Unexplained developmental delay/learning disability: guidelines for best practice protocol for first line assessment and genetic/metabolic/radiological investigations

Intellectual Disabilities and Neurocognitive Impairment in Adult Patients with Inherited Metabolic Diseases: A UK Single Centre Experience

Inherited metabolic diseases (IMDs) are a group of heterogeneous genetic disorders resulting in substrate accumulation, energy deficiency, or complex molecular defects due to the failure of specific molecules to act as enzymes, cofactors, transporters, or receptors in specific metabolic pathways. The pathophysiological changes seen in IMDs are sometimes associated with intellectual disability (ID) or neurocognitive decline, necessitating multidisciplinary input. We here describe our experience at one tertiary metabolic centre in the UK. We reviewed the case prevalence and existing service provision in one adult IMD service covering a multi-ethnic population of 10 million in North England. In our cohort of 2268 IMD patients, 1598 patients had general metabolic conditions (70.5%), and 670 had lysosomal storage disease/disorders (LSD)s (29.5%). The overall prevalence of ID and neurocognitive decline was found to be 15.7% (n = 357), with patients with LSDs accounting for 23.5% (n = 84) of affected patients. Given the prevalence of ID in adults with IMDs, access to multidisciplinary input from neuropsychology and neuropsychiatry services is important. Education of healthcare professionals to diagnose IMDs in patients with ID, in addition to neurocognitive and neuropsychiatric presentations, will avoid missed diagnoses of IMD and will have a positive effect on patient outcomes.

Neurodevelopmental Abnormalities in Patients with Familial Hypocalciuric Hypercalcemia Type 3

OBJECTIVES

To evaluate the prevalence and degree of any neurodevelopmental abnormalities in children with familial hypocalciuric hypercalcemia type 3 (FHH3).

STUDY DESIGN

A formal neurodevelopmental assessment was performed in children diagnosed with FHH3. The Vineland Adaptive Behavior Scales, which is a standardized parent report assessment tool for adaptive behavior, was used to assess communication, social skills, and motor function and to generate a composite score.

RESULTS

Six patients were diagnosed with hypercalcemia between 0.1 and 8 years of age. All had neurodevelopmental abnormalities in childhood consisting of either global developmental delay, motor delay, expressive speech disturbances, learning difficulties, hyperactivity, or autism spectrum disorder. Four out of the 6 probands had a composite Vineland Adaptive Behavior Scales SDS of < -2.0, indicating adaptive malfunctioning. Significant deficits were observed in the domains of communication (mean SDS: -2.0, P < .01), social skills (mean SDS: -1.3, P < .05), and motor skills (mean SDS: 2.6, P < .05). Individuals were equally affected across domains, with no clear genotype-phenotype correlation. All family members affected with FHH3 also described evidence of neurodevelopmental dysfunction, including mild-to-moderate learning difficulties, dyslexia, and hyperactivity.

CONCLUSION

Neurodevelopmental abnormalities appear to be a highly penetrant and common feature of FHH3, and early detection is warranted to provide appropriate educational support. This case series also supports consideration of serum calcium measurement as part of the diagnostic work-up in any child presenting with unexplained neurodevelopmental abnormalities.

Further characterization of the 9q31 microdeletion phenotype; delineation of a common region of overlap containing ZNF462

BACKGROUND

Loss of function variants and whole gene deletions of ZNF462 has been associated with a novel phenotype of developmental delay/intellectual disability and distinctive facial features. Over two dozen cases have been reported to date and the condition is now known as Weiss-Kruszka syndrome (OMIM# 618619). There are several older reports in the literature and DECIPER detailing individuals with interstitial deletions of 9q31 involving the ZNF462 gene. Many of the characteristic facial features described in these microdeletion cases are similar to those who have been diagnosed with Weiss-Kruszka syndrome.

METHODS

We describe three additional patients with overlapping 9q31 deletions and compare the phenotypes of the microdeletion cases reported in the literature to Weiss-Kruszka syndrome.

RESULTS

Phenotypic overlap was observed between patients with 9q31 deletions and Weiss-Kruszka syndrome. Several additional features were noted in 9q31 deletion patients, including hearing loss, small head circumference, palate abnormalities and short stature.

CONCLUSIONS

The common region of overlap of microdeletion cases implicates ZNF462 as the main driver of the recognizable 9q31 microdeletion phenotype. The observation of additional features in patients with 9q31 microdeletions that are not reported in Weiss-Kruszka syndrome further suggests that other genes from the 9q31 region likely act synergistically with ZNF462 to affect phenotypic expression.

Genetic and metabolic investigations for neurodevelopmental disorders: position statement of the Canadian College of Medical Geneticists (CCMG)

PURPOSE AND SCOPE

The aim of this position statement is to provide recommendations for clinicians regarding the use of genetic and metabolic investigations for patients with neurodevelopmental disorders (NDDs), specifically, patients with global developmental delay (GDD), intellectual disability (ID) and/or autism spectrum disorder (ASD). This document also provides guidance for primary care and non-genetics specialists caring for these patients while awaiting consultation with a clinical geneticist or metabolic specialist.

METHODS OF STATEMENT DEVELOPMENT

A multidisciplinary group reviewed existing literature and guidelines on the use of genetic and metabolic investigations for the diagnosis of NDDs and synthesised the evidence to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and to the Canadian Pediatric Society (Mental Health and Developmental Disabilities Committee); following incorporation of feedback, it was approved by the CCMG Board of Directors on 1 September 2022.

RESULTS AND CONCLUSIONS

Chromosomal microarray is recommended as a first-tier test for patients with GDD, ID or ASD. Fragile X testing should also be done as a first-tier test when there are suggestive clinical features or family history. Metabolic investigations should be done if there are clinical features suggestive of an inherited metabolic disease, while the patient awaits consultation with a metabolic physician. Exome sequencing or a comprehensive gene panel is recommended as a second-tier test for patients with GDD or ID. Genetic testing is not recommended for patients with NDDs in the absence of GDD, ID or ASD, unless accompanied by clinical features suggestive of a syndromic aetiology or inherited metabolic disease.

Pathogenic Copy Number Variations Involved in the Genetic Etiology of Syndromic and Non-Syndromic Intellectual Disability-Data from a Romanian Cohort

The investigation of unexplained global developmental delay (GDD)/intellectual disability (ID) is challenging. In low resource settings, patients may not follow a standardized diagnostic process that makes use of the benefits of advanced technologies. Our study aims to explore the contribution of chromosome microarray analysis (CMA) in identifying the genetic etiology of GDD/ID. A total of 371 Romanian patients with syndromic or non-syndromic GDD/ID, without epilepsy, were routinely evaluated in tertiary clinics. A total of 234 males (63.07%) and 137 (36.93%) females, with ages ranging from 6 months to 40 years (median age of 5.5 years), were referred for genetic diagnosis between 2015 and 2022; testing options included CMA and/or karyotyping. Agilent Technologies and Oxford Gene Technology CMA workflows were used. Pathogenic/likely pathogenic copy number variations (pCNVs) were identified in 79 patients (21.29%). Diagnosis yield was comparable between mild ID (17.05%, 22/129) and moderate/severe ID 23.55% (57/242). Higher rates were found in cases where facial dysmorphism (22.97%, 71/309), autism spectrum disorder (ASD) (19.11%, 26/136) and finger anomalies (20%, 27/96) were associated with GDD/ID. GDD/ID plus multiple congenital anomalies (MCA) account for the highest detection rates at 27.42% (17/62). pCNVs represent a significant proportion of the genetic causes of GDD/ID. Our study confirms the utility of CMA in assessing GDD/ID with an uncertain etiology, especially in patients with associated comorbidities.

Children, Adolescents, and Young Adults with Borderline Intellectual Functioning: Etiological, Neurophysiological, and Mri Findings in a Cohort of 651 Patients

This retrospective chart review study explored the etiology, use, and yield of the etiological investigations of 651 children and adolescents diagnosed with borderline intellectual functioning (BIF). Neurological, neurodevelopmental, or neuropsychiatric comorbidities were frequent, and in 23%, the BIF diagnosis evolved into an intellectual disability (ID) by the time of discharge. A primary etiological cause was found in 37.6%, the most prevalent causes being pre- or perinatal conditions, genetic syndromes/chromosomal abnormalities, fetal exposure to maternal substance use, cerebral dysgenesis, and neurological diseases. In total, 79.1% of patients went through one or more investigations during their follow-up. The best etiologic yield leading to a diagnosis in this study population was with exome sequencing, a specific gene panel, microarrays, electroneuromyography, and brain magnetic resonance imaging (MRI). Etiological investigations were performed more frequently among those children receiving an ID diagnosis. Yet, there was no statistically significant difference in the proportion of abnormal findings between the BIF and ID groups. This may mean that the current strategy for determining the need for etiological investigations or current means to gain an etiology is still indecisive. Considering that BIF is defined to include individuals performing between normal cognitive functioning and mild ID, this implies that the prevalence would be anywhere between 7 and 14%. Thus, it could be argued whether in-depth etiological investigations may be justified in cases other than ID in this age group of children over five. With these children and adolescents, the clinicians have to discern between those with a normal variation and those having major difficulties in adaptive behavior affecting everyday life in order to specify and prescribe the rehabilitation or other measures needed. We advocate for a targeted etiological search after careful history-taking and neurological examination. National guidelines that take into account the severity of developmental delay are warranted.

Reduced resource utilization with early use of next-generation sequencing in rare genetic diseases in an Asian cohort

Children with genetic diseases endure a prolonged and costly "diagnostic odyssey." The use of whole exome sequencing (WES) and whole genome sequencing (WGS) has improved the diagnosis rate, ending the odyssey. However, the additional costs associated WES/WGS has impeded their adoption in Asian settings. We aim to estimate the expected change to the mean number of diagnostic tests used, and the associated costs from a decision to use WES early in the diagnostic pathways of pediatric phenotypes, as compared to Existing Practice. Retrospective data from a patient cohort recruited under the Singapore Undiagnosed Disease Program from a tertiary hospital in Singapore, for the period October 2004 to September 2020, was analyzed. Four phenotype-specific subgroups were used: multiple congenital anomalies (MCA) without developmental delay; global developmental delay (GDD); neuromuscular disorder (NMD) and primary immunodeficiency disorder (PID). Patients had undergone a traditional diagnostic pathway and received a diagnosis either through clinical exome or WES or WGS. A costs only analysis was performed, by tabulating the outcomes "test quantity" and "test costs" incurred by patients. The outcomes were compared with alternate diagnostic pathways which incorporates the early introduction of WES trio testing. To include uncertainty in cost outcomes, simulation studies were done on uncertain parameters. Cost outcomes are reported in Singapore dollars (S$). The 92 included patients had MCA (n = 48), GDD (n = 29), NMD (n = 10), or PID (n = 5). Patients were aged between 18 days and 26 years, 52.2% were males. The majority were of Chinese ethnicity (81.5%). If patients had access to WES directly, test quantity reduced by 97.38% for MCA, 96.98% for GDD, 96.56% for NMD, and 99.84% for PID. The expected cost savings per patient were $5940 for MCA (US$4433), $5342 for GDD (US$3986), $4622 for NMD (US$3449), and $58,497 for PID (US$43,654). Uncertainty assessment for MCA and GDD patients showed a respective likelihood of 86.9% and 97.4% for cost savings. Adoption of alternate diagnostic pathways with early WES in selected pediatric subgroups are likelt to reduce costs, when compared to Existing Practice. Benefits arising from earlier diagnosis, and the potential cost savings could mitigate the large initial cost of implementing WES in Asian settings.

Whole exome sequencing based identification of a case of cardiofaciocutaneous syndrome type 3: the benefits of new sequencing technology in children with neurodevelopmental delay

We report the case of a boy with a prolonged diagnostic workup for global developmental delay alongside feeding difficulties, failure to thrive, pulmonary stenosis and macrocephaly. Following a series of diagnostic tests over the first 25 months of life, whole-exome sequencing was performed which diagnosed cardiofaciocutaenous syndrome type 3.Global developmental delay is a common presentation to general paediatric and community paediatric clinics. This prompts the search for an aetiology to describe the child's constellation of symptoms which often consists of a chromosomal microarray, neuroimaging and investigations for an inborn error of metabolism. With developments in genetic testing such as the reducing cost of clinical exome sequencing or whole-exome sequencing, could these testing strategies offer a more comprehensive first line test?This case not only demonstrates the features of cardiofaciocutaneous syndrome type 3 but the added value of modern genetic technologies in the diagnosis of children with global developmental delay.

Prepubertal onset of type 2 diabetes in Shashi-Pena syndrome due to ASXL2 mutation

Type 2 diabetes remains rare in the pediatric population and the majority of cases occur during puberty. A combination of genetic and environmental factors leads to the development of insulin resistance and β-cell failure. An increased prevalence is recognized in a number of rare genetic disorders such as Alström and Bardet-Biedl syndromes. Recently, a rare neurodevelopmental disorder, Shashi-Pena syndrome due to the dominant negative effect of heterozygous mutations in additional Sex-Combs-Like Genes 2 (ASXL2) has been reported. ASXL2 null mice exhibit glucose intolerance, insulin resistance and lipodystrophy. The regulatory role of ASXL2 in glucose and lipid homeostasis occurs through its interaction with peroxisome proliferator-activated receptor gamma (PPARγ), a gene implicated in the pathogenesis of type 2 diabetes on genome-wide association studies. Thiazolidinediones, used for the treatment of type 2 diabetes, exert their effects as direct agonists of PPARγ. We report the first case of type 2 diabetes in Shashi-Pena syndrome, occurring in an 8-year-old prepubertal boy with no family history. In addition, the proband had dyslipidemia, and fatty infiltration of the liver with elevated transaminases. Mutation of ASXL2 in humans, through its interaction with PPARγ appears to cause a phenotype of insulin resistance, type 2 diabetes, and dyslipidemia. Further reported cases will assist in confirming this association.

How paediatricians investigate early developmental impairment in the UK: a qualitative descriptive study

Background

Early developmental impairment (EDI) is common and has many aetiologies and, therefore, potential investigations. There are several published guidelines recommending aetiological investigations, and paediatricians’ views of them varies. Little is known on the thought processes underlying clinical decisions in investigating EDI. This study aimed to describe the thought processes affecting clinical decisions on the investigation of EDI within a nationalised health care system.

Methods

A qualitative descriptive study using semi-structured qualitative interviews performed in person or via video link with paediatricians who see children with EDI in England. As part of the interview, a case study of a fictional disease, Cavorite deficiency, modelled on biotinidase deficiency, was given to participants with the cost of testing, incidence and likelihood it would respond to treatment. This allowed exploration of cost without encumbrance from predisposing views and training on the condition. Thematic analysis was performed by iterative approach. Where participants stated they wanted to redirect money from investigations to treatment, were that even possible, we asked which services they would like to be better funded in their area.

Results

Interviews were conducted with 14 consultant paediatricians: 9 Community / Neurodisability, 2 General paediatricians, and 3 Paediatric Neurologists. Two themes were identified: the value of an aetiological diagnosis to families and managing risk and probability when investigating EDI. The latter contained 4 subthemes: ‘circumspection’ involved blanket investigations chosen irrespective of phenotype and high regard for guidelines; ‘accepting appropriate risk’ involved participants choosing investigations based on clinical phenotype, recognising some aetiologies would be missed; consultants found they ‘transitioned between practices’ during their career; and ‘improved practice’ was thought possible with better evidence on how to stratify investigations based on phenotype. Services that were most frequently reported to need additional funding were therapy services, early community developmental services, management of behaviour, sleep and mental health, and educational support.

Conclusions

There are many factors that influence paediatricians’ choice of aetiological investigation in EDI, but clinical factors are the most important. Paediatricians want better evidence to allow them to select the right investigations for each child without a significant risk of missing an important diagnosis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-022-03233-1.

Urine Organic Acids as Metabolic Indicators for Global Developmental Delay/Intellectual Disability in Chinese Children

Objective: The purpose of this study was to search for differential metabolites in urine organic acids, and to characterize metabolic features that can be used to identify metabolites for exploration of global developmental delay (GDD)/intellectual disability (ID) etiology and pathogenesis. Methods: We screened positive test results that could explain GDD/ID from 1,253 cases, and the major differential metabolites in 132 urine organic acids from the 1,230 cases with negative results (863 GDD cases, 367 ID cases), and 100 typically developing children (TD). Non-supervisory principal component analysis and orthogonal partial least squares discriminant analysis were used to develop models to distinguish GDD/ID from TD children, and to detect major differential metabolites. Results: We get 23 positive results that could identify the cause of GDD/ID from 1253 cases diagnosed with GDD/ID. Among 1,230 negative results, we get the differential metabolites of the GDD group and the ID group had the same trend compared with the TD group. Twenty four differential metabolites were obtained from the GDD group, and 25 from the ID group (VIP > 1.0, p < 0.01). These differential metabolites were mainly related to the following pathways: the synthesis and degradation of ketone bodies, citrate cycle, alanine, aspartate and glutamate metabolism, pyrimidine metabolism, butanoate metabolism, pyruvate metabolism, fatty acid biosynthesis, valine, leucine and isoleucine degradation. Conclusion: The use of metabolomics research methods to detect urine organic acids of children with GDD/ID can discover differential metabolites, which might be valuable for future research on the etiology, pathogenesis, prognosis and possible interventions of GDD/ID. The significantly altered differential metabolites indicators could therefore be potential diagnostic biomarkers for GDD/ID.

Genetic and metabolic investigations for individuals with neurodevelopmental disorders: A survey of Canadian geneticists' practices

Neurodevelopmental disorders (NDDs) are genetically heterogeneous. There are many possible etiological investigations for NDDs, and a lack of clear and current guidelines for such testing. Here we characterize the practices of genetic and metabolic physicians in Canada as it pertains to etiological investigation of patients with NDDs, by means of an online questionnaire. The survey response rate was 30% (n = 46). The most commonly ordered first-line tests for patients with non-syndromic NDDs are chromosomal microarray (98%) and Fragile X testing (85%). The most commonly ordered second-line test for non-syndromic NDDs is a multi-gene panel (78%) or exome sequencing (29%). Biochemical screening is ordered as a first line test by 33% of respondents, second line by 31%, and rarely or never by 36% of respondents. Those respondents with metabolics fellowship training were more likely to order biochemical screening than those without. The number of years of clinical experience generally did not affect the types of tests ordered. For patients with NDDs, test-ordering practice among Canadian clinical geneticists is highly variable, in particular with respect to biochemical screening and use of next-generation sequencing technologies. Evidence-based guidelines should be developed to facilitate best practices in Canada.

Genetic tests by next-generation sequencing in children with developmental delay and/or intellectual disability

Developments in next-generation sequencing (NGS) techogies have assisted in clarifying the diagnosis and treatment of developmental delay/intellectual disability (DD/ID) via molecular genetic testing. Advances in DNA sequencing technology have not only allowed the evolution of targeted panels but also, and more currently enabled genome-wide analyses to progress from research era to clinical practice. Broad acceptance of accuracy- guided targeted gene panel, whole-exome sequencing (WES), and whole-genome sequencing (WGS) for DD/ID need prospective analyses of the increasing cost-effectiveness versus conventional genetic testing. Choosing the appropriate sequencing method requires individual planning. Data are required to guide best-practice recommendations for genomic testing, regarding various clinical phenotypes in an etiologic approach. Targeted panel testing may be recommended as a first-tier testing approach for children with DD/ID. Family-based trio testing by WES/WGS can be used as a second test for DD/ ID in undiagnosed children who previously tested negative on a targeted panel. The role of NGS in molecular diagnostics, treatment, prediction of prognosis will continue to increase further in the coming years. Given the rapid pace of changes in the past 10 years, all medical providers should be aware of the changes in the transformative genetics field.

Inborn Errors of Metabolism in Children with Unexplained Developmental Delay in Misan, Iraq

Objectives

We sought to determine the prevalence of inborn errors of metabolism (IEM) in children with unexplained developmental delay and their types.

Methods

We conducted a cross-sectional study in Misan, Iraq, over a period of one year. A total of 112 infants with unexplained developmental delay were included in the study, and the required information was taken from their parents by direct interview. Tandem mass spectrometry (MS/MS) was done in collaboration with MedLabs’ Referral Laboratory in Amman, Jordan.

Results

Twenty (17.9%) cases had abnormal MS/MS. Disorders of amino acid metabolism represented the majority of IEM (10 cases) in which phenylketonuria and maple syrup urine disease were the most common (found in five cases each). Organic and fatty acid metabolisms were found in five and two cases, respectively. Most cases of IEM had a positive family history and consanguinity, however, family history was the only significant factor (p < 0.001).

Conclusions

A high rate of IEM was detected in children with unexplained developmental delay in Misan. A high clinical suspicion with positive family history and consanguinity supported by the MS/MS results played an essential role in the diagnosis. However, implementation of newborn screening is essential for early diagnosis and to determine appropriate therapy in newborns with IEM in Iraq generally and in Misan in particular.

Current evidence-based recommendations on investigating children with global developmental delay

INTRODUCTION

Global developmental delay (GDD) affects 1%-3% of the population of children under 5 years of age, making it one of the most common conditions presenting in paediatric clinics; causes are exogenous, genetic (non-metabolic) or genetic (metabolic). Recent advances in biotechnology and genetic testing mean that the investigations available to perform for children under 5 years are increasing and are more sensitive than previously. This change in availability and type of testing necessitates an update in the recommendations for investigating GDD.

METHODS

We conducted a review of the literature from 2006 to 2016 to identify articles with evidence relating to the investigation of developmental delay in children under the age of 5 years. We collated the evidence into first-line and second-line investigations and, where available, on their yield and cost implications.

RESULTS

We have provided up-to-date guidance for first-line and second-line investigations for children with GDD under the age of 5 years. Recent evidence demonstrates that genetic testing for all children with unexplained GDD should be first line, if an exogenous cause is not already established. Our review of the literature demonstrates that all patients, irrespective of severity of GDD, should have investigations for treatable conditions. Evidence demonstrates that the yield for treatable conditions is higher than previously thought and that investigations for these metabolic conditions should be considered as first line. Additional second-line investigations can be led by history, examination and developmental trajectories.

DISCUSSION

We may need to update present recommendations in the UK for investigation of developmental delay. This would include microarray testing as first line and a more thorough approach to investigations for metabolic disorders that can be treated. Clinical assessment remains vital for guiding investigations.

Genetics of Schizophrenia: Ready to Translate?

PURPOSE OF REVIEW

This is an era where we have significantly advanced the understanding of the genetic architecture of schizophrenia. In this review, we consider how this knowledge may translate into advances that will improve patient care.

RECENT FINDINGS

Large-scale genome-wide association studies (GWAS) have identified more than a hundred loci each making a small contribution to illness risk. Meta-analysis of copy number variants (CNVs) in the Psychiatric Genomics Consortium (PGC) dataset has confirmed that some variants have a moderate or large impact on risk, although these are rare in the population. Genome sequencing advances allow a much more comprehensive evaluation of genomic variation. We describe the key findings from whole exome studies to date. These studies are happening against a backdrop of growing understanding of the regulation and expression of genes and better functional tools to investigate molecular mechanisms in model systems. We provide an overview of how recent approaches in schizophrenia genetics are converging and consider how they could impact on diagnostics, the development of personalized medicine, and drug discovery.

Incidence of Fragile X syndrome in Ireland

Described as the commonest single gene cause of learning disability internationally, the incidence of Fragile X syndrome (FXS) has never previously been determined in Ireland. The aim of this work was to determine the observed incidence of FXS in the island of Ireland; the Republic of Ireland (ROI) and Northern Ireland (NI) separately and combined. Ascertainment was achieved for a cross-sectional study by a retrospective, clinical and laboratory database review of positive FXS cases, born in either ROI or NI, between years 2000-2009 inclusive. The observed incidence of FXS per 10,000 live births in the island of Ireland in males was 0.94 (95%CI: 0.75-1.13) or ∼1:10,600 and in females was 0.23 (95%CI: 0.14-0.32) or ∼1:43,000. Comparable testing rates for FXS are present in ROI and NI, with on average 1.48% (1.30% in ROI, 1.96% in NI) of live male births and 0.4% (0.35% in ROI, 0.55% in NI) of live female births undergoing analysis which is comparable to other centres internationally. This study demonstrates the observed incidence of FXS in the island of Ireland is (i) approximately half the estimated worldwide incidence in males and is not explained by low levels of testing, and (ii) approximately one quarter the estimated worldwide incidence in females which may be explained by low levels of testing. © 2017 Wiley Periodicals, Inc.