Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics.

MOTIVATION: Phecodes are widely used and easily adapted phenotypes based on International Classification of Diseases codes. The current version of phecodes (v1.2) was designed primarily to study common/complex diseases diagnosed in adults; however, there are numerous limitations in the codes and their structure. RESULTS: Here, we present phecodeX, an expanded version of phecodes with a revised structure and 1,761 new codes. PhecodeX adds granularity to phenotypes in key disease domains that are under-represented in the current phecode structure-including infectious disease, pregnancy, congenital anomalies, and neonatology-and is a more robust representation of the medical phenome for global use in discovery research. AVAILABILITY AND IMPLEMENTATION: phecodeX is available at https://github.com/PheWAS/phecodeX.

Implications of Sleep Health Policy: Daylight Saving and School Start Times.

ABSTRACT: Two proposed public policies, ending seasonal clock change with a transition to permanent Standard Time and moving middle school and high school start times later, are population-based initiatives to improve sleep health. Daylight Saving Time and early school start times are associated with reduced sleep duration and increased circadian misalignment, the effects of which impact not only long-term health outcomes including obesity, cerebrovascular and cardiovascular disease, and cancer, but also mental health, academics, workforce productivity, and safety outcomes. This article highlights studies that led to the endorsement of these public policies by multiple scientific and medical organizations. Neurologists should advocate at the state and federal levels and educate the population about the importance of sleep health.

ECHO autism adult healthcare: Training community clinicians to provide quality care for autistic adults.

Autistic adults experience significant unmet healthcare needs, with opportunities for improvement in both the systems and the practitioners who serve this population. Primary care physicians/practitioners (PCPs) are a natural choice to provide comprehensive care to autistic adults but often lack experience in serving this population. This pilot study developed and tested an Extension for Community Healthcare Outcomes (ECHO) Autism model adapted from our previous work, focused specifically on training PCPs in best-practice care for autistic adults. The project was informed directly by the perspectives and preferences of autistic adults, caregivers, and PCPs. Two consecutive cohorts of PCPs participated in ECHO Autism Adult Healthcare sessions. Each cohort met 1 h twice a month for 6 months, with 37 PCPs (n = 20 in Cohort 1, and n = 17 in Cohort 2) participating. Based on findings from the first cohort, adjustments were made to refine the session preparation, curriculum, conduct of the ECHO, resources, and evaluation. After participation in the ECHO Autism program, PCP self-efficacy and satisfaction improved, while the number of perceived barriers did not change. Knowledge did not improve significantly in Cohort 1, but after adjustments to the training model, participants in Cohort 2 showed significant knowledge gains. While attention to systems of care is critical to addressing barriers in healthcare in the autistic population, the ECHO Autism Adult Healthcare model is feasible and holds promise for improving PCP satisfaction and self-efficacy in working with autistic adults.

The physical and psychiatric health conditions related to autism genetic scores, across genetic ancestries, sexes and age-groups in electronic health records.

BACKGROUND: Although polygenic scores (PGS) for autism have been related to various psychiatric and medical conditions, most studies to date have been conducted in research ascertained populations. We aimed to identify the psychiatric and physical conditions associated with autism PGS in a health care setting. METHODS: We computed PGS for 12,383 unrelated participants of African genetic ancestry (AF) and 65,363 unrelated participants of European genetic ancestry (EU) from Vanderbilt's de-identified biobank. Next, we performed phenome wide association studies of the autism PGS within these two genetic ancestries. RESULTS: Seven associations surpassed the Bonferroni adjusted threshold for statistical significance (p = 0.05/1374 = 3.6 × 10-5) in the EU participants, including mood disorders (OR (95%CI) = 1.08(1.05 to 1.10), p = 1.0 × 10-10), autism (OR (95%CI) = 1.34(1.24 to 1.43), p = 1.2 × 10-9), and breast cancer (OR (95%CI) = 1.09(1.05 to 1.14), 2.6 × 10-5). There was no statistical evidence for PGS-phenotype associations in the AF participants. Conditioning on the diagnosis of autism or on median body mass index (BMI) did not impact the strength of the reported associations. Although we observed some sex differences in the pattern of associations, there was no significant interaction between sex and autism PGS. Finally, the associations between autism PGS and autism diagnosis were stronger in childhood and adolescence, while the associations with mood disorders and breast cancer were stronger in adulthood. DISCUSSION: Our findings indicate that autism PGS is not only related to autism diagnosis but may also be related to adult-onset conditions, including mood disorders and some cancers. CONCLUSIONS: Our study raises the hypothesis that genes associated with autism may also increase the risk for cancers later in life. Future studies are necessary to replicate and extend our findings.

Health conditions in autism: Defining the trajectory from adolescence to early adulthood.

Autistic adults, as compared to non-autistic adults, have increased rates of nearly all medical and psychiatric conditions. Many of these conditions begin in childhood, although few longitudinal studies have been conducted to examine prevalence rates of these conditions from adolescence into early adulthood. In this study, we analyze the longitudinal trajectory of health conditions in autistic youth, compared to age and sex-matched non-autistic youth, transitioning from adolescence into early adulthood in a large integrated health care delivery system. The percent and modeled prevalence of common medical and psychiatric conditions increased from age 14 to 22 years, with autistic youth having a higher prevalence of most conditions than non-autistic youth. The most prevalent conditions in autistic youth at all ages were obesity, neurological disorders, anxiety, and ADHD. The prevalence of obesity and dyslipidemia rose at a faster rate in autistic youth compared to non-autistic youth. By age 22, autistic females showed a higher prevalence of all medical and psychiatric conditions compared to autistic males. Our findings emphasize the importance of screening for medical and psychiatric conditions in autistic youth, coupled with health education targeted at this population, to mitigate the development of adverse health outcomes in autistic adults.

A Practice Pathway for the Treatment of Night Wakings in Children with Autism Spectrum Disorder.

Children with autism spectrum disorder (ASD) report high rates of sleep problems. In 2012, the Autism Treatment Network/ Autism Intervention Research Network on Physical Health (ATN/AIR-P) Sleep Committee developed a pathway to address these concerns. Since its publication, ATN/AIR-P clinicians and parents have identified night wakings as a refractory problem unaddressed by the pathway. We reviewed the existing literature and identified 76 scholarly articles that provided data on night waking in children with ASD. Based on the available literature, we propose an updated practice pathway to identify and treat night wakings in children with ASD.

Pediatric sleep: current knowledge, gaps, and opportunities for the future.

This White Paper addresses the current gaps in knowledge, as well as opportunities for future studies in pediatric sleep. The Sleep Research Society's Pipeline Development Committee assembled a panel of experts tasked to provide information to those interested in learning more about the field of pediatric sleep, including trainees. We cover the scope of pediatric sleep, including epidemiological studies and the development of sleep and circadian rhythms in early childhood and adolescence. Additionally, we discuss current knowledge of insufficient sleep and circadian disruption, addressing the neuropsychological impact (affective functioning) and cardiometabolic consequences. A significant portion of this White Paper explores pediatric sleep disorders (including circadian rhythm disorders, insomnia, restless leg and periodic limb movement disorder, narcolepsy, and sleep apnea), as well as sleep and neurodevelopment disorders (e.g. autism and attention deficit hyperactivity disorder). Finally, we end with a discussion on sleep and public health policy. Although we have made strides in our knowledge of pediatric sleep, it is imperative that we address the gaps to the best of our knowledge and the pitfalls of our methodologies. For example, more work needs to be done to assess pediatric sleep using objective methodologies (i.e. actigraphy and polysomnography), to explore sleep disparities, to improve accessibility to evidence-based treatments, and to identify potential risks and protective markers of disorders in children. Expanding trainee exposure to pediatric sleep and elucidating future directions for study will significantly improve the future of the field.

Health Care Needs, Experiences, and Perspectives of Autistic Adults.

Background: Autistic adults have high rates of co-occurring health conditions, suicide, and premature mortality, yet often experience health care barriers and poor health outcomes. A better understanding of the health care needs and experiences of autistic adults is essential for improving the health care system and patient experience. Methods: This study examined the perspectives of autistic adults regarding their health care experiences in primary care and other settings and their suggestions for improvement using both qualitative and quantitative methods. Twenty autistic adults (aged 18-35 years, 65% male) completed surveys and individual semi-structured interviews. Results: Qualitative data analysis results revealed 10 subthemes across 3 overarching themes: (1) system- and clinic-level factors affect access to care, (2) aspects of the clinic environment affect health care experiences, and (3) provider knowledge and practices affect health care experiences. Within the first theme, participants described barriers to obtaining services, including scheduling logistics, costs and inadequate insurance coverage, and transportation barriers. The second theme focused on aspects of the clinic environment that participants found especially relevant to their health care experiences and that required specific accommodations. This included sensory input, anxiety-provoking situations and procedures, and wait time. Within the third theme, participants emphasized aspects of providers' care that affected their health care experiences. Key factors included provider knowledge about autism, communication, rapport, and individualized care and patient-provider partnerships. Conclusion: Overall, the findings point to a need for provider training and improvements to the health care delivery system to better meet the unique needs of autistic adults.

Why is this an important issue?: Receiving good health care is important for health and well-being. Understanding autistic adults' perspectives on their health care experiences will help identify ways that health care services can be improved to better meet their needs and preferences in the future. What was the purpose of this study?: The purpose of this study was to learn from autistic adults about their health care needs, experiences, and suggestions for improvement. What did the researchers do?: The researchers asked autistic adults in the United States to complete a survey and participate in an interview over Zoom. The survey and interview questions asked about their experiences receiving health care services and suggestions for how to improve health care services for autistic adults. What were the results of the study?: Twenty autistic adults between the ages of 18 and 35 years participated in this study. Most participants were men (65%) and most were White (75%). The participants shared many important insights about their primary health care experiences and experiences in other health care settings. The results fell into main "themes" or ideas that people had in common. These themes are not listed in any particular order. Autistic adults described many factors that make it hard to access to care, such as getting an appointment, finding transportation, or paying for health care. They explained that the clinic environment needs to be better suited to their needs, such as having a quiet place to wait or sensory accommodations. Participants wanted their doctors to know more about autism and to be able to connect and communicate with them. They also wanted their doctors to partner with them to make sure their health care treatment plan is acceptable and understandable. What do these findings add to what was already known?: These findings show that autistic adults in the United States face many barriers in receiving health care. Some recommendations for improvement may be helpful for all patients, such as being able to book appointments online or having a doctor who does not rush you. Other improvements need to be tailored to the unique needs of autistic patients, such sensory accommodations or autism training for doctors and clinic staff. What are potential weaknesses in the study?: Because the study was small and only included adults who were able to share about their experiences during an interview, these results may not apply to all autistic adults. Another limitation is that the study was designed and carried out by non-autistic (allistic) researchers, who have different perspectives from autistic people. We asked participants to help us interpret our findings to help address this limitation. How will these findings help autistic adults in the future?: The insights from this study provide a lot of recommendations about how health care services can be improved to better meet the needs and preferences of autistic adults in the future.

A practical approach to identifying autistic adults within the electronic health record.

The electronic health record (EHR) provides valuable data for understanding physical and mental health conditions in autism. We developed an approach to identify charts of autistic young adults, retrieved from our institution's de-identified EHR database. Clinical notes within two cohorts were identified. Cohort 1 charts had at least one International Classification of Diseases (ICD-CM) autism code. Cohort 2 charts had only autism key terms without ICD-CM codes, and at least four notes per chart. A natural language processing tool parsed medical charts to identify key terms associated with autism diagnoses and mapped them to Unified Medical Language System Concept Unique Identifiers (CUIs). Average scores were calculated for each set of charts based on captured CUIs. Chart review determined whether patients met criteria for autism using a classification rubric. In Cohort 1, of 418 patients, 361 were confirmed to have autism by chart review. Sensitivity was 0.99 and specificity was 0.68 with positive predictive value (PPV) of 0.97. Specificity improved to 0.81 (sensitivity was 0.95; PPV was 0.98) when the number of notes was limited to four or more per chart. In Cohort 2, 48 of 136 patients were confirmed to have autism by chart review. Sensitivity was 0.95, specificity was 0.73, and PPV was 0.70. Our approach, which included using key terms, identified autism charts with high sensitivity, even in the absence of ICD-CM codes. Relying on ICD-CM codes alone may result in inclusion of false positive cases and exclusion of true cases with autism.

Appropriateness, Acceptability, and Feasibility of a Neurodiversity-Based Self-determination Program for Autistic Adults.

Published self-determination programs do not adequately address the needs of autistic adults. We designed a multi-component self-determination program, grounded in the neurodiversity paradigm, to help autistic adults achieve goals to improve their quality of life. The first phase involved 5 days of psychoeducation, practice, and social events; the second phase included 3 months of telecoaching; and the third phase included follow-up. Thirty-four university students coached 31 autistic adults on three evolving goals. On average, participants completed one goal per week. Most participants were satisfied with the program. We found that the program was appropriate, acceptable, and feasible. This program is a promising approach to helping autistic adults gain self-determination skills and improve their quality of life.

It is time to abolish the clock change and adopt permanent standard time in the United States: a Sleep Research Society position statement.

Daylight saving time (DST) refers to the practice of advancing clock time by 1 h each spring, with a return (setting back) to standard time (ST) each fall. Numerous sleep and circadian societies other than the Sleep Research Society have published statements in support of permanent ST, and permanent ST has also received support from multiple medical societies and organizations. This perspective discusses the positive and negative health and economic consequences of permanent DST, permanent ST, and maintaining the status quo (DST for part of the year). After a thorough review of the existing literature, the SRS advocates the adoption of permanent ST.

Investigating the genetic pathways of insomnia in Autism Spectrum Disorder.

BACKGROUND: Sleep problems are common in children with autism spectrum disorder (autism). There is sparse research to date to examine whether insomnia in people with autism is related to autism genetics or insomnia genetics. Moreover, there is a lack of research examining whether circadian-rhythm related genes share potential pathways with autism. AIMS: To address this research gap, we tested whether polygenic scores of insomnia or autism are related to risk of insomnia in people with autism, and whether the circadian genes are associated with insomnia in people with autism. METHODS AND PROCEDURES: We tested these questions using the phenotypically and genotypically rich MSSNG dataset (N = 1049) as well as incorporating in the analyses data from the Vanderbilt University Biobank (BioVU) (N = 349). OUTCOMES AND RESULTS: In our meta-analyzed sample, there was no evidence of associations between the polygenic scores (PGS) for insomnia and a clinical diagnosis of insomnia, or between the PGS of autism and insomnia. We also did not find evidence of a greater burden of rare and disruptive variation in the melatonin and circadian genes in individuals with autism and insomnia compared to individuals with autism without insomnia. CONCLUSIONS AND IMPLICATIONS: Overall, we did not find evidence for strong effects of genetic scores influencing sleep in people with autism, however, we cannot rule out the possibility that smaller genetic effects may play a role in sleep problems. Our study indicated the need for a larger collection of data on sleep problems and sleep quality among people with autism.

Calculating genetic risk for dysfunction in pleiotropic biological processes using whole exome sequencing data.

BACKGROUND: Numerous genes are implicated in autism spectrum disorder (ASD). ASD encompasses a wide-range and severity of symptoms and co-occurring conditions; however, the details of how genetic variation contributes to phenotypic differences are unclear. This creates a challenge for translating genetic evidence into clinically useful knowledge. Sleep disturbances are particularly prevalent co-occurring conditions in ASD, and genetics may inform treatment. Identifying convergent mechanisms with evidence for dysfunction that connect ASD and sleep biology could help identify better treatments for sleep disturbances in these individuals. METHODS: To identify mechanisms that influence risk for ASD and co-occurring sleep disturbances, we analyzed whole exome sequence data from individuals in the Simons Simplex Collection (n = 2380). We predicted protein damaging variants (PDVs) in genes currently implicated in either ASD or sleep duration in typically developing children. We predicted a network of ASD-related proteins with direct evidence for interaction with sleep duration-related proteins encoded by genes with PDVs. Overrepresentation analyses of Gene Ontology-defined biological processes were conducted on the resulting gene set. We calculated the likelihood of dysfunction in the top overrepresented biological process. We then tested if scores reflecting genetic dysfunction in the process were associated with parent-reported sleep duration. RESULTS: There were 29 genes with PDVs in the ASD dataset where variation was reported in the literature to be associated with both ASD and sleep duration. A network of 108 proteins encoded by ASD and sleep duration candidate genes with PDVs was identified. The mechanism overrepresented in PDV-containing genes that encode proteins in the interaction network with the most evidence for dysfunction was cerebral cortex development (GO:0,021,987). Scores reflecting dysfunction in this process were associated with sleep durations; the largest effects were observed in adolescents (p = 4.65 × 10-3). CONCLUSIONS: Our bioinformatic-driven approach detected a biological process enriched for genes encoding a protein-protein interaction network linking ASD gene products with sleep duration gene products where accumulation of potentially damaging variants in individuals with ASD was associated with sleep duration as reported by the parents. Specifically, genetic dysfunction impacting development of the cerebral cortex may affect sleep by disrupting sleep homeostasis which is evidenced to be regulated by this brain region. Future functional assessments and objective measurements of sleep in adolescents with ASD could provide the basis for more informed treatment of sleep problems in these individuals.

A REDCap-based model for online interventional research: Parent sleep education in autism.

INTRODUCTION: The use of online platforms for pediatric healthcare research is timely, given the current pandemic. These platforms facilitate trial efficiency integration including electronic consent, randomization, collection of patient/family survey data, delivery of an intervention, and basic data analysis. METHODS: We created an online digital platform for a multicenter study that delivered an intervention for sleep disorders to parents of children with autism spectrum disorder (ASD). An advisory parent group provided input. Participants were randomized to receive either a sleep education pamphlet only or the sleep education pamphlet plus three quick-tips sheets and two videos that reinforced the material in the pamphlet (multimedia materials). Three measures - Family Inventory of Sleep Habits (FISH), Children's Sleep Habits Questionnaire modified for ASD (CSHQ-ASD), and Parenting Sense of Competence (PSOC) - were completed before and after 12 weeks of sleep education. RESULTS: Enrollment exceeded recruitment goals. Trial efficiency was improved, especially in data entry and automatic notification of participants related to survey completion. Most families commented favorably on the study. While study measures did not improve with treatment in either group (pamphlet or multimedia materials), parents reporting an improvement of ≥3 points in the FISH score showed a significantly improved change in the total CSHQ (P = 0.038). CONCLUSION: Our study demonstrates the feasibility of using online research delivery platforms to support studies in ASD, and more broadly, pediatric clinical and translational research. Online platforms may increase participant inclusion in enrollment and increase convenience and safety for participants and study personnel.

A community-based sleep educational intervention for children with autism spectrum disorder.

BACKGROUND: Sleep problems are common in children with autism spectrum disorder (ASD). Sleep education, effective in improving sleep in ASD, may be difficult to access. We determined if community-based pediatric therapists could successfully deliver sleep educational interventions to caregivers of children with ASD. METHODS: A seven-week feasibility study was conducted consisting of 10 children and caregivers. This feasibility study informed the development of a 16-week preliminary effectiveness study, which consisted of 33 children and caregivers. Children, ages 2-12 years, with a clinical diagnosis of autism and caregiver-reported sleep onset delay of 30 min were included. Community therapists underwent comprehensive training in sleep education and then met with caregiver participants to provide sleep education to each family. Semi-structured qualitative interviews were conducted with all families who completed study procedures.In the feasibility and preliminary effectiveness studies, child participants wore an actigraphy watch (at baseline and after sleep education) and caregivers completed the Child Sleep Habits Questionnaire and Family Inventory of Sleep Habits at baseline and after sleep education; the Child Behavior Checklist was also completed by caregivers in the preliminary effectiveness study. RESULTS: Educator fidelity to the manualized curriculum was maintained. Caregivers showed appropriate understanding, comfort, and implementation of the curriculum. Qualitative and quantitative measures, including caregiver surveys and actigraphy, showed improvements in child sleep and behavior. CONCLUSIONS: Community-based therapists can successfully deliver sleep education to families of children with ASD, which has favorable implications for improving access to care in this population.

Evaluating Sleep Disturbances in Children With Rare Genetic Neurodevelopmental Syndromes.

BACKGROUND: Adequate sleep is important for proper neurodevelopment and positive health outcomes. Sleep disturbances are more prevalent in children with genetically determined neurodevelopmental syndromes compared with typically developing counterparts. We characterize sleep behavior in Rett (RTT), Angelman (AS), and Prader-Willi (PWS) syndromes to identify effective approaches for treating sleep problems in these populations. We compared sleep-related symptoms across individuals with these different syndromes with each other, and with typically developing controls. METHODS: Children were recruited from the Rare Diseases Clinical Research Network consortium registries; unaffected siblings were enrolled as related controls. For each participant, a parent completed multiple sleep questionnaires including Pediatric Sleep Questionnaire (Sleep-Disordered Breathing), Children's Sleep Habits Questionnaire (CSHQ), and Pediatric Daytime Sleepiness Scale. RESULTS: Sleep data were analyzed from 714 participants, aged two to 18 years. Young children with AS had more reported sleep problems than children with RTT or PWS. Older children with RTT had more reported daytime sleepiness than those with AS or PWS. Finally, all individuals with RTT had more evidence of sleep-disordered breathing when compared with individuals with PWS. Notably, typically developing siblings were also reported to have sleep problems, except for sleep-related breathing disturbances, which were associated with each of the genetic syndromes. CONCLUSIONS: Individuals with RTT, AS, and PWS frequently experience sleep problems, including sleep-disordered breathing. Screening for sleep problems in individuals with these and other neurogenetic disorders should be included in clinical assessment and managements. These data may also be useful in developing treatment strategies and in clinical trials.

Recurrence rate of the first nonfebrile seizure in children with autism spectrum disorder.

OBJECTIVE: Epilepsy prevalence is higher in children with Autism Spectrum Disorder (ASD) and is a contributor to morbidity and mortality. Little is known about the recurrence rate after the first nonfebrile seizure in this population, specifically in regard to seizure type and electroencephalogram (EEG) findings. METHODS: We reviewed pediatric medical records at our institution between 2006 and 2016 for subjects with ASD who had a first seizure. We then looked for risk of a recurrent non-provoked seizure within the next two years. RESULTS: Overall, the recurrence rate in this study was 70.9%. This is much higher than the general population. The recurrence rate was higher in patients who had a generalized convulsion compared to those who had a behavioral arrest. When the first seizure was a generalized convulsion, there was an 84% chance of developing a second convulsion, whereas the recurrence rate was 59% for behavioral arrest type seizures (p = 0.002). The odds of having recurrence when the first seizure is a generalized convulsion was 5.36 higher than when it was a behavioral arrest (95% CI 2.14-13.42, p < 0.001). An abnormal EEG was a strong predictor of seizure recurrence in both seizure types. However, even with a normal EEG, generalized convulsions were more likely to recur within 2 years compared to behavioral arrest (OR 6.3, 95% CI 2.1-19). SIGNIFICANCE: The recurrence rate for nonfebrile seizures in children with ASD is much higher than the general population, especially for generalized convulsions. An abnormal EEG has a strong predictive value for seizure recurrence. However, even when the EEG is normal, the recurrence rate for generalized convulsions is quite high. This is an important finding as epilepsy contributes to morbidity and mortality in this group and may impact clinical decisions about when to start anti-seizure medications.