Diagnosis of Genetic White Matter Disorders by Singleton Whole-Exome and Genome Sequencing Using Interactome-Driven Prioritization.

BACKGROUND AND OBJECTIVES: Genetic white matter disorders (GWMD) are of heterogeneous origin, with >100 causal genes identified to date. Classic targeted approaches achieve a molecular diagnosis in only half of all patients. We aimed to determine the clinical utility of singleton whole-exome sequencing and whole-genome sequencing (sWES-WGS) interpreted with a phenotype- and interactome-driven prioritization algorithm to diagnose GWMD while identifying novel phenotypes and candidate genes. METHODS: A case series of patients of all ages with undiagnosed GWMD despite extensive standard-of-care paraclinical studies were recruited between April 2017 and December 2019 in a collaborative study at the Bellvitge Biomedical Research Institute (IDIBELL) and neurology units of tertiary Spanish hospitals. We ran sWES and WGS and applied our interactome-prioritization algorithm based on the network expansion of a seed group of GWMD-related genes derived from the Human Phenotype Ontology terms of each patient. RESULTS: We evaluated 126 patients (101 children and 25 adults) with ages ranging from 1 month to 74 years. We obtained a first molecular diagnosis by singleton WES in 59% of cases, which increased to 68% after annual reanalysis, and reached 72% after WGS was performed in 16 of the remaining negative cases. We identified variants in 57 different genes among 91 diagnosed cases, with the most frequent being RNASEH2B, EIF2B5, POLR3A, and PLP1, and a dual diagnosis underlying complex phenotypes in 6 families, underscoring the importance of genomic analysis to solve these cases. We discovered 9 candidate genes causing novel diseases and propose additional putative novel candidate genes for yet-to-be discovered GWMD. DISCUSSION: Our strategy enables a high diagnostic yield and is a good alternative to trio WES/WGS for GWMD. It shortens the time to diagnosis compared to the classical targeted approach, thus optimizing appropriate management. Furthermore, the interactome-driven prioritization pipeline enables the discovery of novel disease-causing genes and phenotypes, and predicts novel putative candidate genes, shedding light on etiopathogenic mechanisms that are pivotal for myelin generation and maintenance.

[Spanish multicenter study: hyperammonemia not associated with inborn errors of metabolism in children]. / Estudio multicéntrico español: niños con hiperamoniemia no asociada a errores innatos del metabolismo.

INTRODUCTION: The hyperammonemic encephalopathy induced by causes different from inborn errors of metabolism is a relatively uncommon but severe complication. OBJETIVES: To study the characteristics of a secondary hyperammonemia episode to discern the triggering causes to get to the diagnosis, and the development in the therapeutic intervention. METHODS: A multicenter retrospective study of children with hyperammonemia unrelated to inborn errors of metabolism, conducted in Spanish hospitals. RESULTS: Nineteen patients were selected; hyperammonemia developed in infants under one year old in 47% of them, being diagnosed mostly with two or more symptoms. The most common clinical finding was an altered consciousness level similar to that of intoxication symptoms, followed by seizures. These clinical symptoms were present in 14 patients, with one of them or both. Twelve of the 19 patients were in treatment with more than two antiepileptic drugs routinely. All children were treated with protein restriction (n: 10), scavengers (n: 10) and/or carglumic acid (n: 12) for the treatment of hyperammonemia. CONCLUSIONS: This study suggests that secondary hyperammonemia could be underdiagnosed because it is only detected when severe symptoms appear. Risk seems to be higher in those patients receiving antiepileptic drugs or those critically ill with a restricted diet or incremented metabolism. The response to specific treatment is adequate but should be established earlier to avoid neurological sequelae of this entity.

INTRODUCCIÓN: la encefalopatía hiperamoniémica inducida por causas diferentes a los errores innatos del metabolismo es una complicación relativamente infrecuente, pero muy grave. OBJETIVOS: conocer las características de un episodio de hiperamoniemia secundaria, tratar de discernir las causas desencadenantes, cómo se llega al diagnóstico del episodio y cómo se desarrolla la actuación terapéutica. MÉTODOS: es un estudio multicéntrico retrospectivo de casos pediátricos con hiperamoniemia no relacionada con errores innatos del metabolismo, llevado a cabo en hospitales españoles. RESULTADOS: fueron seleccionados 19 pacientes y en un 47% el episodio de hiperamoniemia apareció en menores de un año, que fueron diagnosticados mayoritariamente con dos o más síntomas. La clínica más frecuente fue la de alteración del nivel de conciencia tipo intoxicación, seguida de las crisis convulsivas, sumando en ambas hasta 14 pacientes con alguna de ellas o las dos. Doce de los 19 pacientes utilizaban más de dos fármacos antiepilépticos de forma habitual. Todos los niños recibieron tratamiento con restricción proteica (n: 10), quelantes (n: 10) y/o ácido carglúmico (n: 12) para el tratamiento de la hiperamoniemia. CONCLUSIONES: este estudio sugiere que la hiperamoniemia secundaria puede estar infradiagnosticada y solo se detecta cuando aparece una sintomatología grave. Parecen ser pacientes de riesgo aquellos que reciben fármacos antiepilépticos o aquellos críticos con una alimentación restringida o un metabolismo elevado. La respuesta con tratamiento específico es adecuada pero debe ser precoz para evitar las secuelas neurológicas de esta entidad.

Characterization of human disease phenotypes associated with mutations in TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR, and IFIH1.

Aicardi-Goutières syndrome is an inflammatory disease occurring due to mutations in any of TREX1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, ADAR or IFIH1. We report on 374 patients from 299 families with mutations in these seven genes. Most patients conformed to one of two fairly stereotyped clinical profiles; either exhibiting an in utero disease-onset (74 patients; 22.8% of all patients where data were available), or a post-natal presentation, usually within the first year of life (223 patients; 68.6%), characterized by a sub-acute encephalopathy and a loss of previously acquired skills. Other clinically distinct phenotypes were also observed; particularly, bilateral striatal necrosis (13 patients; 3.6%) and non-syndromic spastic paraparesis (12 patients; 3.4%). We recorded 69 deaths (19.3% of patients with follow-up data). Of 285 patients for whom data were available, 210 (73.7%) were profoundly disabled, with no useful motor, speech and intellectual function. Chilblains, glaucoma, hypothyroidism, cardiomyopathy, intracerebral vasculitis, peripheral neuropathy, bowel inflammation and systemic lupus erythematosus were seen frequently enough to be confirmed as real associations with the Aicardi-Goutieres syndrome phenotype. We observed a robust relationship between mutations in all seven genes with increased type I interferon activity in cerebrospinal fluid and serum, and the increased expression of interferon-stimulated gene transcripts in peripheral blood. We recorded a positive correlation between the level of cerebrospinal fluid interferon activity assayed within one year of disease presentation and the degree of subsequent disability. Interferon-stimulated gene transcripts remained high in most patients, indicating an ongoing disease process. On the basis of substantial morbidity and mortality, our data highlight the urgent need to define coherent treatment strategies for the phenotypes associated with mutations in the Aicardi-Goutières syndrome-related genes. Our findings also make it clear that a window of therapeutic opportunity exists relevant to the majority of affected patients and indicate that the assessment of type I interferon activity might serve as a useful biomarker in future clinical trials.

Urea cycle disorders in Spain: an observational, cross-sectional and multicentric study of 104 cases.

BACKGROUND: Advances in the diagnosis and treatment of urea cycle disorders (UCDs) have led to a higher survival rate. The purpose of this study is to describe the characteristics of patients with urea cycle disorders in Spain. METHODS: Observational, cross-sectional and multicenter study. Clinical, biochemical and genetic data were collected from patients with UCDs, treated in the metabolic diseases centers in Spain between February 2012 and February 2013, covering the entire Spanish population. Heterozygous mothers of patients with OTC deficiency were only included if they were on treatment due to being symptomatic or having biochemistry abnormalities. RESULTS: 104 patients from 98 families were included. Ornithine transcarbamylase deficiency was the most frequent condition (64.4%) (61.2% female) followed by type 1 citrullinemia (21.1%) and argininosuccinic aciduria (9.6%). Only 13 patients (12.5%) were diagnosed in a pre-symptomatic state. 63% of the cases presented with type intoxication encephalopathy. The median ammonia level at onset was 298 µmol/L (169-615). The genotype of 75 patients is known, with 18 new mutations having been described. During the data collection period four patients died, three of them in the early days of life. The median current age is 9.96 years (5.29-18), with 25 patients over 18 years of age. Anthropometric data, expressed as median and z-score for the Spanish population is shown. 52.5% of the cases present neurological sequelae, which have been linked to the type of disease, neonatal onset, hepatic failure at diagnosis and ammonia values at diagnosis. 93 patients are following a protein restrictive diet, 0.84 g/kg/day (0.67-1.10), 50 are receiving essential amino acid supplements, 0.25 g/kg/day (0.20-0.45), 58 arginine, 156 mg/kg/day (109-305) and 45 citrulline, 150 mg/kg/day (105-199). 65 patients are being treated with drugs: 4 with sodium benzoate, 50 with sodium phenylbutyrate, 10 with both drugs and 1 with carglumic acid. CONCLUSIONS: Studies like this make it possible to analyze the frequency, natural history and clinical practices in the area of rare diseases, with the purpose of knowing the needs of the patients and thus planning their care.