A Review of the Genomic Analysis of Children Presenting with Developmental Delay/Intellectual Disability and Associated Dysmorphic Features

Genetic and phenotypic analysis of 225 Chinese children with developmental delay and/or intellectual disability using whole-exome sequencing

Developmental delay (DD), or intellectual disability (ID) is a very large group of early onset disorders that affects 1-2% of children worldwide, which have diverse genetic causes that should be identified. Genetic studies can elucidate the pathogenesis underlying DD/ID. In this study, whole-exome sequencing (WES) was performed on 225 Chinese DD/ID children (208 cases were sequenced as proband-parent trio) who were classified into seven phenotype subgroups. The phenotype and genomic data of patients with DD/ID were further retrospectively analyzed. There were 96/225 (42.67%; 95% confidence interval [CI] 36.15-49.18%) patients were found to have causative single nucleotide variants (SNVs) and small insertions/deletions (Indels) associated with DD/ID based on WES data. The diagnostic yields among the seven subgroups ranged from 31.25 to 71.43%. Three specific clinical features, hearing loss, visual loss, and facial dysmorphism, can significantly increase the diagnostic yield of WES in patients with DD/ID (P = 0.005, P = 0.005, and P = 0.039, respectively). Of note, hearing loss (odds ratio [OR] = 1.86%; 95% CI = 1.00-3.46, P = 0.046) or abnormal brainstem auditory evoked potential (BAEP) (OR = 1.91, 95% CI = 1.02-3.50, P = 0.042) was independently associated with causative genetic variants in DD/ID children. Our findings enrich the variation spectrums of SNVs/Indels associated with DD/ID, highlight the value genetic testing for DD/ID children, stress the importance of BAEP screen in DD/ID children, and help to facilitate early diagnose, clinical management and reproductive decisions, improve therapeutic response to medical treatment.

Urban-rural difference in factors associated with childhood functional difficulty in Bangladesh: a cross-sectional study

Objective

Early childhood functional difficulty poses a substantial worldwide public health challenge, leading to adverse effects on children's quality of life and overall productivity. Moreover, it represents a significant social and economic problem in Bangladesh. Therefore, the current study aimed to identify factors contributing to childhood functional difficulty in Bangladesh within the context of urban-rural areas.

Methods

A nationally representative cross-sectional survey data from Multiple Indicator Cluster Survey (MICS), 2019 in Bangladesh was used in this study. Chi-square test and multivariable logistic regression analyses were carried out to identify factors associated with childhood functional difficulty.

Results

Functional difficulties were found in approximately 3.3% of children 2-4 years of age in urban areas and 2.5% in rural areas. Having a mother with functional difficulties and undernutrition were identified as significant factors common in both urban and rural areas. Further, mothers who had no formal education (AOR = 2.76, 95%CI = 1.18-6.45) and experienced infant death (AOR = 1.94, 95%CI = 1.01-3.70) were identified as significant factors of functional difficulty in urban areas. On the other hand, in rural areas, no access to mass media, children with acute respiratory infection (ARI) (AOR = 2.13, 95%CI = 1.39-3.28), female sex (AOR = 0.69, 95%CI = 0.53-0.91), child undernutrition (AOR = 1.73, 95%CI = 1.32-2.27) and poorer socio-economic status (AOR = 1.95, 95%CI = 1.08-3.55) were found significant factors.

Conclusion

Functional difficulty was found to be present in one out of every 35 children age 2 to 4 years in Bangladesh. Childhood functional difficulties were reported slightly higher in urban areas as compared to rural areas. Reducing childhood difficulties in urban areas demands comprehensive strategies: quality healthcare, inclusive education, community support, better information systems, and collaboration. To achieve urban-rural parity in child health, address disparities in economic development, healthcare, and education, especially for girls.

Neurodevelopmental Disorder, Obesity, Pancytopenia, Diabetes Mellitus, Cirrhosis, and Renal Failure in ACBD6-Associated Syndrome: A Case Report

OBJECTIVES

Neurodevelopmental disorders (NDDs) are a group of conditions that are clinically and etiologically heterogeneous. Biallelic variants in ACBD6 were previously reported in 7 patients with NDDs. Unfortunately, their clinical information remains very limited with descriptions of only their neurologic and craniofacial features. The purpose of this report is to expand the clinical phenotype of the ACBD6-associated NDDs.

METHODS

We identified 2 Thai siblings with NDDs. Clinical and radiologic features of the proband were described. The affected siblings and parents underwent whole-exome sequencing and PCR-Sanger sequencing.

RESULTS

Clinical manifestations that have never been previously reported include morbid obesity, pancytopenia with severe infections, diabetes mellitus, cirrhosis, and renal failure, leading to deaths in their early 30s. Molecular studies identified a novel homozygous 1 base-pair duplication (c.360dup; p.Leu121Thrfs*27) in the ACBD6 gene.

DISCUSSION

This study reported 1 novel single base-pair duplication, expanding the mutational spectrum, and described the clinical features establishing the entity of ACBD6-associated NDDs.

Trio-based exome sequencing reveals a high rate of the de novo variants in intellectual disability

Intellectual disability (ID), a neurodevelopmental disorder affecting 1-3% of the general population, is characterized by limitations in both intellectual function and adaptive skills. The high number of conditions associated with ID underlines its heterogeneous origin and reveals the difficulty of obtaining a rapid and accurate genetic diagnosis. However, the Next Generation Sequencing, and the whole exome sequencing (WES) in particular, has boosted the diagnosis rate associated with ID. In this study, WES performed on 244 trios of patients clinically diagnosed with isolated or syndromic ID and their respective unaffected parents has allowed the identification of the underlying genetic basis of ID in 64 patients, yielding a diagnosis rate of 25.2%. Our results suggest that trio-based WES facilitates ID's genetic diagnosis, particularly in patients who have been extensively waiting for a definitive molecular diagnosis. Moreover, genotypic information from parents provided by trio-based WES enabled the detection of a high percentage (61.5%) of de novo variants inside our cohort. Establishing a quick genetic diagnosis of ID would allow early intervention and better clinical management, thus improving the quality of life of these patients and their families.

Copy number variants calling from WES data through eXome hidden Markov model (XHMM) identifies additional 2.5% pathogenic genomic imbalances smaller than 30 kb undetected by array-CGH

It has been estimated that Copy Number Variants (CNVs) account for 10%-20% of patients affected by Developmental Disorder (DD)/Intellectual Disability (ID). Although array comparative genomic hybridization (array-CGH) represents the gold-standard for the detection of genomic imbalances, common Agilent array-CGH 4 × 180 kb arrays fail to detect CNVs smaller than 30 kb. Whole Exome sequencing (WES) is becoming the reference application for the detection of gene variants and makes it possible also to infer genomic imbalances at single exon resolution. However, the contribution of small CNVs in DD/ID is still underinvestigated. We made use of the eXome Hidden Markov Model (XHMM) software, a tool utilized by the ExAC consortium, to detect CNVs from whole exome sequencing data, in a cohort of 200 unsolved DD/DI patients after array-CGH and WES-based single nucleotide/indel variant analyses. In five out of 200 patients (2.5%), we identified pathogenic CNV(s) smaller than 30 kb, ranging from one to six exons. They included two heterozygous deletions in TCF4 and STXBP1 and three homozygous deletions in PPT1, CLCN2, and PIGN. After reverse phenotyping, all variants were reported as causative. This study shows the interest in applying sequencing-based CNV detection, from available WES data, to reduce the diagnostic odyssey of additional patients unsolved DD/DI patients and compare the CNV-detection yield of Agilent array-CGH 4 × 180kb versus whole exome sequencing.

Risk factors for early childhood disability in Bangladesh: Evidence from Multiple Indicator Cluster Survey 2019

INTRODUCTION

Early childhood is a vital part of human life because most of the brain developments occur in this particular period. Early childhood disability is a significant global public health burden, which can negatively impact the children's quality of life and their overall productivity. It is also a major social and economic problem in Bangladesh. Therefore, it is very important to understand the associated factors for early childhood disability, which may help disability prevention, better management and policy formulation. The main objective of this study is to investigate the child, family, and community-level factors associated with early childhood disability in Bangladesh.

METHODS

A cross sectional nationally representative data was derived from Multiple Indicator Cluster Survey (MICS), 2019. A total of 14,072 Bangladeshi children under five years of age were selected for this study. Various types of statistical analysis (simple, bivariate, multivariable) were performed. To assess the bivariate relationship between chosen categorical variables (independent) and early childhood disability (dependent), a chi-square test was used. The multivariable ordinal logistic regression was used to find out the association of disability with child, family, and community-level factors.

RESULTS

The results show that 2.0% of the children have at least one disability and 0.8% have more disabilities. Several factors namely not attending in early childhood education [Odds Ratio (OR) = 0.65; 95% confidence interval (CI) = 0.13-1.17 Ρ = 0.01], having mother's functional difficulty (OR = 1.23; 95% (CI) = 0.58-1.88 Ρ <0.001), unhappy mother's life (OR = 0.85; 95% CI = 0.30-1.39 Ρ <0.001), parents without internet access (OR = 0.68; 95% CI = 0.06-1.29 Ρ = 0.03) and parents using mobile phone (OR = 0.52; 95% CI = 0.09-0.95 Ρ = 0.02) were found to be important for early childhood disability in Bangladesh.

CONCLUSION

Early childhood disability is still neglected in Bangladesh and further epidemiological studies are recommended. The findings of this study may help policy makers and relevant stakeholders to develop interventions for reducing the overall burden of early childhood disability.

Correlates of child functional difficulties status in Ghana: A further analysis of the 2017/18 multiple indicator cluster survey

BACKGROUND

Functional difficulties have long-term implications for children's physical, cognitive, emotional, social, and academic growth and development. Although the subject of functional difficulties has received enough scholarly attention in the developed world, few studies have addressed the issue in Ghana. Therefore, the study aimed to regress child, maternal and household and geographical level factors associated with the functional difficulty of children in Ghana.

METHOD

We analysed the 2017/18 multiple indicator cluster survey dataset. The study sample consists of weighted cases of 21,871 children within the ages of 5-17 years. Summary statistics were produced for the study variables. Bivariate analyses were performed to select significant correlates for the multivariate analysis. We accounted for sample design and weight before using Poisson regression techniques to do the bivariate and multivariate analysis.

RESULTS

These factors were significantly associated with functional difficulties among 5-17 years old children in Ghana: not covered with health insurance, mothers who have a functional difficulty and those without information on their functional difficulty status, and children who dwelt in richer households compared to the richest households. Compared to the northern region, children from the remaining nine regions in Ghana were more likely to have had a child functional difficulty.

CONCLUSION

Given the results, the government of Ghana and other development partners should promote policies and programs to reduce the consequences of disability or functional difficulties in children by taking into consideration factors like mothers' functional difficulty, access to health insurance, and regional and economic disparities in Ghana.

Further Delineation of the TRAPPC6B Disorder: Report on a New Family and Review

Pathogenic variants in the TRAPPC6B gene were recently found to be associated in three consanguineous families, with microcephaly, epilepsy, and brain malformations. Here, we report on a 3.5-year-old boy, born to consanguineous Lebanese parents, who presented with developmental delay, lactic acidosis, postnatal microcephaly, and abnormal brain magnetic resonance imaging. By whole exome sequencing, a novel homozygous likely pathogenic variant in exon 1 of the TRAPPC6B gene (c.23T > A; [p.Leu8*]) was identified. A review of the clinical description and literature is discussed, pointing out the phenotypic heterogeneity associated with mutations in this gene.