Integration of emerging epigenetic information with autism spectrum disorder (ASD) genetic results may elucidate functional insights not possible via either type of information in isolation. Here we use the genotype and DNA methylation (DNAm) data from cord blood and peripheral blood to identify SNPs associated with DNA methylation (meQTL lists). Additionally, we use publicly available fetal brain and lung meQTL lists to assess enrichment of ASD GWAS results for tissue-specific meQTLs. ASD-associated SNPs are enriched for fetal brain (OR = 3.55; P < 0.001) and peripheral blood meQTLs (OR = 1.58; P < 0.001). The CpG targets of ASD meQTLs across cord, blood, and brain tissues are enriched for immune-related pathways, consistent with other expression and DNAm results in ASD, and reveal pathways not implicated by genetic findings. This joint analysis of genotype and DNAm demonstrates the potential of both brain and blood-based DNAm for insights into ASD and psychiatric phenotypes more broadly.
Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive behaviors that typically emerge by 24 months of age. To develop effective early interventions that can potentially ameliorate the defining deficits of ASD and improve long-term outcomes, early detection is essential. Using prospective neuroimaging of 59 6-month-old infants with a high familial risk for ASD, we show that functional connectivity magnetic resonance imaging correctly identified which individual children would receive a research clinical best-estimate diagnosis of ASD at 24 months of age. Functional brain connections were defined in 6-month-old infants that correlated with 24-month scores on measures of social behavior, language, motor development, and repetitive behavior, which are all features common to the diagnosis of ASD. A fully cross-validated machine learning algorithm applied at age 6 months had a positive predictive value of 100% [95% confidence interval (CI), 62.9 to 100], correctly predicting 9 of 11 infants who received a diagnosis of ASD at 24 months (sensitivity, 81.8%; 95% CI, 47.8 to 96.8). All 48 6-month-old infants who were not diagnosed with ASD were correctly classified [specificity, 100% (95% CI, 90.8 to 100); negative predictive value, 96.0% (95% CI, 85.1 to 99.3)]. These findings have clinical implications for early risk assessment and the feasibility of developing early preventative interventions for ASD.
Genetic and environmental factors contribute to the etiologies of autism spectrum disorder (ASD), but evidence of specific environmental and susceptibility windows is limited. Here we study monozygotic and dizygotic twins discordant for ASD to test whether fetal and postnatal metal dysregulation increases ASD risk. Using validated tooth-matrix biomarkers, we estimate pre- and post-natal exposure profiles of essential and toxic elements. Significant divergences are apparent in metal uptake between ASD cases and their control siblings, but only during discrete developmental per. Cases have reduced uptake of essential elements manganese and zinc, and higher uptake of the neurotoxin lead. Manganese and lead are also correlated with ASD severity and autistic traits. Our study suggests that metal toxicant uptake and essential element deficiency during specific developmental windows increases ASD risk and severity, supporting the hypothesis of systemic elemental dysregulation in ASD. Independent replication in population-based studies is needed to extend these findings.
Racial differences in parent report of concerns about their child’s development to healthcare providers may contribute to delayed autism spectrum disorder diagnoses in Black children. We tested the hypotheses that compared to White parents, Black parents of children with autism spectrum disorder would report fewer concerns about autism symptoms and would be more likely to report concerns about disruptive behaviors. A sample of 18- to 40-month-old toddlers ( N = 174) with autism spectrum disorder and their parent participated. After screening positive for autism spectrum disorder risk, but prior to a diagnostic evaluation, parents completed free-response questions soliciting concerns about their child’s development. Parent responses were coded for the presence or the absence of 10 possible concerns, which were grouped into autism concerns (e.g. social and restricted and repetitive behavior concerns) or non-autism concerns (e.g. general developmental and disruptive behavior concerns). Compared to White parents, Black parents reported significantly fewer autism concerns and fewer social and restricted and repetitive behavior concerns. However, Black parents did not report significantly fewer non-autism concerns. Race did not influence parent report of disruptive behavior concerns. Lower reporting of autism concerns by Black parents may impact providers’ abilities to identify children who need further screening or evaluation.
Autism spectrum disorder (ASD) is a complex and heterogeneous disorder, diagnosed on the basis of behavioral symptoms during the second year of life or later. Finding scalable biomarkers for early detection is challenging because of the variability in presentation of the disorder and the need for simple measurements that could be implemented routinely during well-baby checkups. EEG is a relatively easy-to-use, low cost brain measurement tool that is being increasingly explored as a potential clinical tool for monitoring atypical brain development. EEG measurements were collected from 99 infants with an older sibling diagnosed with ASD, and 89 low risk controls, beginning at 3 months of age and continuing until 36 months of age. Nonlinear features were computed from EEG signals and used as input to statistical learning methods. Prediction of the clinical diagnostic outcome of ASD or not ASD was highly accurate when using EEG measurements from as early as 3 months of age. Specificity, sensitivity and PPV were high, exceeding 95% at some ages. Prediction of ADOS calibrated severity scores for all infants in the study using only EEG data taken as early as 3 months of age was strongly correlated with the actual measured scores. This suggests that useful digital biomarkers might be extracted from EEG measurements.
Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic organization in diseased brains are limited. In this work, we integrated genotypes and RNA sequencing in brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, and bipolar disorder, as well as controls. More than 25% of the transcriptome exhibits differential splicing or expression, with isoform-level changes capturing the largest disease effects and genetic enrichments. Coexpression networks isolate disease-specific neuronal alterations, as well as microglial, astrocyte, and interferon-response modules defining previously unidentified neural-immune mechanisms. We integrated genetic and genomic data to perform a transcriptome-wide association study, prioritizing disease loci likely mediated by cis effects on brain expression. This transcriptome-wide characterization of the molecular pathology across three major psychiatric disorders provides a comprehensive resource for mechanistic insight and therapeutic development.
The role of de novo mutations in regulatory elements affecting genes associated with developmental disorders, or other genes, has been essentially unexplored. We identified de novo mutations in three classes of putative regulatory elements in almost 8,000 patients with developmental disorders. Here we show that de novo mutations in highly evolutionarily conserved fetal brain-active elements are significantly and specifically enriched in neurodevelopmental disorders. We identified a significant twofold enrichment of recurrently mutated elements. We estimate that, genome-wide, 1-3% of patients without a diagnostic coding variant carry pathogenic de novo mutations in fetal brain-active regulatory elements and that only 0.15% of all possible mutations within highly conserved fetal brain-active elements cause neurodevelopmental disorders with a dominant mechanism. Our findings represent a robust estimate of the contribution of de novo mutations in regulatory elements to this genetically heterogeneous set of disorders, and emphasize the importance of combining functional and evolutionary evidence to identify regulatory causes of genetic disorders.
OBJECTIVE: This cluster randomized trial (CRT) evaluated the efficacy of the Classroom Social, Communication, Emotional Regulation, and Transactional Support (SCERTS) Intervention (CSI) compared with usual school-based education with autism training modules (ATM).
METHOD: Sixty schools with 197 students with autism spectrum disorder (ASD) in 129 classrooms were randomly assigned to CSI or ATM. Mean student age was 6.79 years (SD 1.05) and 81.2% were male. CSI teachers were trained on the model and provided coaching throughout the school year to assist with implementation. A CRT, with students nested within general and special education classrooms nested within schools, was used to evaluate student outcomes.
RESULTS: The CSI group showed significantly better outcomes than the ATM group on observed measures of classroom active engagement with respect to social interaction. The CSI group also had significantly better outcomes on measures of adaptive communication, social skills, and executive functioning with Cohen’s d effect sizes ranging from 0.31 to 0.45.
CONCLUSION: These findings support the preliminary efficacy of CSI, a classroom-based, teacher-implemented intervention for improving active engagement, adaptive communication, social skills, executive functioning, and problem behavior within a heterogeneous sample of students with ASD. This makes a significant contribution to the literature by demonstrating efficacy of a classroom-based teacher-implemented intervention with a heterogeneous group of students with ASD using both observed and reported measures. (PsycINFO Database Record
A number of studies of parent-mediated interventions in autism spectrum disorder have been published in the last 15 years. We reviewed 19 randomized clinical trials of parent-mediated interventions for children with autism spectrum disorder between the ages of 1 and 6 years and conducted a meta-analysis on their efficacy. Meta-analysis outcomes were autism spectrum disorder symptom severity, socialization, communication-language, and cognition. Quality of evidence was rated as moderate for autism spectrum disorder symptom severity, communication-language, and cognition, and very low for socialization. Weighted Hedges’ g varied from 0.18 (communication-language) to 0.27 (socialization) and averaged 0.23 across domains. We also examined the relationship between outcome and dose of parent training, type of control group, and type of informant (parent and clinician). Outcomes were not significantly different based on dose of treatment. Comparing parent training to treatment-as-usual did not result in significantly different treatment effects than when parent training was compared to an active comparison group. Based on parent report only, treatment effects were significant for communication-language and non-significant for socialization, yet the opposite was found based on clinician-rated tools. This meta-analysis suggests that while most outcome domains of parent-delivered intervention are associated with small effects, the quality of research is improving.
Despite reports have noted that children severely affected by autism spectrum disorder (ASD) appear to have been understudied. Rigorous analysis of this observation has been limited, and the representation of severity has not been well-described. We assessed three domains of severity (communication ability, cognitive functioning, and adaptive functioning) in 367 treatment studies of children with ASD published 1991-2013. We found that the proportion of studies that included the severely affected population decreased significantly over time, as well as wide variability in measurement and reporting. Inadequate representation of the full autism spectrum in the literature could lead to an unbalanced picture of ASD and leave behind those with arguably the greatest need.
OBJECTIVE: Many states with mandates requiring commercial insurers to cover autism spectrum disorder (ASD) health services specify upper age limits above which coverage is no longer mandated. It is unknown what effects these age caps have on health service use and spending among adolescents who have exceeded the age cap.
METHOD: Using administrative claims data from 3 national commercial insurers, a difference-in-differences approach was used to estimate effects of age caps on health service use and spending among adolescents with ASD. Statistical models compared changes in use and spending between those above versus below the age cap among individuals eligible versus ineligible for mandated coverage. The analytic sample included data from 2008 through 2012 on 7,845 individuals (151,976 person-months) ages 10 to 21 years in 11 states imposing mandate age caps going into effect during adolescence.
RESULTS: Age caps were associated with 4.2 percentage point (95% CI = -7.0, -1.5) lower probability of any ASD-specific service use in a month and $69 less (95% CI = -112, -$26) in average monthly spending on ASD-specific services than would have been expected given concomitant pre-post age cap differences among individuals in the same states who were never eligible for mandate-covered services. In addition, age caps were associated with $99 (95% CI = -$168, -$30) lower average monthly spending on all health care services.
CONCLUSION: Insurance mandates that include age caps going into effect during adolescence reduce health service use and spending among individuals with ASD during a critical phase of the life course.
OBJECTIVES: To investigate if children after receiving an ASD diagnosis obtain their remaining scheduled vaccines according to the Advisory Committee on Immunization Practices (ACIP) recommendations and to compare the vaccination patterns of younger siblings of children with ASD with the vaccination patterns of younger siblings of children without ASD.
DESIGN, SETTING, AND PARTICIPANTS: This investigation was a retrospective matched cohort study. The setting was 6 integrated health care delivery systems across the United States within the Vaccine Safety Datalink. Participants were children born between January 1, 1995, and September 30, 2010, and their younger siblings born between January 1, 1997, and September 30, 2014. The end of follow-up was September 30, 2015.
EXPOSURES: Recommended childhood vaccines between ages 1 month and 12 years.
MAIN OUTCOME AND MEASURE: The proportion of children who received all of their vaccine doses according to ACIP recommendations.
RESULTS: The study included 3729 children with ASD (676 [18.1%] female), 592 907 children without ASD, and their respective younger siblings. Among children without ASD, 250 193 (42.2%) were female. For vaccines recommended between ages 4 and 6 years, children with ASD were significantly less likely to be fully vaccinated compared with children without ASD (adjusted rate ratio, 0.87; 95% CI, 0.85-0.88). Within each age category, vaccination rates were significantly lower among younger siblings of children with ASD compared with younger siblings of children without ASD. The adjusted rate ratios varied from 0.86 for siblings younger than 1 year to 0.96 for those 11 to 12 years old. Parents who had a child with ASD were more likely to refuse at least 1 recommended vaccine for that child’s younger sibling and to limit the number of vaccines administered during the younger sibling’s first year of life.
CONCLUSIONS AND RELEVANCE: Children with ASD and their younger siblings were undervaccinated compared with the general population. The results of this study suggest that children with ASD and their younger siblings are at increased risk of vaccine-preventable diseases.
IMPORTANCE: In recent years, rates of vaccination have been declining. Whether this phenomenon disproportionately affects children with autism spectrum disorder (ASD) or their younger siblings is unknown.
OBJECTIVES: To investigate if children after receiving an ASD diagnosis obtain their remaining scheduled vaccines according to the Advisory Committee on Immunization Practices (ACIP) recommendations and to compare the vaccination patterns of younger siblings of children with ASD with the vaccination patterns of younger siblings of children without ASD.
DESIGN, SETTING, AND PARTICIPANTS: This investigation was a retrospective matched cohort study. The setting was 6 integrated health care delivery systems across the United States within the Vaccine Safety Datalink. Participants were children born between January 1, 1995, and September 30, 2010, and their younger siblings born between January 1, 1997, and September 30, 2014. The end of follow-up was September 30, 2015.
EXPOSURES: Recommended childhood vaccines between ages 1 month and 12 years.
MAIN OUTCOME AND MEASURE: The proportion of children who received all of their vaccine doses according to ACIP recommendations.
RESULTS: The study included 3729 children with ASD (676 [18.1%] female), 592 907 children without ASD, and their respective younger siblings. Among children without ASD, 250 193 (42.2%) were female. For vaccines recommended between ages 4 and 6 years, children with ASD were significantly less likely to be fully vaccinated compared with children without ASD (adjusted rate ratio, 0.87; 95% CI, 0.85-0.88). Within each age category, vaccination rates were significantly lower among younger siblings of children with ASD compared with younger siblings of children without ASD. The adjusted rate ratios varied from 0.86 for siblings younger than 1 year to 0.96 for those 11 to 12 years old. Parents who had a child with ASD were more likely to refuse at least 1 recommended vaccine for that child’s younger sibling and to limit the number of vaccines administered during the younger sibling’s first year of life.
CONCLUSIONS AND RELEVANCE: Children with ASD and their younger siblings were undervaccinated compared with the general population. The results of this study suggest that children with ASD and their younger siblings are at increased risk of vaccine-preventable diseases.