State of the Art of Genetic Testing for Patients With Autism: A Practical Guide for Clinicians

2023 clinical practice guidelines on autism spectrum disorder in children and adolescents in Singapore

Introduction

Autism is a neurodevelopmental condition that is increasing in prevalence worldwide. There has been an exponential increase in autism-related research since 2010, when the first Singapore Clinical Practice Guidelines (CPG) on autism was published. Understanding of autism has since evolved to adopt a lifespan approach beyond that of a childhood condition. The aim of this CPG was to provide an updated set of recommendations for children and adolescents to aid clinical practice for professionals.

Method

A multidisciplinary workgroup that comprised representatives from various sectors worked on this CPG. Clinical questions were organised into 10 different sections, each with its own subgroup of members. Seventeen existing international guidelines were evaluated using the Appraisal of Guidelines for REsearch & Evaluation II (AGREE-II) framework, of which 4 met criteria to act as references. Literature review across multiple databases was conducted between January 2011 to 2023; Grading of Recommendations, Assessment, Development and Evaluation (GRADE-like) methodology was used to synthesise evidence. Recommendation statements were derived, following Delphi-style consensus surveys among the workgroup. The draft guidelines underwent external review and public consultation before being formalised.

Results

Recommendation and good practice statements pertaining to care of children and adolescents on the autism spectrum across 10 different sections were developed. Evidence matrices complement these recommendations and detail relevant evidence behind each recommendation statement.

Conclusion

It is intended for these guidelines to promote effective management and healthcare services for children and adolescents on the autism spectrum, by reinforcing good and evidence-based clinical practice within our national context.

Exploring genetic testing requests, genetic alterations and clinical associations in a cohort of children with autism spectrum disorder

Several studies show great heterogeneity in the type of genetic test requested and in the clinicopathological characteristics of patients with ASD. The following study aims, firstly, to explore the factors that might influence professionals' decisions about the appropriateness of requesting genetic testing for their patients with ASD and, secondly, to determine the prevalence of genetic alterations in a representative sample of children with a diagnosis of ASD. Methods: We studied the clinical factors associated with the request for genetic testing in a sample of 440 children with ASD and the clinical factors of present genetic alterations. Even though the main guidelines recommend genetic testing all children with an ASD diagnosis, only 56% of children with an ASD diagnosis were genetically tested. The prevalence of genetic alterations was 17.5%. These alterations were more often associated with intellectual disability and dysmorphic features. There are no objective data to explicitly justify the request for genetic testing, nor are there objective data to justify requesting one genetic study versus multiple studies. Remarkably, only 28% of males were genetically tested with the recommended tests (fragile X and CMA). Children with dysmorphic features and organic comorbidities were more likely to be genetic tested than those without. Previous diagnosis of ASD (family history of ASD) and attendance at specialist services were also associated with Genetically tested Autism Spectrum Disorder GTASD. Our findings emphasize the importance of establishing algorithms to facilitate targeted genetic consultation for individuals with ASD who are likely to benefit, considering clinical phenotypes, efficiency, ethics, and benefits.

Provider-reported experiences, barriers, and perspectives on genetic testing as part of autism diagnosis

Several professional organizations recommend conducting genetic testing as part of the autism diagnosis process, as it can provide additional information and benefits for autistic people and their families. However, there is disagreement among autism communities about whether genetic testing reflects autistic people's best interests. In practice, rates of clinical genetic testing for autism are much lower than diagnoses, creating a large gap between clinical guidelines and real clinical encounters. To investigate one potential source of this gap, we interviewed 14 healthcare providers about the autism diagnostic process and their actions related to autism genetic testing. We recruited a sample of primarily Ph.D. level-psychologists and analyzed our qualitative data using a five-step framework analysis method. Participants generally had positive or mixed views of genetic testing in autism. They described their current experiences of implementation of genetic testing, including that they did not often find it changed their clinical practice. Only some providers recommended it to everyone receiving an autism diagnosis. They also listed factors which discourage families from getting testing, including high costs, families feeling overwhelmed, other support needs taking priority, and ethical implications. Notably, providers highlighted a trend of referring patients to research genetic testing rather than clinical testing, which may provide a cheaper and easier alternative but is not likely to return results to participants. Finally, participants felt they needed more training in genetics and listed specific topics of uncertainty. Our research highlights a need to further educate clinicians in the uses and limitations of genetic testing for autism and suggests content areas of focus for genetics educators.

Reanalysis of Trio Whole-Genome Sequencing Data Doubles the Yield in Autism Spectrum Disorder: De Novo Variants Present in Half

Autism spectrum disorder (ASD) is a common condition with lifelong implications. The last decade has seen dramatic improvements in DNA sequencing and related bioinformatics and databases. We analyzed the raw DNA sequencing files on the Variantyx® bioinformatics platform for the last 50 ASD patients evaluated with trio whole-genome sequencing (trio-WGS). "Qualified" variants were defined as coding, rare, and evolutionarily conserved. Primary Diagnostic Variants (PDV), additionally, were present in genes directly linked to ASD and matched clinical correlation. A PDV was identified in 34/50 (68%) of cases, including 25 (50%) cases with heterozygous de novo and 10 (20%) with inherited variants. De novo variants in genes directly associated with ASD were far more likely to be Qualifying than non-Qualifying versus a control group of genes (p = 0.0002), validating that most are indeed disease related. Sequence reanalysis increased diagnostic yield from 28% to 68%, mostly through inclusion of de novo PDVs in genes not yet reported as ASD associated. Thirty-three subjects (66%) had treatment recommendation(s) based on DNA analyses. Our results demonstrate a high yield of trio-WGS for revealing molecular diagnoses in ASD, which is greatly enhanced by reanalyzing DNA sequencing files. In contrast to previous reports, de novo variants dominate the findings, mostly representing novel conditions. This has implications to the cause and rising prevalence of autism.

Ethical challenges in autism genomics: Recommendations for researchers

Equitable and just genetic research and clinical translation require an examination of the ethical questions pertaining to vulnerable and marginalized communities. Autism research and advocate communities have expressed concerns over current practices of genetics research, urging the field to shift towards paradigms and practices that ensure benefits and avoid harm to research participants and the wider autistic community. Building upon a framework of bioethical principles, we provide the background for the concerns and present recommendations for ethically sustainable and justice-oriented genetic and genomic autism research. With the primary goal of enhancing the health, well-being, and autonomy of autistic persons, we make recommendations to guide priority setting, responsible research conduct, and informed consent practices. Further, we discuss the ethical challenges particularly pertaining to research involving highly vulnerable individuals and groups, such as those with impaired cognitive or communication ability. Finally, we consider the clinical translation of autism genetics studies, including the use of genetic testing. These guidelines, developed by an interdisciplinary working group comprising autistic and non-autistic individuals, will aid in leveraging the potential of genetics research to enhance the quality of life of autistic individuals and are widely applicable across stigmatized traits and vulnerable communities.

Analysis of the Brazilian-Portuguese Content on Autism Spectrum Disorder Available on YouTube Videos

AIMS

Information about Autism Spectrum Disorder (ASD) is available in different videos on YouTube. However, these videos might present inaccurate or outdated information. The aims of this study were to 1) identify characteristics of Brazilian-Portuguese videos about ASD (i.e., type of content, number of views, likes, and dislikes); 2) analyze the content of informative videos about ASD, by assessing their trustworthiness and overall quality; and 3) investigate the most popular topics of informative videos about ASD over time.

METHODS

This is a cross-sectional study that investigated Brazilian-Portuguese ASD content on YouTube. Videos were selected by two examiners and categorized as experiential or informative. The Discern checklist and the Global Quality Score (GQS) were used to analyze the trustworthiness and quality of informative videos.

RESULTS

In total, 216 videos were analyzed, of which 19.5% and 85% were classified as experiential and informative, respectively. The majority of informative videos presented moderate trustworthiness and quality. Videos about ASD clinical aspects were the most popular.

CONCLUSION

YouTube offers a large number of experiential and informative videos on ASD. However, some of these videos fail to present reliable and additional sources of information for stakeholders. Efforts to promote knowledge translation about ASD on YouTube are necessary.

Synchrony 2022: Catalyzing Research and Treatments to Benefit Individuals with Neurodevelopmental Disorders including Autism Spectrum Disorders

A unique translational medicine conference for research into treatments that can benefit individuals with neurodevelopmental disorders (NDD), including autism spectrum disorder (ASD), has been developed and hosted by The BRAIN Foundation (Pleasanton, CA, USA) since 2019 [...]

Saudi Expert Consensus-Based Autism Spectrum Disorder Statement: From Screening to Management

Background: There is a large gap between the needs of individuals diagnosed with autism spectrum disorder (ASD) and the currently available services in Saudi Arabia. Services are often difficult to access, inconsistent in quality, incomplete, unsatisfactory, and costly. As such, there is a national need for expert consensus on the appropriate standards for the assessment and management of children on the autism spectrum. Methodology: A guideline development group (GDC) was formed by professionals representing all related specialties and institutions involved in the management of individuals on the autism spectrum in Saudi Arabia. They met on a regular basis over 21 months. The guideline development process consisted of five steps starting from reviewing existing guidelines and ending with discussing and writing this manuscript. A formal voting process was utilized and recommendations were discussed until a consensus was reached. Results: There was consensus on the following: A specialized diagnostic assessment needs to be carried out by an experienced multidisciplinary team for children referred to assess for ASD. They should be assessed for medical etiology, their behavioral history carefully reviewed, and symptoms directly observed. Longitudinal assessments are encouraged to reflect the effects of symptoms on the individual’s ability to function while with their family, among peers, and in school settings. An additional formal assessment of language, cognitive, and adaptive abilities as well as sensory status is essential to complete the diagnostic process. Interventions should be individualized, developmentally appropriate, and intensive, with performance data relevant to intervention goals to evaluate and adjust interventions. Target symptoms must be identified to address and develop monitoring systems to track change. Conclusion: ASD is a complex condition with widely varying clinical manifestations, thus requiring evaluation and intervention by a range of professionals working in coordination. Behavioral and environmental interventions are the key to optimal outcomes, in conjunction with medications when indicated for specific symptoms. Parental involvement in interventions is vital to sustaining therapeutic gains.

Potential Cross Talk between Autism Risk Genes and Neurovascular Molecules: A Pilot Study on Impact of Blood Brain Barrier Integrity

Autism Spectrum Disorder (ASD) is a common pediatric neurobiological disorder with up to 80% of genetic etiologies. Systems biology approaches may make it possible to test novel therapeutic strategies targeting molecular pathways to alleviate ASD symptoms. A clinical database of autism subjects was queried for individuals with a copy number variation (CNV) on microarray, Vineland, and Parent Concern Questionnaire scores. Pathway analyses of genes from pathogenic CNVs yielded 659 genes whose protein-protein interactions and mRNA expression mapped 121 genes with maximal antenatal expression in 12 brain regions. A Research Domain Criteria (RDoC)-derived neural circuits map revealed significant differences in anxiety, motor, and activities of daily living skills scores between altered CNV genes and normal microarrays subjects, involving Positive Valence (reward), Cognition (IQ), and Social Processes. Vascular signaling was identified as a biological process that may influence these neural circuits. Neuroinflammation, microglial activation, iNOS and 3-nitrotyrosine increase in the brain of Semaphorin 3F- Neuropilin 2 (Sema 3F-NRP2) KO, an ASD mouse model, agree with previous reports in the brain of ASD individuals. Signs of platelet deposition, activation, release of serotonin, and albumin leakage in ASD-relevant brain regions suggest possible blood brain barrier (BBB) deficits. Disruption of neurovascular signaling and BBB with neuroinflammation may mediate causative pathophysiology in some ASD subgroups. Although preliminary, these data demonstrate the potential for developing novel therapeutic strategies based on clinically derived data, genomics, cognitive neuroscience, and basic neuroscience methods.

Modern Biomarkers for Autism Spectrum Disorder: Future Directions

Autism spectrum disorder is an increasingly prevalent neurodevelopmental disorder in the world today, with an estimated 2% of the population being affected in the USA. A major complicating factor in diagnosing, treating, and understanding autism spectrum disorder is that defining the disorder is solely based on the observation of behavior. Thus, recent research has focused on identifying specific biological abnormalities in autism spectrum disorder that can provide clues to diagnosis and treatment. Biomarkers are an objective way to identify and measure biological abnormalities for diagnostic purposes as well as to measure changes resulting from treatment. This current opinion paper discusses the state of research of various biomarkers currently in development for autism spectrum disorder. The types of biomarkers identified include prenatal history, genetics, neurological including neuroimaging, neurophysiologic, and visual attention, metabolic including abnormalities in mitochondrial, folate, trans-methylation, and trans-sulfuration pathways, immune including autoantibodies and cytokine dysregulation, autonomic nervous system, and nutritional. Many of these biomarkers have promising preliminary evidence for prenatal and post-natal pre-symptomatic risk assessment, confirmation of diagnosis, subtyping, and treatment response. However, most biomarkers have not undergone validation studies and most studies do not investigate biomarkers with clinically relevant comparison groups. Although the field of biomarker research in autism spectrum disorder is promising, it appears that it is currently in the early stages of development.

Impact of Genetic and Genomic Testing on the Clinical Management of Patients with Autism Spectrum Disorder

Research has shown that genetics play a key role in the development of autism spectrum disorder (ASD). ASD has been linked to many genes and is a prominent feature in numerous genetic disorders. A genetic evaluation should be offered to any patient who receives a diagnosis of ASD, including deep phenotyping and genetic testing when clinically indicated. When insurance does not cover genetic testing for ASD patients, the lack of medical utility is often cited as a reason for prior authorization request denial. However, ample evidence exists that genetic testing has the power to change clinical management in many of these patients. Genetic testing that results in a diagnosis guides clinicians to screen for associated medical conditions and can direct targeted medical interventions. Given the potential for clinically actionable results, it is important that genetic testing be available and accessible to all patients with ASD.

Duration of untreated autism in rural America: emerging public health crisis

The rural areas have been at the receiving end amidst mental health disparity across the USA. There is a serious and concerning divide among ones with autism spectrum disorders (ASDs) living in underserved areas as compared to urban residents. With the higher than ever prevalence of ASD as per the recent reports of the Centers for Disease Control and Prevention; there is a need for a closer look at the prevailing issues. The trends are reflecting marked underdiagnosis, late diagnosis, lack of evidence-based diagnostic measures and interventions. These factors interplay in worsening the mental health crisis and there is an urgent need for corrective measures to address these highly modifiable problems.

Challenging Case: The Role of Genetic Testing in Complex Autism

CASE

S is a 12-year-old boy with autism spectrum disorder (ASD), seizure disorder, cerebral palsy, and intellectual disability who presented to the primary care clinician for a preventative care visit.S was born at full term after an unremarkable pregnancy. His developmental delays were first noted at around 8 months, when he could not sit independently and had intermittently poor eye contact. He was referred to Part C Early Intervention and subsequently evaluated by a neurodevelopmental pediatrician, where he was noted to be hypotonic, with delayed motor and cognitive skills. Initial genetics evaluation included karyotype, fragile X testing, Angelman and Prader-Willi DNA fluorescence in situ hybridization probes, POLG sequencing, MECP2 testing, a microarray, creatinine kinase, very long-chain fatty acids, lymphocyte arylsulfatase, urine organic acids, and plasma amino acids, all of which were normal.As time progressed, S continued to have motor and communication delays and developed choreic movements. He also developed episodes concerning for seizure, including periods of staring while awake and episodes of extremity shaking lasting a few seconds with associated eye deviation, which eventually progressed to generalized seizures. He also developed periods of lethargy. Outpatient workup included several EEGs, which were notable for foci in the right frontal and left temporal regions. He has had several brain MRIs showing generalized volume loss and had critical laboratory tests during a period of lethargy, which were unconcerning. He was treated with multiple antiseizure medications. He was diagnosed with ASD at age 5 years because of delayed language, poor social communication, and repetitive behaviors.Over time, S continued to experience global developmental delays and autistic-like behaviors and remained minimally verbal. However, clinicians noted a number of developmental strengths, including a generally positive mood, a willingness to participate in therapy, improved receptive language skills, attachment to his mother, and a love of nature and the outdoors. He participated in a number of therapy modalities including speech/language therapy, occupational therapy, physical therapy, applied behavioral analysis, aqua therapy, partner-assisted scanning, and therapeutic horseback riding.In 2019, whole-exome sequencing was newly covered by the state Medicaid program, and testing was obtained in 2020. Whole-exome sequencing revealed a de novo STXBP1 pathogenic variant c.874C>T (p.Arg292Cys), which is associated with developmental and epileptic encephalopathy. His presentation is consistent with STXBP1 encephalopathy including refractory epilepsy, ASD, intellectual disability, and movement disorders.What are important considerations in genetic testing for children with autism? How does a genetic testing result alter management for clinicians and families?

Access, utilization, and awareness for clinical genetic testing in autism spectrum disorder in Sweden: A survey study

Clinical genetic testing is recommended for individuals diagnosed with autism spectrum disorder. There are only a few reports of how these recommendations are followed and especially missing for European countries. We aimed to analyze the rate of access, utilization, and awareness of clinical genetic testing among autistic individuals in Sweden through online surveys targeting parents with at least one autistic child and autistic adolescents (from 15 years) and adults. In total, 868 parents of autistic children and 213 autistic adolescents or adults completed the survey. Only 9.1% (n = 79) of parents and 2.8% (n = 6) of autistic adolescents/adults reported having received a referral for clinical genetic testing after autism spectrum disorder diagnosis. The autistic children offered a referral were younger at diagnosis (p < 0.001) and more likely to have an additional neurodevelopmental diagnosis (p < 0.01), including intellectual disability (p < 0.001) or a language disorder (p < 0.001). Genetic counseling was provided to less than half of the families that were referred for clinical genetic testing. Finally, we report that both respondent groups preferred to be informed by written text and an expert in genetics about clinical genetic testing. This study highlights a lack of awareness and access to clinical genetic testing after autism spectrum disorder diagnosis in Sweden and demonstrates the need for additional studies on how clinical guidelines for genetic testing are followed in different countries.

Awareness and perception of medical genetic services among Malaysian parents of autism spectrum disorders children: the lessons to be learned

Purpose

Autism spectrum disorder (ASD) is a group of complex neurodevelopmental disorders with uncertain etiology. Evidence shows that genetic testing can explain about 20% of cases. This study aims to assess the level of awareness and perception of medical genetic services among Malaysian parents with ASD children.

Design/methodology/approach

A cross-sectional survey using an interviewer-administered questionnaire was done among 111 parents of children with ASD from August 2017 to September 2019 in two clinics in Malaysia.

Findings

A majority of children with ASD (80.20%) were male and diagnosed at the age of 3–4 years old (47.80%). When the autistic child was born, most mothers and fathers were aged 26–30 (40.50%) and 31–35 years old (42.30%), respectively. Another child with ASD in nuclear and extended families was reported for 11.70% and 13.50%, respectively. Only 24.30% have seen a professional genetic consultant, and 19.8% have done genetic testing for affected children. The mean score of awareness of genetic services for ASD was 2.48 ± 3.30. Having medical insurance and another child with ASD in the nuclear family was significantly associated with a higher level of awareness (p = 0.01 and p < 0.001, respectively). Most of the participants have a positive perception of these services.

Originality/value

Regardless of demographic factors, participants have poor awareness of genetic services for ASD, likely because the primary physician did not recommend it upon diagnosis. Increasing health-care providers’ knowledge about the current potential of genetic testing for ASD and educational campaigns for the public are critical components of using available genetic tests to improve ASD management.

[Genetic risk factors and their influence on neural development in autism spectrum disorders]

Genetic risk factors and their influence on neural development in autism spectrum disorders Abstract. Abstract. Autism spectrum disorders are etiologically based on genetic and specific gene x biologically relevant environmental risk factors. They are diagnosed based on behavioral characteristics, such as impaired social communication and stereotyped, repetitive behavior and sensory as well as special interests. The genetic background is heterogeneous, i. e., it comprises diverse genetic risk factors across the disorder and high interindividual differences of specific genetic risk factors. Nevertheless, risk factors converge regarding underlying biological mechanisms and shared pathways, which likely cause the autism-specific behavioral characteristics. The current selective literature review summarizes differential genetic risk factors and focuses particularly on mechanisms and pathways currently being discussed by international research. In conclusion, clinically relevant aspects and open translational research questions are presented.

Diagnostic Utility of Genome-Wide DNA Methylation Analysis in Mendelian Neurodevelopmental Disorders

Mendelian neurodevelopmental disorders customarily present with complex and overlapping symptoms, complicating the clinical diagnosis. Individuals with a growing number of the so-called rare disorders exhibit unique, disorder-specific DNA methylation patterns, consequent to the underlying gene defects. Besides providing insights to the pathophysiology and molecular biology of these disorders, we can use these epigenetic patterns as functional biomarkers for the screening and diagnosis of these conditions. This review summarizes our current understanding of DNA methylation episignatures in rare disorders and describes the underlying technology and analytical approaches. We discuss the computational parameters, including statistical and machine learning methods, used for the screening and classification of genetic variants of uncertain clinical significance. Describing the rationale and principles applied to the specific computational models that are used to develop and adapt the DNA methylation episignatures for the diagnosis of rare disorders, we highlight the opportunities and challenges in this emerging branch of diagnostic medicine.

The Creatine Transporter Unfolded: A Knotty Premise in the Cerebral Creatine Deficiency Syndrome

Creatine provides cells with high-energy phosphates for the rapid reconstitution of hydrolyzed adenosine triphosphate. The eponymous creatine transporter (CRT1/SLC6A8) belongs to a family of solute carrier 6 (SLC6) proteins. The key role of CRT1 is to translocate creatine across tissue barriers and into target cells, such as neurons and myocytes. Individuals harboring mutations in the coding sequence of the human CRT1 gene develop creatine transporter deficiency (CTD), one of the pivotal underlying causes of cerebral creatine deficiency syndrome. CTD encompasses an array of clinical manifestations, including severe intellectual disability, epilepsy, autism, development delay, and motor dysfunction. CTD is characterized by the absence of cerebral creatine, which implies an indispensable role for CRT1 in supplying the brain cells with creatine. CTD-associated variants dramatically reduce or abolish creatine transport activity by CRT1. Many of these are point mutations that are known to trigger folding defects, leading to the retention of encoded CRT1 proteins in the endoplasmic reticulum and precluding their delivery to the cell surface. Misfolding of several related SLC6 transporters also gives rise to detrimental pathologic conditions in people; e.g., mutations in the dopamine transporter induce infantile parkinsonism/dystonia, while mutations in the GABA transporter 1 cause treatment-resistant epilepsy. In some cases, folding defects are amenable to rescue by small molecules, known as pharmacological and chemical chaperones, which restore the cell surface expression and transport activity of the previously non-functional proteins. Insights from the recent molecular, animal and human case studies of CTD add toward our understanding of this complex disorder and reveal the wide-ranging effects elicited upon CRT1 dysfunction. This grants novel therapeutic prospects for the treatment of patients afflicted with CTD, e.g., modifying the creatine molecule to facilitate CRT1-independent entry into brain cells, or correcting folding-deficient and loss-of-function CTD variants using pharmacochaperones and/or allosteric modulators. The latter justifies a search for additional compounds with a capacity to correct mutation-specific defects.

The Mitochondrial Dysfunction Hypothesis in Autism Spectrum Disorders: Current Status and Future Perspectives

Autism spectrum disorders (ASDs) constitute a set of heterogeneous neurodevelopmental conditions, characterized by a wide genetic variability that has led to hypothesize a polygenic origin. The metabolic profiles of patients with ASD suggest a possible implication of mitochondrial pathways. Although different physiological and biochemical studies reported deficits in mitochondrial oxidative phosphorylation in subjects with ASD, the role of mitochondrial DNA variations has remained relatively unexplored. In this review, we report and discuss very recent evidence to demonstrate the key role of mitochondrial disorders in the development of ASD.