The clinical utility of rapid exome sequencing in a consanguineous population

Arab founder variants: Contributions to clinical genomics and precision medicine

BACKGROUND

Founder variants are ancestral variants shared by individuals who are not closely related. The large effect size of some of these variants in the context of Mendelian disorders offers numerous precision medicine opportunities.

METHODS

Using one of the largest datasets on Mendelian disorders in the Middle East, we identified 2,908 medically relevant founder variants derived from 18,360 exomes and genomes and investigated their contribution to the clinical annotation of the human genome.

FINDINGS

Strikingly, ∼34% of Arab founder variants are absent in gnomAD. We found a strong contribution of Arab founder variants to the identification of novel gene-disease links (n = 224) and the support/dispute (n = 81 support, n = 101 dispute) of previously reported candidate gene-disease links. The powerful segregation evidence generated by Arab founder variants allowed many ClinVar and Human Gene Mutation Database variants to be reclassified. Overall, 39.5% of diagnostic reports from our clinical lab are based on founder variants, and 19.41% of tested individuals carry at least one pathogenic founder variant. The presumptive loss-of-function mechanism that typically underlies autosomal recessive diseases means that Arab founder variants also offer unique opportunities in "druggable genome" research. Arab founder variants were also informative of migration patterns in the Middle East consistent with documented historical accounts.

CONCLUSIONS

We highlight the contribution of founder variants from an under-represented population group to precision medicine and inform future prevention programs. Our study also sheds light on the added value of these variants in supplementing other lines of research in tracing population history.

FUNDING

There is no funding for this work.

Genetic Study for Identifying Beta Thalassemia Trait in Relatives of Children with Beta Thalassemia Major

BACKGROUND

The most common inherited illness, thalassemia, is thought to have a detrimental effect on public health, particularly in endemic areas. Children with beta thalassemia disease have several mutations. Prevention and premarital examination are still the most effective measures to lessen the burden of beta thalassemia.

OBJECTIVES

This study primarily aimed to determine the beta thalassemia carriers in relatives of beta thalassemia major children, the role of gene study in the confirmation of beta thalassemia trait diagnosis, and to detect the genetic defect in the relatives of beta thalassemia major children.

MATERIALS AND METHODS

The cross-sectional study was conducted on 109 healthy children, aged between six months and 18 years, who were the relatives (second and fourth degree) of beta thalassemia major cases.

RESULTS

Gene screening, using the amplification refractory mutation system (ARMS) polymerase chain reaction (PCR), covered the most common 22 alleles in the Mediterranean region, and was successful in detecting 61.5% of beta-globin chain mutations of studied participants, in addition to high prevalence (34.8%) of beta thalassemia carriers among the relatives of beta thalassemia children.

CONCLUSION

The beta thalassemia carrier rate was found to be highly prevalent among relatives of beta thalassemia major children. Despite the accuracy of gene screening in the detection of beta thalassemia carriers, the use of the most common 22 alleles can only detect 61.5% of carriers; hence, the value of tested gene study is still limited in the detection of carrier rates.

Deciphering the Complexities of Sodium Voltage-Gated Channel Alpha Subunit 1 (SCN1A) Mutation: A Case of Intractable Epilepsy in a Five-and-a-Half-Month-Old Male

If the sodium voltage-gated channel alpha subunit 1 (SCN1A) gene, which encodes Nav1.1 protein, undergoes pathological mutation, it results in a wide range of epileptic syndrome, including febrile seizure, genetic epilepsy with febrile seizure plus (GEFS+), and developmental and epileptic encephalopathy (DEE), including Dravet syndrome. We present the case of a five-and-a-half-month-old boy with SCN1A gene-related epileptic seizures, starting as focal seizures and progressing to generalized tonic-clonic seizures. Despite treating the seizures with multiple antiepileptic drugs, including phenytoin, sodium valproate, levetiracetam, perampanel, and clobazam, it was very difficult to control the seizures, and genetic testing was suggested. The SCN1A mutation leads to either loss of function, including GEFS+ and Dravet syndrome, or gain of function, including familial hemiplegic migraine type 3. The case emphasizes the importance of genetic testing in refractory epilepsy management to provide medical strategies for the diagnosis. It focuses on the difficulties faced in diagnostic and treatment strategies for the management of SCN1A-related epilepsy. It emphasizes the importance of monitoring and personalized treatment strategies to reduce the incidence of refractory epilepsy.

Insight into prevalence, etiology, and modalities of pediatric chronic dialysis: a comprehensive nationwide analysis

BACKGROUND

This study aimed to determine the prevalence and etiology of kidney failure (KF) among children below 15 years of age receiving chronic dialysis in Saudi Arabia and describe their dialysis modalities.

METHODS

This cross-sectional descriptive study was conducted on 8 August 2022, encompassing all 23 pediatric dialysis centers in Saudi Arabia. Data gathered comprised patient demographics, causes of KF, and the dialysis methods employed. Collected data underwent analysis to determine prevalence of children undergoing chronic dialysis, discern underlying causes of KF, and evaluate distribution of patients across different dialysis modalities.

RESULTS

The prevalence of children on chronic dialysis is 77.6 per million children living in Saudi Arabia, equating to 419 children. The predominant underlying cause of KF was congenital anomalies of the kidneys and urinary tract (CAKUT), representing a substantial 41% of cases. Following this, others or unknown etiologies accounted for a noteworthy 25% of cases, with focal segmental glomerulosclerosis (FSGS) comprising 13%, glomerulonephritis at 11%, and congenital nephrotic syndrome contributing 10% to etiological distribution. Regarding dialysis modalities employed, 67% of patients were on peritoneal dialysis (PD), while the remaining 33% were on hemodialysis (HD).

CONCLUSIONS

This first nationwide study of pediatric chronic dialysis in Saudi Arabia sheds light on the prevalence of children undergoing chronic dialysis and underlying causes of their KF, thereby contributing to our understanding of clinical management considerations. This research serves as a stepping stone for the development of national registries.

Case Report: A rare treatable metabolic syndrome (Brown-Vialetto-Van Laere syndrome) masquerading as chronic inflammatory demyelinating polyneuropathy from Saudi Arabia

Background

Brown-Vialetto-Van Laere (BVVL) syndrome is an extremely rare autosomal recessive progressive motoneuron disease that is caused by a defect in the riboflavin transporter genes SLC52A2 and SLC52A3. BVVL syndrome has a variable age of presentation, and it is characterized by progressive auditory neuropathy, bulbar palsy, stridor, muscle weakness, and respiratory compromise secondary to diaphragmatic and vocal cord paralysis. BVVL syndrome has a poor prognosis in the absence of treatment, including morbidity with quadriparesis and sensorineural hearing loss, with mortality in the younger age group. Early administration of riboflavin is associated with prolonged survival, low morbidity, and reversal of some clinical manifestations.

Case presentation

We describe an 18-month-old male infant with progressive pontobulbar palsy, loss of developmental milestones, and a clinical picture suggestive of chronic inflammatory demyelinating neuropathy. A nerve conduction study revealed axonal neuropathy, while molecular analysis revealed a homozygous mutation in one of the riboflavin transporter genes, SLC52A3, confirming BVVL syndrome. The patient needed long-term respiratory support and a gastrostomy tube to support feeding. With high-dose riboflavin supplementation, he experienced moderate recovery of motor function.

Conclusion

This report highlights the importance of considering BVVL syndrome in any patient who presents with the clinical phenotype of pontobulbar palsy and peripheral axonal neuropathy, as early riboflavin treatment may improve or halt disease progression, thus reducing the associated mortality and morbidity.

Unplanned Readmissions in Children with Medical Complexity in Saudi Arabia: A Large Multicenter Study

Background

Children with medical complexity (CMC) account for a substantial proportion of healthcare spending, and one-third of their expenditures are due to readmissions. However, knowledge regarding the healthcare-resource utilization and characteristics of CMC in Saudi Arabia is limited.

Objectives

To describe hospitalization patterns and characteristics of Saudi CMC with an unplanned 30-day readmission.

Methodology

This retrospective study included Saudi CMC (aged 0-14 years) who had an unplanned 30-day readmission at six tertiary centers in Riyadh, Jeddah, Dammam, Alahsa, and Almadina between January 2016 and December 2020. Hospital-based inclusion criteria focused on CMC with multiple complex chronic conditions (CCCs) and technology assistance (TA) device use. CMC were compared across demographics, clinical characteristics, and hospital-resource utilization.

Results

A total of 9139 pediatric patients had unplanned 30-day readmission during the study period, of which 680 (7.4%) met the inclusion criteria. Genetic conditions were the most predominant primary pathology (66.3%), with one-third of cases (33.7%) involving the neuromuscular system. During the index admission, pneumonia was the most common diagnosis (33.1%). Approximately 35.1% of the readmissions were after 2 weeks. Pneumonia accounted for 32.5% of the readmissions. After readmission, 16.9% of patients were diagnosed with another CCC or received a new TA device, and the in-hospital mortality rate was 6.6%.

Conclusion

The rate of unplanned 30-day readmissions in children with medical complexity in Saudi Arabia is 7.4%, which is lower than those reported from developed countries. Saudi children with CCCs and TA devices were readmitted approximately within similar post-discharge time and showed distinct hospitalization patterns associated with specific diagnoses. To effectively reduce the risk of 30-day readmissions, targeted measures must be introduced both during the hospitalization period and after discharge.

Emerging significance of butyrylcholinesterase

Butyrylcholinesterase (BChE; EC 3.1.1.8), an enzyme structurally related to acetylcholinesterase, is widely distributed in the human body. It plays a role in the detoxification of chemicals such as succinylcholine, a muscle relaxant used in anesthetic practice. BChE is well-known due to variant forms of the enzyme with little or no hydrolytic activity which exist in some endogamous communities and result in prolonged apnea following the administration of succinylcholine. Its other functions include the ability to hydrolyze acetylcholine, the cholinergic neurotransmitter in the brain, when its primary hydrolytic enzyme, acetylcholinesterase, is absent. To assess its potential roles, BChE was studied in relation to insulin resistance, type 2 diabetes mellitus, cognition, hepatic disorders, cardiovascular and cerebrovascular diseases, and inflammatory conditions. Individuals who lack the enzyme activity of BChE are otherwise healthy, until they are given drugs hydrolyzed by this enzyme. Therefore, BChE is a candidate for the study of loss-of-function mutations in humans. Studying individuals with variant forms of BChE can provide insights into whether they are protected against metabolic diseases. The potential utility of the enzyme as a biomarker for Alzheimer's disease and the response to its drug treatment can also be assessed.

Exome sequencing improves the molecular diagnostics of paediatric unexplained neurodevelopmental disorders

BACKGROUND

Neurodevelopmental disorders (NDDs) and/or associated multiple congenital abnormalities (MCAs) represent a genetically heterogeneous group of conditions with an adverse prognosis for the quality of intellectual and social abilities and common daily functioning. The rapid development of exome sequencing (ES) techniques, together with trio-based analysis, nowadays leads to up to 50% diagnostic yield. Therefore, it is considered as the state-of-the-art approach in these diagnoses.

RESULTS

In our study, we present the results of ES in a cohort of 85 families with 90 children with severe NDDs and MCAs. The interconnection of the in-house bioinformatic pipeline and a unique algorithm for variant prioritization resulted in a diagnostic yield of up to 48.9% (44/90), including rare and novel causative variants (41/90) and intragenic copy-number variations (CNVs) (3/90). Of the total number of 47 causative variants, 53.2% (25/47) were novel, highlighting the clinical benefit of ES for unexplained NDDs. Moreover, trio-based ES was verified as a reliable tool for the detection of rare CNVs, ranging from intragenic exon deletions (GRIN2A, ZC4H2 genes) to a 6-Mb duplication. The functional analysis using PANTHER Gene Ontology confirmed the involvement of genes with causative variants in a wide spectrum of developmental processes and molecular pathways, which form essential structural and functional components of the central nervous system.

CONCLUSION

Taken together, we present one of the first ES studies of this scale from the central European region. Based on the high diagnostic yield for paediatric NDDs in this study, 48.9%, we confirm trio-based ES as an effective and reliable first-tier diagnostic test in the genetic evaluation of children with NDDs.

A Rare Sparkle: A Case of Calcified Kidneys in a Young Infant With Renal Failure

Primary hyperoxaluria-1 (PH1) is an autosomal recessively inherited rare genetic condition due to the deficiency of the hepatic enzyme alanine:glyoxylate aminotransferase which leads to high systemic levels of oxalate and subsequently, early end-stage renal disease and death. Here, we present a case of a three-month-old male infant who presented with loose stools, reduced oral intake, and decreased activity for 12-13 days along with edema and a peeling rash on cheeks, lips, and genitalia. During the entire duration of the inpatient stay, the child was oligoanuric. Kidney ultrasound (USG) was suggestive of bilateral hyperechoic kidneys with increased cortical echogenicity and a computed tomography scan showed bilateral diffusely calcified renal cortices with well-preserved renal architecture. A diagnosis of "oxalate nephropathy" was made from renal biopsy and genetic testing confirmed it to be "primary hyperoxaluria-1". The child was initially managed conservatively, and then peritoneal dialysis was done, following which the child was shifted to intermittent hemodialysis.