Clinical Genetic Testing in Autism Spectrum Disorder in a Large Community-Based Population Sample

Views of Genetic Testing for Autism Among Autism Self-Advocates: A Qualitative Study

BACKGROUND

Autism self-advocates' views regarding genetic tests for autism are important, but critical questions about their perspectives arise.

METHODS

We interviewed 11 autism self-advocates, recruited through autism self-advocacy websites, for 1 h each.

RESULTS

Interviewees viewed genetic testing and its potential pros and cons through the lens of their own indiviudal perceived challenges, needs and struggles, especially concerning stigma and discrimination, lack of accommodations and misunderstandings from society about autism, their particular needs for services, and being blamed by others and by themselves for autistic traits. Their views of genetic testing tended not to be binary, but rather depended on how the genetic test results would be used. Interviewees perceived pros of genetic testing both in general and with regard to themselves (e.g., by providing "scientific proof" of autism as a diagnosis and possibly increasing availability of services). But they also perceived disadvantages and limitations of testing (e.g., possible eugenic applications). Participants distinguished between what they felt would be best for themselves and for the autistic community as a whole. When asked if they would undergo testing for themselves, if offered, interviewees added several considerations (e.g., undergoing testing because they support science in general). Interviewees were divided whether a genetic diagnosis would or should reduce self-blame, and several were wary of testing unless treatment, prevention or societal attitudes changed. Weighing these competing pros and cons could be difficult.

CONCLUSIONS

This study, the first to use in-depth qualitative interviews to assess views of autism self-advocates regarding genetic testing, highlights key complexities. Respondents felt that such testing is neither wholly good or bad in itself, but rather may be acceptable depending on how it is used, and should be employed in beneficial, not harmful ways. These findings have important implications for practice, education of multiple stakeholders, research, and policy.

Genetic Testing History in Adults with Autism Spectrum Disorder

Background & Objectives

Many genes have been identified in autism spectrum disorder (ASD). Yet little is known about how many adults with ASD receive recommended genetic testing and their outcomes. We investigated the percentage of adults with ASD who received genetic testing using recommended methods in our ASD specialty clinic and the percentage with positive findings.

Methods

Potentially eligible adults were identified through search of our health system data repository and ASD diagnoses confirmed using review of relevant medical records by consensus of psychiatrists specializing in ASD. Patients were included (N=630) who had at least one visit with a qualifying clinician between 5/1/2010 and 12/15/2020 and demographic data available. Data were collected through manual retrospective review of the electronic health record.

Results

Only 41% of the adults with ASD (261/630) had a history of genetic testing documented in the medical record. Genetic testing was declined by patients or families for 11% (72) of records and not recorded in 47% (297). Mean (SD; range) age for the 261 adults with testing documented was 28.5 (5.3; 22-58) years. Sixty-seven (26%) were identified as female, 14 (6%) as Asian, 8 (3%) as Black or African American, 226 (89%) as White, 6 (2%) as other race, and 2 (1%) as Hispanic. 189 (73%) had intellectual disability. Ninety-one percent (236) had the genetic testing method recorded. Only 54% (95% CI: 46%, 61%) of patients had testing using a recommended method (chromosomal array, autism/intellectual disability sequencing panel, or exome sequencing). Few adults had received testing with sequencing technologies. A genetic cause of ASD was found in 28% (95% CI: 19%, 39%) of the 121 adults with results from ASD-related genetic testing recorded.

Conclusions

Genetic testing can offer clinical and research insights. Yet it is underutilized in this population of adults with ASD. Nearly half of the adults in our sample lacked documentation of genetic testing. Thus, the percentage of adults with confirmed ASD who had any recommended genetic testing may be even lower than reported. Adults with ASD may benefit from having their genetic testing history reviewed in the clinic and the latest genetic testing performed.

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.

Factors Associated With Underutilization of Genetic Testing in Autism Spectrum Disorders

BACKGROUND

We sought to identify patient and provider factors associated with low completion of genetic testing, specifically chromosomal microarray (CMA), for autism spectrum disorder (ASD).

METHODS

Medical record review was conducted of children newly diagnosed with ASD without prior genetic testing at a single academic medical center from February 2015 through January 2016.

RESULTS

Only 41.9% of individuals with ASD completed CMA testing over at least 18 months from diagnosis (n = 140 of 334). Time to CMA completion varied, with a median of 86.5 days (interquartile range 2 to 214.5 days). Provider recommendation of genetic testing at the diagnostic visit and greater number of follow-up visits were associated with CMA completion. On multivariate regression, CMA completion was inversely associated with age (odds ratio [OR] = 0.8 for each year older, 95% confidence interval [CI] 0.7, 0.9; P = 0.001) and directly associated with intellectual disability or global developmental delay (OR = 2.2, 95% CI 1.3, 3.8; P = 0.004), first-degree relative with ASD (OR = 2.5, 95% CI 1.0, 6.0; P = 0.044), and public insurance (OR = 1.7, 95% CI 1.0, 2.9; P = 0.037). Parental concern and cost/insurance coverage were the most frequently documented barriers.

CONCLUSIONS

Workflows to support early genetic testing recommendation and ordering soon after diagnosis may increase utilization, incorporating both family and provider perspectives. Genetic counseling highlighting the utility of genetic testing across the life span, phenotypic variability of genetic disorders, and possibility of de novo variants in ASD may also improve utilization.

Spanish mental health residents' perspectives about residency education on the genetics of psychiatric disorders: A cross-sectional survey

Despite compelling evidence that some patients with a psychiatric diagnosis could benefit from genetic assessment, genetic testing for psychiatric patients is underutilized. Few studies have reported psychiatric genetics training for mental health specialists, and such research is especially lacking in Spain. We aimed to gather the opinions of Spanish mental health residents, including resident intern nurses (RINs), doctors (RIDs) and psychologists (RIPs). A short survey was prepared by an expert team and distributed to all mental health residency centers in Spain during the first semester of 2021. Of the 2028 residents, 18% responded. Participants were mainly females (71%), in their first year of residency (37%) and within the 27-31-year age range. While participants received little theoretical (13.4%) and practical (4.6%) training on average, RIDs had the most affirmative responses. Notably, RINs and RIDs were interested in genetics during residency (>40%) and strongly believed (85.0%) that genetics training using both theoretical and practical methodologies should be incorporated into residency training. However, RIPs were less interested (20%), and only 60% believed that genetics training should be incorporated. Spanish mental health residents, although interested in genetics in psychiatry, receive little training on this topic. They strongly believe that genetics training using theoretical and practical methodologies should be incorporated.

Newborn Screening for Neurodevelopmental Disorders May Exacerbate Health Disparities

Newborn screening (NBS) began in the early 1960s with screening for phenylketonuria on blood collected on filter paper. The number of conditions included in NBS programs expanded significantly with the adoption of tandem mass spectrometry. The recommended uniform screening panel provides national guidance and has reduced state variability. Universality and uniformity have been supported to promote equity. Recently, a number of researchers have suggested expanding NBS to include genomic sequencing to identify all genetic disorders in newborns. This has been specifically suggested for genes that increase the risk for neurodevelopmental disorders (NDDs), with the presumption that early identification in the newborn period would reduce disabilities. We offer arguments to show that genomic sequencing of newborns for NDDs risks exacerbating disparities. First, the diagnosis of NDD requires clinical expertise, and both genetic and neurodevelopmental expertise are in short supply, leading to disparities in access to timely follow-up. Second, therapies for children with NDDs are insufficient to meet their needs. Increasing early identification for those at risk who may never manifest developmental delays could shift limited resources to those children whose parents are more poised to advocate, worsening disparities in access to services. Rather, we suggest an alternative: genomic sequencing of all children with diagnosed NDDs. This focused strategy would have the potential to target genomic sequencing at children who manifest NDDs across diverse populations which could better improve our understanding of contributory genes to NDDs.

Linkage of whole genome sequencing and administrative health data in autism: A proof of concept study

Whether genetic testing in autism can help understand longitudinal health outcomes and health service needs is unclear. The objective of this study was to determine whether carrying an autism-associated rare genetic variant is associated with differences in health system utilization by autistic children and youth. This retrospective cohort study examined 415 autistic children/youth who underwent genome sequencing and data collection through a translational neuroscience program (Province of Ontario Neurodevelopmental Disorders Network). Participant data were linked to provincial health administrative databases to identify historical health service utilization, health care costs, and complex chronic medical conditions during a 3-year period. Health administrative data were compared between participants with and without a rare genetic variant in at least 1 of 74 genes associated with autism. Participants with a rare variant impacting an autism-associated gene (n = 83, 20%) were less likely to have received psychiatric care (at least one psychiatrist visit: 19.3% vs. 34.3%, p = 0.01; outpatient mental health visit: 66% vs. 77%, p = 0.04). Health care costs were similar between groups (median: $5589 vs. $4938, p = 0.4) and genetic status was not associated with odds of being a high-cost participant (top 20%) in this cohort. There were no differences in the proportion with complex chronic medical conditions between those with and without an autism-associated genetic variant. Our study highlights the feasibility and potential value of genomic and health system data linkage to understand health service needs, disparities, and health trajectories in individuals with neurodevelopmental conditions.

Child and adolescent psychiatrists' use, attitudes, and understanding of genetic testing and pharmacogenetics in clinical practice

The purpose of this study was to report current practices and attitudes of child and adolescent psychiatrists (CAP) regarding diagnostic genetic and pharmacogenetic (PGx) testing. We surveyed 958 US-based practicing CAP. 54.9% of respondents indicated that they had ordered/referred for a genetic test in the past 12 months. 87% of respondents agreed that it is their role to discuss genetic information regarding psychiatric conditions with their patients; however, 45% rated their knowledge of genetic testing practice guidelines as poor/very poor. The most ordered test was PGx (32.2%), followed by chromosomal microarray (23.0%). 73.4% reported that PGx is at least slightly useful in child and adolescent psychiatry. Most (62.8%) were asked by a patient/family to order PGx in the past 12 months and 41.7% reported they would order PGx in response to a family request. Those who ordered a PGx test were more likely to have been asked by a patient/family and to work in private practice. 13.8% of respondents agreed/strongly agreed that a PGx test can predict the effectiveness of specific antidepressants. Some respondents also indicated they would make clinical changes based on PGx information even if a medication was currently effective and there were no side effects. Genetic testing has become routine clinical care in child and adolescent psychiatry. Despite this, many providers rate their associated knowledge as poor/very poor. Patient requests were associated with ordering practices and providers misinterpretation of PGx may be leading to unnecessary changes in clinical management. There is need for further education and support for clinicians.

Candidate biomarkers in psychiatric disorders: state of the field

The field of psychiatry is hampered by a lack of robust, reliable and valid biomarkers that can aid in objectively diagnosing patients and providing individualized treatment recommendations. Here we review and critically evaluate the evidence for the most promising biomarkers in the psychiatric neuroscience literature for autism spectrum disorder, schizophrenia, anxiety disorders and post-traumatic stress disorder, major depression and bipolar disorder, and substance use disorders. Candidate biomarkers reviewed include various neuroimaging, genetic, molecular and peripheral assays, for the purposes of determining susceptibility or presence of illness, and predicting treatment response or safety. This review highlights a critical gap in the biomarker validation process. An enormous societal investment over the past 50 years has identified numerous candidate biomarkers. However, to date, the overwhelming majority of these measures have not been proven sufficiently reliable, valid and useful to be adopted clinically. It is time to consider whether strategic investments might break this impasse, focusing on a limited number of promising candidates to advance through a process of definitive testing for a specific indication. Some promising candidates for definitive testing include the N170 signal, an event-related brain potential measured using electroencephalography, for subgroup identification within autism spectrum disorder; striatal resting-state functional magnetic resonance imaging (fMRI) measures, such as the striatal connectivity index (SCI) and the functional striatal abnormalities (FSA) index, for prediction of treatment response in schizophrenia; error-related negativity (ERN), an electrophysiological index, for prediction of first onset of generalized anxiety disorder, and resting-state and structural brain connectomic measures for prediction of treatment response in social anxiety disorder. Alternate forms of classification may be useful for conceptualizing and testing potential biomarkers. Collaborative efforts allowing the inclusion of biosystems beyond genetics and neuroimaging are needed, and online remote acquisition of selected measures in a naturalistic setting using mobile health tools may significantly advance the field. Setting specific benchmarks for well-defined target application, along with development of appropriate funding and partnership mechanisms, would also be crucial. Finally, it should never be forgotten that, for a biomarker to be actionable, it will need to be clinically predictive at the individual level and viable in clinical settings.

Knowledge, attitudes and experiences of genetic testing for autism spectrum disorders among caregivers, patients, and health providers: A systematic review

BACKGROUND

Several genetic testing techniques have been recommended as a first-tier diagnostic tool in clinical practice for diagnosing autism spectrum disorder (ASD). However, the actual usage rate varies dramatically. This is due to various reasons, including knowledge and attitudes of caregivers, patients, and health providers toward genetic testing. Several studies have therefore been conducted worldwide to investigate the knowledge, experiences, and attitudes toward genetic testing among caregivers of children with ASD, adolescent and adult ASD patients, and health providers who provide medical services for them. However, no systematic review has been done.

AIM

To systematically review research on knowledge, experiences, and attitudes towards genetic testing among caregivers of children with ASD, adolescent and adult ASD patients, and health providers.

METHODS

We followed the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines and searched the literature in three English language databases (PubMed, Web of Science, and PsychInfo) and two Chinese databases (CNKI and Wanfang). Searched literature was screened independently by two reviewers and discussed when inconsistency existed. Information on characteristics of the study, characteristics of participants, and main findings regarding knowledge, experience, and attitudes of caregivers of children with ASD, adolescent and adult ASD patients, and health providers concerning ASD genetic testing were extracted from included papers into a charting form for analysis.

RESULTS

We included 30 studies published between 2012 and 2022 and conducted in 9 countries. Most of the studies (n = 29) investigated caregivers of children with ASD, one study also included adolescent and adult patients, and two covered health providers. Most (51.0%-100%) of the caregivers/patients knew there was a genetic cause for ASD and 17.0% to 78.1% were aware of ASD genetic testing. However, they lacked full understanding of genetic testing. They acquired relevant and necessary information from physicians, the internet, ASD organizations, and other caregivers. Between 9.1% to 72.7% of caregivers in different studies were referred for genetic testing, and between 17.4% to 61.7% actually obtained genetic testing. Most caregivers agreed there are potential benefits following genetic testing, including benefits for children, families, and others. However, two studies compared perceived pre-test and post-test benefits with conflicting findings. Caregivers concerns included high costs, unhelpful results, negative influences (e.g., causing family conflicts, causing stress/risk/pain to children etc.) prevented some caregivers from using genetic testing. Nevertheless, 46.7% to 95.0% caregivers without previous genetic testing experience intended to obtain it in the future, and 50.5% to 59.6% of parents previously obtaining genetic testing would recommend it to other parents. In a single study of child and adolescent psychiatrists, 54.9% of respondents had ordered ASD genetic testing for their patients in the prior 12 mo, which was associated with greater knowledge of genetic testing.

CONCLUSION

Most caregivers are willing to learn about and use genetic testing. However, the review showed their current knowledge is limited and usage rates varied widely in different studies.

Child and Adolescent Psychiatrists' Use, Attitudes, and Understanding of Genetic Tests in Clinical Practice

Objective

To report current practices and attitudes of child and adolescent psychiatrists (CAP) regarding diagnostic genetic and pharmacogenetic (PGx) testing.

Methods

Survey of 958 US-based practicing CAP.

Results

54.9% of respondents indicated that they had ordered/referred for a genetic test in the past 12 months. 87% of respondents agreed that it is their role to discuss genetic information regarding psychiatric conditions with their patients; however, 45% rated their knowledge of genetic testing practice guidelines as poor/very poor. The most ordered test was PGx (32.2%), followed by chromosomal microarray (23.0%). 73.4% reported that PGx is at least slightly useful in child and adolescent psychiatry. Most (62.8%) were asked by a patient/family to order PGx in the past 12 months and 41.7% reported they would order PGx in response to a family request. Those who ordered a PGx test were more likely to have been asked by a patient/family and to work in private practice. 13.8% of respondents agreed/strongly agreed that a PGx test can predict the effectiveness of specific antidepressants. Some respondents also indicated they would make clinical changes based on PGx information even if a medication was currently effective and there were no side effects.

Conclusions

Genetic testing has become routine clinical care in child and adolescent psychiatry. Despite this, many providers rate their associated knowledge as poor/very poor. Patient requests were associated with ordering practices and providers misinterpretation of PGx may be leading to unnecessary changes in clinical management. There is need for further education and support for clinicians.

Barriers to genetic testing in clinical psychiatry and ways to overcome them: from clinicians' attitudes to sociocultural differences between patients across the globe

Genetic testing has evolved rapidly over recent years and new developments have the potential to provide insights that could improve the ability to diagnose, treat, and prevent diseases. Information obtained through genetic testing has proven useful in other specialties, such as cardiology and oncology. Nonetheless, a range of barriers impedes techniques, such as whole-exome or whole-genome sequencing, pharmacogenomics, and polygenic risk scoring, from being implemented in psychiatric practice. These barriers may be procedural (e.g., limitations in extrapolating results to the individual level), economic (e.g., perceived relatively elevated costs precluding insurance coverage), or related to clinicians' knowledge, attitudes, and practices (e.g., perceived unfavorable cost-effectiveness, insufficient understanding of probability statistics, and concerns regarding genetic counseling). Additionally, several ethical concerns may arise (e.g., increased stigma and discrimination through exclusion from health insurance). Here, we provide an overview of potential barriers for the implementation of genetic testing in psychiatry, as well as an in-depth discussion of strategies to address these challenges.

Advancing artificial intelligence-assisted pre-screening for fragile X syndrome

BACKGROUND

Fragile X syndrome (FXS), the most common inherited cause of intellectual disability and autism, is significantly underdiagnosed in the general population. Diagnosing FXS is challenging due to the heterogeneity of the condition, subtle physical characteristics at the time of birth and similarity of phenotypes to other conditions. The medical complexity of FXS underscores an urgent need to develop more efficient and effective screening methods to identify individuals with FXS. In this study, we evaluate the effectiveness of using artificial intelligence (AI) and electronic health records (EHRs) to accelerate FXS diagnosis.

METHODS

The EHRs of 2.1 million patients served by the University of Wisconsin Health System (UW Health) were the main data source for this retrospective study. UW Health includes patients from south central Wisconsin, with approximately 33 years (1988-2021) of digitized health data. We identified all participants who received a code for FXS in the form of International Classification of Diseases (ICD), Ninth or Tenth Revision (ICD9 = 759.83, ICD10 = Q99.2). Only individuals who received the FXS code on at least two occasions ("Rule of 2") were classified as clinically diagnosed cases. To ensure the availability of sufficient data prior to clinical diagnosis to test the model, only individuals who were diagnosed after age 10 were included in the analysis. A supervised random forest classifier was used to create an AI-assisted pre-screening tool to identify cases with FXS, 5 years earlier than the time of clinical diagnosis based on their medical records. The area under receiver operating characteristic curve (AUROC) was reported. The AUROC shows the level of success in identification of cases and controls (AUROC = 1 represents perfect classification).

RESULTS

52 individuals were identified as target cases and matched with 5200 controls. AI-assisted pre-screening tool successfully identified cases with FXS, 5 years earlier than the time of clinical diagnosis with an AUROC of 0.717. A separate model trained and tested on UW Health cases achieved the AUROC of 0.798.

CONCLUSIONS

This result shows the potential utility of our tool in accelerating FXS diagnosis in real clinical settings. Earlier diagnosis can lead to more timely intervention and access to services with the goal of improving patients' health outcomes.

Testing and extending strategies for identifying genetic disease-related encounters in pediatric patients

PURPOSE

To better understand health care utilization and develop decision support tools, methods for identifying patients with suspected genetic diseases (GDs) are needed. Previous studies had identified inpatient-relevant International Classification of Diseases (ICD) codes that were possibly, probably, or definitely indicative of GDs. We assessed whether these codes identified GD-related inpatient, outpatient, and emergency department encounters among pediatric patients with suspected GDs from a previous study (the North Carolina Clinical Genomic Evaluation by Next-Generation Exome Sequencing [NCGENES] study).

METHODS

Using the electronic medical records of 140 pediatric patients from the NCGENES study, we characterized the presence of ICD codes representing possible, probable, or definite GD-related diagnoses across encounter types. In addition, we examined codes from encounters for which initially no GD-related codes had been found and determined whether these codes were indicative of a GD.

RESULTS

Among NCGENES patients with visits between 2014 and 2017, 92% of inpatient, 75% of emergency department, and 63% of outpatient encounters included ≥1 GD-related code. Encounters with highly specific (ie, definite) GD codes had fewer low-specificity GD codes than encounters with only low-specificity GD codes. We identified an additional 32 ICD-9 and 56 ICD-10 codes possibly indicative of a GD.

CONCLUSION

Code-based strategies can be refined to assess health care utilization among pediatric patients and may contribute to a systematic approach to identify patients with suspected GDs.

Genes To Mental Health (G2MH): A Framework to Map the Combined Effects of Rare and Common Variants on Dimensions of Cognition and Psychopathology

Rare genomic disorders (RGDs) confer elevated risk for neurodevelopmental psychiatric disorders. In this era of intense genomics discoveries, the landscape of RGDs is rapidly evolving. However, there has not been comparable progress to date in scalable, harmonized phenotyping methods. As a result, beyond associations with categorical diagnoses, the effects on dimensional traits remain unclear for many RGDs. The nature and specificity of RGD effects on cognitive and behavioral traits is an area of intense investigation: RGDs are frequently associated with more than one psychiatric condition, and those studied to date affect, to varying degrees, a broad range of developmental and cognitive functions. Although many RGDs have large effects, phenotypic expression is typically influenced by additional genomic and environmental factors. There is emerging evidence that using polygenic risk scores in individuals with RGDs offers opportunities to refine prediction, thus allowing for the identification of those at greatest risk of psychiatric illness. However, translation into the clinic is hindered by roadblocks, which include limited genetic testing in clinical psychiatry, and the lack of guidelines for following individuals with RGDs, who are at high risk of developing psychiatric symptoms. The Genes to Mental Health Network (G2MH) is a newly funded National Institute of Mental Health initiative that will collect, share, and analyze large-scale data sets combining genomics and dimensional measures of psychopathology spanning diverse populations and geography. The authors present here the most recent understanding of the effects of RGDs on dimensional behavioral traits and risk for psychiatric conditions and discuss strategies that will be pursued within the G2MH network, as well as how expected results can be translated into clinical practice to improve patient outcomes.

Rare variants in the outcome of social skills group training for autism

Exome sequencing has been proposed as the first-tier genetic testing in autism spectrum disorder (ASD). Here, we performed exome sequencing in autistic individuals with average to high intellectual abilities (N = 207) to identify molecular diagnoses and genetic modifiers of intervention outcomes of social skills group training (SSGT) or standard care. We prioritized variants of clinical significance (VCS), variants of uncertain significance (VUS) and generated a pilot scheme to calculate genetic scores of rare and common variants in ASD-related gene pathways. Mixed linear models were used to test the association between the carrier status of VCS/VUS or the genetic scores with intervention outcomes measured by the social responsiveness scale. Additionally, we combined behavioral and genetic features using a machine learning (ML) model to predict the individual response. We showed a rate of 4.4% and 11.3% of VCS and VUS in the cohort, respectively. Individuals with VCS or VUS had improved significantly less after standard care than non-carriers at post-intervention (β = 9.35; p = 0.036), while no such association was observed for SSGT (β = -2.50; p = 0.65). Higher rare variant genetic scores for synaptic transmission and regulation of transcription from RNA polymerase II were separately associated with less beneficial (β = 8.30, p = 0.0044) or more beneficial (β = -6.79, p = 0.014) effects after SSGT compared with standard care at follow-up, respectively. Our ML model showed the importance of rare variants for outcome prediction. Further studies are needed to understand genetic predisposition to intervention outcomes in ASD.

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.

Prevalence of Underdiagnosed Fragile X Syndrome in 2 Health Systems

This cross-sectional study examines the gap between best estimates of prevalence and clinical diagnosis of fragile X syndrome by mining the electronic health records of 3.8 million people in Wisconsin.

Harnessing rare variants in neuropsychiatric and neurodevelopment disorders-a Keystone Symposia report

Neurodevelopmental neuropsychiatric disorders, such as autism spectrum disorder and schizophrenia, have strong genetic risk components, but the underlying mechanisms have proven difficult to decipher. Rare, high-risk variants may offer an opportunity to delineate the biological mechanisms responsible more clearly for more common idiopathic diseases. Indeed, different rare variants can cause the same behavioral phenotype, demonstrating genetic heterogeneity, while the same rare variant can cause different behavioral phenotypes, demonstrating variable expressivity. These observations suggest convergent underlying biological and neurological mechanisms; identification of these mechanisms may ultimately reveal new therapeutic targets. At the 2021 Keystone eSymposium "Neuropsychiatric and Neurodevelopmental Disorders: Harnessing Rare Variants" a panel of experts in the field described significant progress in genomic discovery and human phenotyping and raised several consistent issues, including the need for detailed natural history studies of rare disorders, the challenges in cohort recruitment, and the importance of viewing phenotypes as quantitative traits that are impacted by rare variants.

Genetic evaluation of children with autism spectrum disorders in developing and low-resource areas

LAY ABSTRACT

Autism is the most common neurodevelopmental disorder in children worldwide. Genetic factors play an important role in the risk of developing autism. Determining the genetic cause of autism is key to understanding the biological processes that lead to the clinical manifestations of autism, and can inform the management and even prevention of this condition. Establishing genetic causes of autism requires collection of genetic data on a global scale. Limited research on genetic testing for individuals with autism is available from developing countries in low-resource regions. In this study, we explored the types of investigations ordered for Jordanian children with autism by their physicians. A representative sample of parents of children with autism in Jordan was questioned about the studies that their children received. We found that the recommended genetic testing was only performed in a small number of children with autism. In contrast, most children in the sample received non-genetic testing, which is not routinely recommended. We also explored the sociocultural factors that may influence the decision to perform genetic testing in this population. We discuss our findings in light of the data available from other developing and developed 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.

Phenotypic signatures in clinical data enable systematic identification of patients for genetic testing

Around 5% of the population is affected by a rare genetic disease, yet most endure years of uncertainty before receiving a genetic test. A common feature of genetic diseases is the presence of multiple rare phenotypes that often span organ systems. Here, we use diagnostic billing information from longitudinal clinical data in the electronic health records (EHRs) of 2,286 patients who received a chromosomal microarray test, and 9,144 matched controls, to build a model to predict who should receive a genetic test. The model achieved high prediction accuracies in a held-out test sample (area under the receiver operating characteristic curve (AUROC), 0.97; area under the precision-recall curve (AUPRC), 0.92), in an independent hospital system (AUROC, 0.95; AUPRC, 0.62), and in an independent set of 172,265 patients in which cases were broadly defined as having an interaction with a genetics provider (AUROC, 0.9; AUPRC, 0.63). Patients carrying a putative pathogenic copy number variant were also accurately identified by the model. Compared with current approaches for genetic test determination, our model could identify more patients for testing while also increasing the proportion of those tested who have a genetic disease. We demonstrate that phenotypic patterns representative of a wide range of genetic diseases can be captured from EHRs to systematize decision-making for genetic testing, with the potential to speed up diagnosis, improve care and reduce costs.

Child and Adolescent Psychiatrists' Perceptions of Utility and Self-rated Knowledge of Genetic Testing Predict Usage for Autism Spectrum Disorder

Autism spectrum disorder (ASD) is associated with numerous genetic syndromes.1 Practice guidelines from various medical specialty societies, such as American Academy of Child and Adolescent Psychiatry (AACAP), American College of Medical Genetics, American Neurological Association, and American Academy of Pediatrics, indicate that genetic testing should be part of the evaluation for ASD.1-4 Studies have shown, however, that many patients do not receive indicated genetic testing; reported rates of testing vary widely, ranging from 1.5% to 60% of patients receiving genetic testing as part of the evaluation for ASD.4-8 Child and adolescent psychiatrists practicing in the United States (approximately 8300)9 far outnumber developmental behavioral pediatricians (approximately 900) and child neurologists (approximately 900), but in 1 study child and adolescent psychiatrists were the least likely to order genetic testing during the evaluation of patients with ASD diagnoses.6 Thus, it is critical to understand attitudes of child and adolescent psychiatrists toward genetic testing and other barriers to genetic testing to optimize adherence to practice guidelines for appropriate genetic testing in people with ASD. A survey to capture the current practice, knowledge, and perceptions toward genetic testing was developed by content matter experts that included child and adolescent psychiatrists, psychologists, and genetic counselors as well as lawyers, anthropologists, and bioethicists with expertise in ethical, legal, and social implications of genetics.

Genetic Testing in Neurodevelopmental Disorders

Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.

Comprehensive Genetic Analysis of Non-syndromic Autism Spectrum Disorder in Clinical Settings

Although genetic factors are involved in the etiology of autism spectrum disorder (ASD), the significance of genetic analysis in clinical settings is unclear. Forty-nine subjects diagnosed with non-syndromic ASD were analyzed by microarray comparative genomic hybridization (CGH) analysis, whole-exome sequencing (WES) analysis, and panel sequencing analysis for 52 common causative genes of ASD to detect inherited rare variants. Genetic analysis by microarray CGH and WES analyses showed conclusive results in about 10% of patients, however, many inherited variants detected by panel sequencing analysis were difficult to interpret and apply in clinical practice in the majority of patients. Further improvement of interpretation of many variants detected would be necessary for combined genetic tests to be used in clinical settings.

Diagnostic genetic testing for neurodevelopmental psychiatric disorders: closing the gap between recommendation and clinical implementation

Advances in laboratory testing have significantly increased the detection of rare genetic etiologies of neurodevelopmental psychiatric disorders (NPD), particularly developmental delay/ intellectual disability, autism spectrum disorder, and schizophrenia. Establishing a genetic diagnosis has important medical and personal utility for individuals with these conditions. Diagnostic genetic tests for NPD are clinically available but underutilized outside of medical genetics settings. Without clear multidisciplinary consensus recommendations, active involvement of medical specialists working with NPD patients, and practical education and training, the implementation of genetic testing for NPD will continue to lag behind other areas of medicine. In the long-term, collaborative efforts to address educational, logistical, and workforce obstacles will improve patient care and pave the way for targeted, effective NPD treatments.