Yield of additional metabolic studies in neurodevelopmental disorders

Diagnostic yield from routine metabolic screening tests in evaluation of global developmental delay and intellectual disability

Global developmental delay and intellectual disability (GDD/ID) affect 3% of the paediatric population. Although inborn errors of metabolism (IEM) are not a common cause of GDD/ID, early therapeutic intervention can improve neurodevelopmental manifestations. In 2012, a first-tier test panel, including specialized metabolic and routine chemistry tests, was piloted to community-based paediatricians in British Columbia with aims to achieve earlier diagnosis of treatable IEM.

Objective

The aim of this retrospective review was to evaluate the diagnostic yield from these first-tier tests in the 7 years before (2006 to 2012) and after (2013 to 2019) implementation at the community paediatrician level.

Results

Prior and postimplementation diagnostic yield of an IEM from first-tier metabolic testing was 9 out of 986 (0.91%) and 11 out of 4,345 children (0.25%), respectively. Disorders of creatine metabolism and organic acidurias were the most frequently established diagnoses in both time periods. No diagnoses were established through acylcarnitine copper/ceruloplasmin, lactate, or ammonia testing. Twenty out of 24 patients had specific neurological or other red flag signs in addition to GDD/ID. Four boys diagnosed with an x-linked creatine transporter defect (CTD) had speech-language delay as the most prominent finding.

Conclusions

The expansion of first-tier metabolic testing to community-based paediatricians in BC did not yield an increase in IEM diagnoses. A modified first-tier test panel should be offered to patients with GDD/ID, neurologic, and/or red flag signs. Urine creatine testing in boys with speech-language delay warrants consideration to detect CTD.

Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance

Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.

The diagnosis of inborn errors of metabolism in previously undiagnosed adults referred for medical genetics evaluation

Traditionally thought of as a pediatric diagnostic and therapeutic dilemma, the diagnostic rate and spectrum of inborn errors of metabolism (IEM) in the adult population is largely unknown. A retrospective chart review of patients seen by the Michigan Medicine Adult Medical Genetics Clinic for clinical evaluation from 2014 to 2018 was conducted. Patients referred for a primary indication possibly consistent with an IEM were considered. Variables included age at genetic evaluation, symptom onset age, sex, clinical course, organ systems involved, developmental history, family history and prior genetic testing. Of patients evaluated during the study period, 112 were referred for an indication possibly consistent with an IEM and underwent a complete biochemical workup with an IEM diagnostic rate of 9.8% achieved. An additional 9.8% were diagnosed with a non-IEM genetic diagnosis. Management changes were implemented in all IEM diagnoses. Metabolic disorders in the adult population are under-recognized and under-diagnosed. This report demonstrates the need for clinicians to consider these diagnoses in adults and either refer to a genetics clinic or initiate a biochemical workup. As advances in diagnosis, treatment, and life expectancy of patients with IEMs increases, recognizing and diagnosing these conditions can significantly impact care.

Clinical Validation of Targeted and Untargeted Metabolomics Testing for Genetic Disorders: A 3 Year Comparative Study

Global untargeted metabolomics (GUM) has entered clinical diagnostics for genetic disorders. We compared the clinical utility of GUM with traditional targeted metabolomics (TM) as a screening tool in patients with established genetic disorders and determined the scope of GUM as a discovery tool in patients with no diagnosis under investigation. We compared TM and GUM data in 226 patients. The first cohort (n = 87) included patients with confirmed inborn errors of metabolism (IEM) and genetic syndromes; the second cohort (n = 139) included patients without diagnosis who were undergoing evaluation for a genetic disorder. In patients with known disorders (n = 87), GUM performed with a sensitivity of 86% (95% CI: 78–91) compared with TM for the detection of 51 diagnostic metabolites. The diagnostic yield of GUM in patients under evaluation with no established diagnosis (n = 139) was 0.7%. GUM successfully detected the majority of diagnostic compounds associated with known IEMs. The diagnostic yield of both targeted and untargeted metabolomics studies is low when assessing patients with non-specific, neurological phenotypes. GUM shows promise as a validation tool for variants of unknown significance in candidate genes in patients with non-specific phenotypes.

Diagnostic contribution of metabolic workup for neonatal inherited metabolic disorders in the absence of expanded newborn screening

Inherited metabolic disorders (IMDs) in neonates are a diagnostic and therapeutic challenge for the neonatologist, with the priority being to rapidly flag the treatable diseases. The objective of this study was to evaluate the contribution of targeted metabolic testing for diagnosing suspected IMDs on the basis of suggestive clinical setting or family history in neonates. We conducted an observational study over five years, from January 1st, 2010 to December 31, 2014 in the neonatal intensive care unit (NICU) at Robert Debré University Hospital, Paris, France. We assessed the number of neonates for whom a metabolic testing was performed, the indication for each metabolic test and the diagnostic yield of this selected metabolic workup for diagnosing an IMD. Metabolic testing comprised at least one of the following testings: plasma, urine or cerebrospinal fluid amino acids, urine organic acids, plasma acylcarnitine profile, and urine mucopolysaccharides and oligosaccharides. 11,301 neonates were admitted at the neonatal ICU during the study period. One hundred and ninety six neonates underwent metabolic testing. Eleven cases of IMDs were diagnosed. This diagnostic approach allowed the diagnosis, treatment and survival of 4 neonates (maple syrup urine disease, propionic acidemia, carnitine-acylcarnitine translocase deficiency and type 1 tyrosinemia). In total, metabolic testing was performed for 1.7% of the total number of neonates admitted in the NICU over the study period. These included 23% finally unaffected neonates with transient abnormalities, 5.6% neonates suffering from an identified IMD, 45.4% neonates suffering from a non-metabolic identified disease and 26% neonates with chronic abnormalities but for whom no final causal diagnosis could be made. In conclusion, as expected, such a metabolic targeted workup allowed the diagnosis of classical neonatal onset IMDs in symptomatic newborns. However, this workup remained normal or unspecific for 94.4% of the tested patients. It allowed excluding an IMD in 68.4% of the tested neonates. In spite of the high rate of normal results, such a strategy seems acceptable due to the severity of the symptoms and the need for immediate treatment when available in neonatal IMDs. However, its cost-effectiveness remains low especially in a clinically targeted population in a country where newborn screening is still unavailable for IMDs except for phenylketonuria in 2019.

Failure to shorten the diagnostic delay in two ultra-orphan diseases (mucopolysaccharidosis types I and III): potential causes and implications

Background

Rare diseases are often un- or misdiagnosed for extended periods, resulting in a long diagnostic delay that may significantly add to the burden of the disease. An early diagnosis is particularly essential if a disease-modifying treatment is available. The purpose of this study was to assess the extent of the diagnostic delay in the two ultra-rare diseases, i.e., mucopolysaccharidosis I (MPS I) and III (MPS III), both of which are lysosomal storage disorders with different phenotypic severities (MPS 1 is characterized by the severe Hurler and the more attenuated non-Hurler phenotypes, MPS III is characterized by the severe rapidly progressing (RP) phenotype and more attenuated slowly progressing (SP) phenotype). We investigated whether the diagnostic delay changed over the previous decades.

Results

The diagnostic delay, which is defined as the time between the first visit to a medical doctor for disease-related symptoms and the final diagnosis, was assessed using telephone interviews with patients diagnosed between 1988 and 2017 and/or their parents or legal guardian(s). In addition, the medical charts were reviewed. For MPS I (n = 29), the median diagnostic delay was 8 months (range 1-24 months) for Hurler patients and 28 months (range 2-147 months) for non-Hurler patients. For MPS III (n = 46), the median diagnostic delay was 33 months (range 1-365 months). No difference was observed between the RP and SP phenotypic groups. Comparing the diagnostic delay over time using 5-year time intervals, no reduction in the diagnostic delay was observed for MPS I or MPS III.

Conclusions

In the Netherlands, the time to diagnosis for patients with MPS I and MPS III has not changed between 1988 and 2017, and an extensive delay still exists between the first visit to a medical doctor for disease-related symptoms and the final diagnosis. The numerous campaigns launched to increase awareness, leading to earlier diagnosis of these rare disorders, particularly of MPS I, have failed to achieve their goal. Robust selected screening protocols embedded in national guidelines and newborn screening for disorders that meet the criteria for population screening may be the only effective approaches for reducing the diagnostic delay.

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.

Genetic Approach to Diagnosis of Intellectual Disability

Intellectual disability is a non-specific phenotype present in a genetically heterogeneous group of disorders. It is characterized by deficits in intellectual and adaptive functioning, presenting before 18 y of age. Identifying the cause of ID is important to provide treatment where available, genetic counseling, recurrence risks and reproductive options for subsequent pregnancies. Advances in technology, especially next generation sequencing and microarrays, have greatly increased the diagnostic yield of evaluation in cases of ID. This paper describes the points in history taking and examination in the evaluation of a proband, and discusses the proper use of newer diagnostic technologies.

Metabolic evaluation of children with global developmental delay

Global developmental delay (GDD) is a relatively common early-onset chronic neurological condition, which may have prenatal, perinatal, postnatal, or undetermined causes. Family history, physical and neurological examinations, and detailed history of environmental risk factors might suggest a specific disease. However, diagnostic laboratory tests, brain imaging, and other evidence-based evaluations are necessary in most cases to elucidate the causes. Diagnosis of GDD has recently improved because of remarkable advances in genetic technology, but this is an exhaustive and expensive evaluation that may not lead to therapeutic benefits in the majority of GDD patients. Inborn metabolic errors are one of the main targets for the treatment of GDD, although only a small proportion of GDD patients have this type of error. Nevertheless, diagnosis is often challenging because the phenotypes of many genetic or metabolic diseases often overlap, and their clinical spectra are much broader than currently known. Appropriate and cost-effective strategies including up-to-date information for the early identification of the "treatable" causes of GDD are needed for the development of well-timed therapeutic applications with the potential to improve neurodevelopmental outcomes.

Diagnostic Value of a Multidisciplinary Clinic for Intellectual Disability

Background:

Identification of the underlying cause of intellectual disability (ID) is important as it improves genetic counselling, management, adaptation; yet its etiologic heterogeneity is challenging and often leads to an expensive work-up.

Methods:

To improve this diagnostic trajectory, the multidisciplinary Complex Diagnostic Clinic (CDC) was established for ID patients with unexplained complex systemic and/or neurologic features that were referred to the CDC and evaluated by three medical specialists followed by multi-disciplinary rounds. Analyses included surveys and interviews, (retrospective) chart review, costs calculations and comparison.

Results:

24 children (9 male) were evaluated during seven clinics held over 16 months. The average patient age was 7 years 11 months (range 9 months-18 years). All the children had previously been seen by 2–10 specialist services. The diagnostic yield of the CDC was higher than expected with confirmed and working diagnoses in 11 (46%) and 9 (38%) children respectively. Cost-savings included fewer trips to hospital and fewer tests via more streamlined evaluations. Positive feedback was received from both families and medical professionals.

Conclusions:

The CDC represents an innovative model of personalized care. Specialist collaboration in the interpretation of relevant clinical, biochemical and genomic data resulted in diagnoses, where none had previously been possible.

Comprehensive evaluation of the child with intellectual disability or global developmental delays

Global developmental delay and intellectual disability are relatively common pediatric conditions. This report describes the recommended clinical genetics diagnostic approach. The report is based on a review of published reports, most consisting of medium to large case series of diagnostic tests used, and the proportion of those that led to a diagnosis in such patients. Chromosome microarray is designated as a first-line test and replaces the standard karyotype and fluorescent in situ hybridization subtelomere tests for the child with intellectual disability of unknown etiology. Fragile X testing remains an important first-line test. The importance of considering testing for inborn errors of metabolism in this population is supported by a recent systematic review of the literature and several case series recently published. The role of brain MRI remains important in certain patients. There is also a discussion of the emerging literature on the use of whole-exome sequencing as a diagnostic test in this population. Finally, the importance of intentional comanagement among families, the medical home, and the clinical genetics specialty clinic is discussed.

The metabolic evaluation of the child with an intellectual developmental disorder: diagnostic algorithm for identification of treatable causes and new digital resource

Intellectual developmental disorders (IDD), characterized by significant impairment of cognitive functions, with limitations of learning, adaptive behavior and skills, are frequent (2.5% of the population affected) and present with significant co-morbidity. The burden of IDD, in terms of emotional suffering and associated health care costs, is significant; prevention and treatment therefore are important. A systematic literature review, updated in 2013, identified 89 inborn errors of metabolism (IEMs), which present with IDD as prominent feature and are amenable to causal therapy. Therapeutic effects include improvement and/or stabilization of psychomotor/cognitive development, behavior/psychiatric disturbances, seizures, neurologic and systemic manifestations. The levels of available evidence for the various treatments range from Level 1b, c (n=5); Level 2a, b, c (n=14); Level 4 (n=53), and Levels 4-5 (n=27). For a target audience comprising clinical and biochemical geneticists, child neurologists and developmental pediatricians, five experts translated....this data into a 2-tiered diagnostic algorithm: The first tier comprises metabolic "screening" tests in urine and blood, which are relatively accessible, affordable, less invasive, and have the potential to identify 60% of all treatable IEMs. The second tier investigations for the remaining disorders are ordered based on individual clinical signs and symptoms. This algorithm is supported by an App www.treatable-id.org, which comprises up-to-date information on all 89 IEMs, relevant diagnostic tests, therapies and a search function based on signs and symptoms. These recommendations support the clinician in early identification of treatable IEMs in the child with IDD, allowing for timely initiation of therapy with the potential to improve neurodevelopmental outcomes. The need for future studies to determine yield and usefulness of these recommendations, with subsequent updates and improvements to developments in the field, is outlined.

The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders

PURPOSE

The purpose of this study was to assess the diagnostic yield of the traditional, comprehensive clinical evaluation and targeted genetic testing, within a general genetics clinic. These data are critically needed to develop clinically and economically grounded diagnostic algorithms that consider presenting phenotype, traditional genetics testing, and the emerging role of next-generation sequencing (whole-exome/genome sequencing).

METHODS

We retrospectively analyzed a cohort of 500 unselected consecutive patients who received traditional genetic diagnostic evaluations at a tertiary medical center. We calculated the diagnosis rate, number of visits to diagnosis, genetic tests, and the cost of testing.

RESULTS

Thirty-nine patients were determined to not have a genetic disorder; 212 of the remaining 461 (46%) received a genetic diagnosis, and 72% of these were diagnosed on the first visit. The cost per subsequent successful genetic diagnosis was estimated at $25,000.

CONCLUSION

Almost half of the patients were diagnosed using the traditional approach, most at the initial visit. For those remaining undiagnosed, next-generation sequencing may be clinically and economically beneficial. Estimating a 50% success rate for next-generation sequencing in undiagnosed genetic disorders, its application after the first clinical visit could result in a higher rate of genetic diagnosis at a considerable cost savings per successful diagnosis.

Treatable inborn errors of metabolism causing intellectual disability: a systematic literature review

BACKGROUND

Intellectual disability ('developmental delay' at age<5 years) affects 2.5% of population worldwide. Recommendations to investigate genetic causes of intellectual disability are based on frequencies of single conditions and on the yield of diagnostic methods, rather than availability of causal therapy. Inborn errors of metabolism constitute a subgroup of rare genetic conditions for which an increasing number of treatments has become available. To identify all currently treatable inborn errors of metabolism presenting with predominantly intellectual disability, we performed a systematic literature review.

METHODS

We applied Cochrane Collaboration guidelines in formulation of PICO and definitions, and searched in Pubmed (1960-2011) and relevant (online) textbooks to identify 'all inborn errors of metabolism presenting with intellectual disability as major feature'. We assessed levels of evidence of treatments and characterised the effect of treatments on IQ/development and related outcomes.

RESULTS

We identified a total of 81 'treatable inborn errors of metabolism' presenting with intellectual disability as a major feature, including disorders of amino acids (n=12), cholesterol and bile acid (n=2), creatine (n=3), fatty aldehydes (n=1); glucose homeostasis and transport (n=2); hyperhomocysteinemia (n=7); lysosomes (n=12), metals (n=3), mitochondria (n=2), neurotransmission (n=7); organic acids (n=19), peroxisomes (n=1), pyrimidines (n=2), urea cycle (n=7), and vitamins/co-factors (n=8). 62% (n=50) of all disorders are identified by metabolic screening tests in blood (plasma amino acids, homocysteine) and urine (creatine metabolites, glycosaminoglycans, oligosaccharides, organic acids, pyrimidines). For the remaining disorders (n=31) a 'single test per single disease' approach including primary molecular analysis is required. Therapeutic modalities include: sick-day management, diet, co-factor/vitamin supplements, substrate inhibition, stemcell transplant, gene therapy. Therapeutic effects include improvement and/or stabilisation of psychomotor/cognitive development, behaviour/psychiatric disturbances, seizures, neurologic and systemic manifestations. The levels of available evidence for the various treatments range from Level 1b,c (n=5); Level 2a,b,c (n=14); Level 4 (n=45), Level 4-5 (n=27). In clinical practice more than 60% of treatments with evidence level 4-5 is internationally accepted as 'standard of care'.

CONCLUSION

This literature review generated the evidence to prioritise treatability in the diagnostic evaluation of intellectual disability. Our results were translated into digital information tools for the clinician (www.treatable-id.org), which are part of a diagnostic protocol, currently implemented for evaluation of effectiveness in our institution. Treatments for these disorders are relatively accessible, affordable and with acceptable side-effects. Evidence for the majority of the therapies is limited however; international collaborations, patient registries, and novel trial methodologies are key in turning the tide for rare diseases such as these.

Medical comorbidities in autism: challenges to diagnosis and treatment

Ever since its original description by Leo Kanner in l943, autism has been generally defined by its clinical characteristics and core symptoms that include impaired social skills, isolated areas of interest, and delayed and disordered language. Over time, it has become apparent that autism is a heterogeneous disorder with regard to its clinical presentation, etiology, underlying neurobiology, and degree of severity. As a result, the termed diagnosis of autism spectrum disorders (ASDs) has come into common usage. With advancements in clinical care, there has come the appreciation that many ASD children, adolescents, and adults may have medically relevant disorders that may negatively impact their developmental progress and behavior, but which frequently go undetected. Many of these medical conditions are treatable, often resulting in improved developmental gains and quality of life for the patient and family. In addition, the possibility exists that some of these medical conditions may suggest the presence of important genetic and/or biologic markers, which, if identified, can refine our ability to be more precise in categorizing clinical and genetic subtypes within the autism spectrum.