relation is suggested. Aside from lactic acidosis and cardiomyopathy, developmental delay and other phenotypic features affecting multiple organ systems are often present in these patients, suggesting a broader spectrum than hitherto reported. The diagnosis should be suspected on clinical features and the presence of markers of mitochondrial dysfunction in body fluids, especially low residual complex I, III and IV activity in muscle. Molecular confirmation is required and targeted genomic testing may be the most efficient approach. Although subjective clinical improvement was observed in a small number of patients on therapies such as ketogenic diet and dichloroacetate, no evidence-based effective therapy exists.

Implementing an integrated multi-technology platform for drug checking: Social, scientific, and technological considerations.

The illicit drug overdose crisis in North America continues to devastate communities with fentanyl detected in the majority of illicit drug overdose deaths. The COVID-19 pandemic has heightened concerns of even greater unpredictability in the drug supplies and unprecedented rates of overdoses. Portable drug-checking technologies are increasingly being integrated within overdose prevention strategies. These emerging responses are raising new questions about which technologies to pursue and what service models can respond to the current risks and contexts. In what has been referred to as the epicenter of the overdose crisis in Canada, a multi-technology platform for drug checking is being piloted in community settings using a suite of chemical analytical methods to provide real-time harm reduction. These include infrared absorption, Raman scattering, gas chromatography with mass spectrometry, and antibody-based test strips. In this Perspective, we illustrate some advantages and challenges of using multiple techniques for the analysis of the same sample, and provide an example of a data analysis and visualization platform that can unify the presentation of the results and enable deeper analysis of the results. We also highlight the implementation of a various service models that co-exist in a research setting, with particular emphasis on the way that drug checking technicians and harm reduction workers interact with service users. Finally, we provide a description of the challenges associated with data interpretation and the communication of results to a diverse audience.

Initial results of a drug checking pilot program to detect fentanyl adulteration in a Canadian setting.

BACKGROUND: Opioid overdose deaths in North America have been rising largely as a result of fentanyl adulteration in the illegal drug supply. Drug checking is an established harm reduction intervention in some European settings but has not been broadly implemented or evaluated in North America. We are evaluating a pilot program offering drug checking for people who use street drugs in Vancouver, British Columbia. METHODS: Drug checking services were implemented at two locations in Vancouver between November 2017 and April 2018 using a Fourier transform infrared (FTIR) spectrometer and fentanyl immunoassay strips. We report on the findings generated by this technological combination during the study period. RESULTS: During the study period, a total of 1714 samples were tested. Of 907 samples expected to be heroin, only 160 (17.6%) contained the expected substance, and 822 (90.6%) tested positive for fentanyl. Of 256 samples expected to be speed or crystal meth, 225 (87.9%) contained amphetamine or methamphetamine, and 15 (5.9%) tested positive for fentanyl. The FTIR also found unexpected and potentially dangerous substances and adulterants other than fentanyl. CONCLUSIONS: This pilot program has demonstrated the feasibility of drug checking for identifying individual drug samples containing unexpected or hazardous substances, including fentanyl. By identifying the range of adulterants and diluents and giving an estimate of their prevalence in different drug types, it has also provided information about the composition of the illicit drug supply in an urban North American setting.

A novel deletion in the iron-response element of the L-ferritin gene, causing hyperferritinaemia cataract syndrome.

A 47-year-old woman, presenting to her family physician with fatigue, was incidentally found to have persistently elevated ferritin. There was clinically no suggestion of iron overload, and laboratory testing showed transferrin saturation at the low end of the reference range. After ruling out acquired causes of hyperferritinaemia, as well as laboratory interference, further questioning revealed a history of bilateral early-onset cataracts, allowing a diagnosis of hyperferritinaemia cataract syndrome to be made. DNA sequencing of the 5' untranslated region of the L-ferritin gene revealed a novel 4-base deletion in the iron response element, within a region known to be crucial for binding iron regulatory protein.