Diagnostic Yield and Economic Implications of Whole-Exome Sequencing for ASD Diagnosis in Israel

A meta-analysis of diagnostic yield and clinical utility of genome and exome sequencing in pediatric rare and undiagnosed genetic diseases

PURPOSE

To systematically evaluate the diagnostic yield and clinical utility of genome sequencing (GS) and exome sequencing (ES; genome-wide sequencing [GWS]) in pediatric patients with rare and undiagnosed genetic diseases.

METHODS

We conducted a meta-analysis of studies published between 2011 and 2023. To address study heterogeneity, comparative analyses included within-cohort studies using random-effects models.

RESULTS

We identified 108 studies including 24,631 probands with diverse clinical indications. The pooled diagnostic yield among within-cohort studies (N = 13) for GWS was 34.2% (95% CI: 27.6-41.5; I2: 86%) vs 18.1% (95% CI: 13.1-24.6; I2: 89%) for non-GWS, with 2.4-times odds of diagnosis (95% CI: 1.40-4.04; P < .05). The pooled diagnostic yield among within-cohort studies (N = 3) for GS was 30.6% (95% CI: 18.6-45.9; I2: 79%) vs 23.2% (95% CI: 18.5-28.7; I2: 58%) for ES, with 1.7-times the odds of diagnosis (95% CI: 0.94-2.92; P = .13). In first-line testing, the diagnostic yield tended to be higher for GS than for ES across clinical subgroups. The pooled clinical utility among patients with a positive diagnosis was 58.7% (95% CI: 47.3-69.2; I2: 81%) for GS and 54.5% (95% CI: 40.7-67.6; I2: 87%) for ES.

CONCLUSION

GS appears to have a higher diagnostic yield than ES, with similar clinical utility per positive diagnosis.

Community-oriented, hospital level genetics: a new approach to improve access for underserved communities

BACKGROUND

Certain populations are at increased risk for genetic syndromes but have limited access to genetic testing.

METHODS

We founded a community-based, pediatric genetics clinic in the Muslim-Arab city of Tayibe, Israel. Children with suspected genetic conditions of consanguineous parents, or families with two or more affected siblings were referred by local staff. The clinic was staffed by a Meir Medical Center (MMC) clinical geneticist. Blood samples were collected during the initial visit. Tests were publicly funded, with no parental involvement in administrative procedures required. A control group consisted of MMC pediatric genetics clinic patients.

RESULTS

During the first year, 30 children were assessed. No patients were lost to follow-up, compared to 8 (28%) in the MMC control group. The average time to test results was shorter in the Tayibe group and the diagnostic rate was higher, with 27.6% receiving a diagnosis (42.9%, excluding autism cases).

CONCLUSION

Our first-year experience shows the success and promising results of this model, with advantages in almost all parameters, compared to the traditional, hospital-based clinic. Factors such as faster time-to-results, greater family adherence and satisfaction, and zero lost to follow-up rate suggest considering implementing this model for providing genetic services to other underserved populations.

IMPACT

A community-oriented approach for a pediatric genetics clinic allowed reaching high-risk populations, with increased adherence, faster results and a higher yield. Our clinic relied solely on available public funding and staff, requiring no additional contributions. The current dogma of hospital-based genetics services should be reconsidered.

Association between rare, genetic variants linked to autism and ultrasonography fetal anomalies in children with autism spectrum disorder

BACKGROUND

Recent evidence suggests that certain fetal anomalies detected upon prenatal ultrasound screenings are associated with autism spectrum disorder (ASD). In this cross-sectional study, we aimed to identify genetic variants associated with fetal ultrasound anomalies (UFAs) in children with ASD.

METHODS

The study included all children with ASD who are registered in the database of the Azrieli National Center of Autism and Neurodevelopment and for whom both prenatal ultrasound and whole exome sequencing (WES) data were available. We applied our in-house integrative bioinformatics pipeline, AutScore, to these WES data to prioritize rare, gene-disrupting variants (GDVs) probably contributing to ASD susceptibily. Univariate statistics and multivariable regression were used to assess the associations between UFAs and GDVs identified in these children.

RESULTS

The study sample comprised 126 children, of whom 43 (34.1%) had at least one UFA detected in the prenatal ultrasound scan. A total of 87 candidate ASD genetic variants were detected in 60 children, with 24 (40%) children carrying multiple variants. Children with UFAs were more likely to have loss-of-function (LoF) mutations (aOR = 2.55, 95%CI: 1.13-5.80). This association was particularly noticeable when children with structural anomalies or children with UFAs in their head and brain scans were compared to children without UFAs (any mutation: aOR = 8.28, 95%CI: 2.29-30.01; LoF: aOR = 5.72, 95%CI: 2.08-15.71 and any mutation: aOR = 6.39, 95%CI: 1.34-30.47; LoF: aOR = 4.50, 95%CI: 1.32-15.35, respectively). GDVs associated with UFAs were enriched in genes highly expressed across all tissues (aOR = 2.76, 95%CI: 1.14-6.68). There was a weak, but significant, correlation between the number of mutations and the number of abnormalities detected in the same children (r = 0.21, P = 0.016).

CONCLUSIONS

The results provide valuable insights into the potential genetic basis of prenatal organogenesis abnormalities associated with ASD and shed light on the complex interplay between genetic factors and fetal development.

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.

Economic evaluation of next-generation sequencing techniques in diagnosis of genetic disorders: A systematic review

In recent years, massively parallel sequencing or next generation sequencing (NGS) has considerably changed both the research and diagnostic fields, and rapid developments have led to the combination of NGS techniques in clinical practice, ease of analysis, and detection of genetic mutations. This article aimed at reviewing the economic evaluation studies of the NGS techniques in the diagnosis of genetic diseases. In this systematic review, scientific databases (PubMed, EMBASE, Web of Science, Cochrane, Scopus, and CEA registry) were searched from 2005 to 2022 to identify the related literature on the economic evaluation of NGS techniques in the diagnosis of genetic diseases. Full-text reviews and data extraction were all performed by two independent researchers. The quality of all the articles included in this study was evaluated using the Checklist of Quality of Health Economic Studies (QHES). Out of 20 521 screened abstracts, 36 studies met the inclusion criteria. The mean score of the QHES checklist for the studies was 0.78 (high quality). Seventeen studies were conducted based on modeling. Cost-effectiveness analysis, cost-utility analysis, and cost-minimization analysis were done in 26 studies, 13 studies, and 1 study, respectively. Based on the available evidence and findings, exome sequencing, which is one of the NGS techniques, could have the potential to be used as a cost-effective genomic test to diagnose children with suspected genetic diseases. The results of the present study support the cost-effectiveness of exome sequencing in diagnosing suspected genetic disorders. However, the use of exome sequencing as a first- or second-line diagnostic test is still controversial. Most studies have been conducted in high-income countries, and research on the cost-effectiveness of NGS methods is recommended in low- and middle-income countries.

Proband only exome sequencing in 403 Indian children with neurodevelopmental disorders: Diagnostic yield, utility and challenges in a resource-limited setting

Whole exome sequencing is recommended as the first tier test for neurodevelopmental disorders (NDDs) with trio being an ideal option for the detection of de novo variants. Cost constraints have led to adoption of sequential testing i.e. proband-only whole exome followed by targeted testing of parents. The reported diagnostic yield for proband exome approach ranges between 31 and 53%. Typically, these study designs have aptly incorporated targeted parental segregation before concluding a genetic diagnosis to be confirmed. The reported estimates however do not accurately reflect the yield of proband only standalone whole -exome, a question commonly posed to the referring clinician in self pay medical systems like India. To assess the utility of standalone proband exome (without follow up targeted parental testing), we retrospectively evaluated 403 cases of neurodevelopmental disorders referred for proband-only whole exome sequencing at Neuberg Centre for Genomic Medicine (NCGM), Ahmedabad during the period of January 2019 and December 2021. A diagnosis was considered confirmed only upon the detection of Pathogenic/Likely Pathogenic variants in concordance with patient's phenotype as well as established inheritance pattern. Targeted parental/familial segregation analysis was recommended as a follow up test where applicable. The diagnostic yield of the proband-only standalone whole exome was 31.5%. Only 20 families submitted samples for follow up targeted testing, and a genetic diagnosis was confirmed in twelve cases increasing the yield to 34.5%. To understand factors leading to poor uptake of sequential parental testing, we focused on cases where an ultra-rare variant was detected in hitherto described de novo dominant neurodevelopmental disorder. A total of 40 novel variants in genes associated with de novo autosomal dominant disorders could not be reclassified as parental segregation was denied. Semi-structured telephonic interviews were conducted upon informed consent to comprehend reasons for denial. Major factors influencing decision making included lack of definitive cure in the detected disorders; especially when couples not planning further conception and financial constraints to fund further targeted testing. Our study thus depicts the utility and challenges of proband-only exome approach and highlights the need for larger studies to understand factors influencing decision making in sequential testing.

A Personalized Multidisciplinary Approach to Evaluating and Treating Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder without a known cure. Current standard-of-care treatments focus on addressing core symptoms directly but have provided limited benefits. In many cases, individuals with ASD have abnormalities in multiple organs, including the brain, immune and gastrointestinal system, and multiple physiological systems including redox and metabolic systems. Additionally, multiple aspects of the environment can adversely affect children with ASD including the sensory environment, psychosocial stress, dietary limitations and exposures to allergens and toxicants. Although it is not clear whether these medical abnormalities and environmental factors are related to the etiology of ASD, there is evidence that many of these factors can modulate ASD symptoms, making them a potential treatment target for improving core and associated ASD-related symptoms and improving functional limitation. Additionally, addressing underlying biological disturbances that drive pathophysiology has the potential to be disease modifying. This article describes a systematic approach using clinical history and biomarkers to personalize medical treatment for children with ASD. This approach is medically comprehensive, making it attractive for a multidisciplinary approach. By concentrating on treatable conditions in ASD, it is possible to improve functional ability and quality of life, thus providing optimal outcomes.