Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries.

Balanced chromosomal abnormalities (BCAs) represent a relatively untapped reservoir of single-gene disruptions in neurodevelopmental disorders (NDDs). We sequenced BCAs in patients with autism or related NDDs, revealing disruption of 33 loci in four general categories: (1) genes previously associated with abnormal neurodevelopment (e.g., AUTS2, FOXP1, and CDKL5), (2) single-gene contributors to microdeletion syndromes (MBD5, SATB2, EHMT1, and SNURF-SNRPN), (3) novel risk loci (e.g., CHD8, KIRREL3, and ZNF507), and (4) genes associated with later-onset psychiatric disorders (e.g., TCF4, ZNF804A, PDE10A, GRIN2B, and ANK3). We also discovered among neurodevelopmental cases a profoundly increased burden of copy-number variants from these 33 loci and a significant enrichment of polygenic risk alleles from genome-wide association studies of autism and schizophrenia. Our findings suggest a polygenic risk model of autism and reveal that some neurodevelopmental genes are sensitive to perturbation by multiple mutational mechanisms, leading to variable phenotypic outcomes that manifest at different life stages.

Heritable genotype contrast mining reveals novel gene associations specific to autism subgroups.

Though the genetic etiology of autism is complex, our understanding can be improved by identifying genes and gene-gene interactions that contribute to the development of specific autism subtypes. Identifying such gene groupings will allow individuals to be diagnosed and treated according to their precise characteristics. To this end, we developed a method to associate gene combinations with groups with shared autism traits, targeting genetic elements that distinguish patient populations with opposing phenotypes. Our computational method prioritizes genetic variants for genome-wide association, then utilizes Frequent Pattern Mining to highlight potential interactions between variants. We introduce a novel genotype assessment metric, the Unique Inherited Combination support, which accounts for inheritance patterns observed in the nuclear family while estimating the impact of genetic variation on phenotype manifestation at the individual level. High-contrast variant combinations are tested for significant subgroup associations. We apply this method by contrasting autism subgroups defined by severe or mild manifestations of a phenotype. Significant associations connected 286 genes to the subgroups, including 193 novel autism candidates. 71 pairs of genes have joint associations with subgroups, presenting opportunities to investigate interacting functions. This study analyzed 12 autism subgroups, but our informatics method can explore other meaningful divisions of autism patients, and can further be applied to reveal precise genetic associations within other phenotypically heterogeneous disorders, such as Alzheimer's disease.

ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons.

Miles-Carpenter syndrome (MCS) was described in 1991 as an XLID syndrome with fingertip arches and contractures and mapped to proximal Xq. Patients had microcephaly, short stature, mild spasticity, thoracic scoliosis, hyperextendable MCP joints, rocker-bottom feet, hyperextended elbows and knees. A mutation, p.L66H, in ZC4H2, was identified in a XLID re-sequencing project. Additional screening of linked families and next generation sequencing of XLID families identified three ZC4H2 mutations: p.R18K, p.R213W and p.V75in15aa. The families shared some relevant clinical features. In silico modeling of the mutant proteins indicated all alterations would destabilize the protein. Knockout mutations in zc4h2 were created in zebrafish and homozygous mutant larvae exhibited abnormal swimming, increased twitching, defective eye movement and pectoral fin contractures. Because several of the behavioral defects were consistent with hyperactivity, we examined the underlying neuronal defects and found that sensory neurons and motoneurons appeared normal. However, we observed a striking reduction in GABAergic interneurons. Analysis of cell-type-specific markers showed a specific loss of V2 interneurons in the brain and spinal cord, likely arising from mis-specification of neural progenitors. Injected human wt ZC4H2 rescued the mutant phenotype. Mutant zebrafish injected with human p.L66H or p.R213W mRNA failed to be rescued, while the p.R18K mRNA was able to rescue the interneuron defect. Our findings clearly support ZC4H2 as a novel XLID gene with a required function in interneuron development. Loss of function of ZC4H2 thus likely results in altered connectivity of many brain and spinal circuits.

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors.

Truncating mutations of chromodomain helicase DNA-binding protein 8 (CHD8), and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA sequencing) with genome-wide CHD8 binding (ChIP sequencing). Suppressing CHD8 to levels comparable with the loss of a single allele caused altered expression of 1,756 genes, 64.9% of which were up-regulated. CHD8 showed widespread binding to chromatin, with 7,324 replicated sites that marked 5,658 genes. Integration of these data suggests that a limited array of direct regulatory effects of CHD8 produced a much larger network of secondary expression changes. Genes indirectly down-regulated (i.e., without CHD8-binding sites) reflect pathways involved in brain development, including synapse formation, neuron differentiation, cell adhesion, and axon guidance, whereas CHD8-bound genes are strongly associated with chromatin modification and transcriptional regulation. Genes associated with ASD were strongly enriched among indirectly down-regulated loci (P < 10(-8)) and CHD8-bound genes (P = 0.0043), which align with previously identified coexpression modules during fetal development. We also find an intriguing enrichment of cancer-related gene sets among CHD8-bound genes (P < 10(-10)). In vivo suppression of chd8 in zebrafish produced macrocephaly comparable to that of humans with inactivating mutations. These data indicate that heterozygous disruption of CHD8 precipitates a network of gene-expression changes involved in neurodevelopmental pathways in which many ASD-associated genes may converge on shared mechanisms of pathogenesis.

rPLR: an imaging system for measuring pupillary light reflex at a distance.

Pupillary light reflex (PLR) is a simple noninvasive neurological test that can reveal a great amount of information of the neural system. We report here a novel imaging system for measuring PLR without using any restraints to limit the subject's movement. Our system incorporates a tracking component that can locate the subject's eye position and redirect the pupillary imaging component to follow the subject's movement. This system can measure PLR, at a distance from the subject, with high spatial resolution (<50 µm) and temporal resolution (120 Hz). Because this new PLR device can accommodate the subject's movement, it is well positioned to test in young children and other people who have difficulty remaining voluntarily still during tests.

Investigation of NRXN1 deletions: clinical and molecular characterization.

Deletions at 2p16.3 involving exons of NRXN1 are associated with susceptibility for autism and schizophrenia, and similar deletions have been identified in individuals with developmental delay and dysmorphic features. We have identified 34 probands with exonic NRXN1 deletions following referral for clinical microarray-based comparative genomic hybridization. To more firmly establish the full phenotypic spectrum associated with exonic NRXN1 deletions, we report the clinical features of 27 individuals with NRXN1 deletions, who represent 23 of these 34 families. The frequency of exonic NRXN1 deletions among our postnatally diagnosed patients (0.11%) is significantly higher than the frequency among reported controls (0.02%; P = 6.08 × 10(-7) ), supporting a role for these deletions in the development of abnormal phenotypes. Generally, most individuals with NRXN1 exonic deletions have developmental delay (particularly speech), abnormal behaviors, and mild dysmorphic features. In our cohort, autism spectrum disorders were diagnosed in 43% (10/23), and 16% (4/25) had epilepsy. The presence of NRXN1 deletions in normal parents and siblings suggests reduced penetrance and/or variable expressivity, which may be influenced by genetic, environmental, and/or stochastic factors. The pathogenicity of these deletions may also be affected by the location of the deletion within the gene. Counseling should appropriately represent this spectrum of possibilities when discussing recurrence risks or expectations for a child found to have a deletion in NRXN1.

Brief Report: A Preliminary Study of the Relationship between Repetitive Behaviors and Concurrent Executive Function Demands in Children with Autism Spectrum Disorder.

The present study evaluated the hypothesis that the strength of the relationship between executive function (EF) and repetitive behaviors and restricted interests (RBRI) symptomatology is moderated by the degree to which concurrent demands are placed on multiple aspects of EF. An eye movement task was used to evaluate inhibition and task switching ability (both together and in isolation) in a sample of 22 children with autism spectrum disorder (ASD). The Repetitive Behavior Scale-Revised (RBS-R) was used to assess the severity of RBRI symptoms. Results provide preliminary support for the aforementioned hypothesis. RBS-R scores were significantly correlated with task performance when simultaneous demands were placed on switching and inhibition; however, no such relationship was found for inhibition-only or switching-only task conditions.

Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder.

Defining different genetic subtypes of autism spectrum disorder (ASD) can enable the prediction of developmental outcomes. Based on minor physical and major congenital anomalies, we categorize 325 Canadian children with ASD into dysmorphic and nondysmorphic subgroups. We develop a method for calculating a patient-level, genome-wide rare variant score (GRVS) from whole-genome sequencing (WGS) data. GRVS is a sum of the number of variants in morphology-associated coding and non-coding regions, weighted by their effect sizes. Probands with dysmorphic ASD have a significantly higher GRVS compared to those with nondysmorphic ASD (P = 0.03). Using the polygenic transmission disequilibrium test, we observe an over-transmission of ASD-associated common variants in nondysmorphic ASD probands (P = 2.9 × 10-3). These findings replicate using WGS data from 442 ASD probands with accompanying morphology data from the Simons Simplex Collection. Our results provide support for an alternative genomic classification of ASD subgroups using morphology data, which may inform intervention protocols.

Autism spectrum disorders--a genetics review.

Autism is an etiologically and clinically heterogeneous group of disorders, diagnosed solely by the complex behavioral phenotype. On the basis of the high-heritability index, geneticists are confident that autism will be the first behavioral disorder for which the genetic basis can be well established. Although it was initially assumed that major genome-wide and candidate gene association studies would lead most directly to common autism genes, progress has been slow. Rather, most discoveries have come from studies of known genetic disorders associated with the behavioral phenotype. New technology, especially array chromosomal genomic hybridization, has both increased the identification of putative autism genes and raised to approximately 25%, the percentage of children for whom an autism-related genetic change can be identified. Incorporating clinical geneticists into the diagnostic and autism research arenas is vital to the field. Interpreting this new technology and deciphering autism's genetic montage require the skill set of the clinical geneticist including knowing how to acquire and interpret family pedigrees, how to analyze complex morphologic, neurologic, and medical phenotypes, sorting out heterogeneity, developing rational genetic models, and designing studies. The current emphasis on deciphering autism spectrum disorders has accelerated the field of neuroscience and demonstrated the necessity of multidisciplinary research that must include clinical geneticists both in the clinics and in the design and implementation of basic, clinical, and translational research.

Detecting corpus callosum abnormalities in autism based on anatomical landmarks.

Autism is a severe developmental disorder whose neurological basis is largely unknown. The aim of this study was to identify the shape differences of the corpus callosum between patients with autism and control subjects. Anatomical landmarks were collected from midsagittal magnetic resonance images of 25 patients and 18 controls. Euclidean distance matrix analysis and thin-plate spline analyses were used to examine the landmark forms. Point-by-point shape comparison was performed both globally and locally. A new local shape comparison scheme was proposed which compared each part of the shape in its local coordinate system. Point correspondence was established among individual shapes based on the inherent landmark correspondence. No significant difference was found in the landmark form between patients and controls, but the distance between the interior genu and the posterior-most section was found to be significantly shorter in patients. Thin-plate spline analysis showed significant group differences between the landmark configurations in terms of the deformation from the overall mean configuration. Significant global shape differences were found in the anterior lower body and posterior bottom, and there was a local shape difference in the anterior bottom. This study can serve as both a clinical reference and a detailed procedural guideline for similar studies in the future.

A longitudinal study of pupillary light reflex in 6- to 24-month children.

Pupillary light reflex (PLR) is an involuntary response where the pupil size changes with luminance. Studies have shown that PLR response was altered in children with autism spectrum disorders (ASDs) and other neurological disorders. However, PLR in infants and toddlers is still understudied. We conducted a longitudinal study to investigate PLR in children of 6-24 months using a remote pupillography device. The participants are categorized into two groups. The 'high risk' (HR) group includes children with one or more siblings diagnosed with ASDs; whereas the 'low risk' (LR) group includes children without an ASD diagnosis in the family history. The participants' PLR was measured every six months until the age of 24 months. The results indicated a significant age effect in multiple PLR parameters including resting pupil radius, minimal pupil radius, relative constriction, latency, and response time. In addition, the HR group had a significantly larger resting and minimal pupil size than the LR group. The experimental data acquired in this study revealed not only general age-related PLR changes in infants and toddlers, but also different PLRs in children with a higher risk of ASD.

Catatonia in Down syndrome: systematic approach to diagnosis, treatment and outcome assessment based on a case series of seven patients.

OBJECTIVE: The goal is to expand our knowledge of catatonia occurring in adolescents and young adults with Down syndrome (DS) by describing the first prospective, consecutive, well-characterized cohort of seven young people with DS diagnosed with catatonia and treated between 2013 and 2018, and to assess each patient's treatment responses. Longitudinal assessment of each patient's response to treatment is intended to provide clinicians and psychiatrists a firm foundation from which assess treatment efficacy. STUDY DESIGN: Young adults with Down syndrome were consecutively enrolled in the study as they were diagnosed with catatonia. A comprehensive data set included medical, laboratory, developmental, demographic, family, social and genetic data, including query into disorders for which individuals with DS are at risk. Catatonia was diagnosed based on an unequivocal history of regression, positive Bush-Francis Catatonia Rating Scale and positive response to intravenous lorazepam. Patients' longitudinal progress was monitored using the Catatonia Impact Scale (CIS) developed for this purpose. RESULTS: Seven consecutive DS patients, who presented with unequivocal regression were diagnosed with catatonia and treated for 2.7-6 years using standard-of-care therapies; primarily GABA agonist, lorazepam, electroconvulsive therapy (ECT) and glutamate antagonists (dextromethorphan/quinidine, memantine, minocycline). Responses to each treatment modality were assessed at clinic visits and through weekly electronic CIS reports. CONCLUSION: Seven young adults with DS were diagnosed with catatonia; all responded to Lorazepam and/or ECT therapy with good to very good results. Though ECT most dramatically returned patients to baseline, symptoms often returned requiring additional ECT. Dextromethorphan/quinidine, not used until mid-2017, appeared to reduce the reoccurrence of symptoms following ECT. Though all seven patients improved significantly, each continues to require some form of treatment to maintain a good level of functioning. Findings of a significant number of autoimmune disorders and laboratory markers of immune activation in this population may guide new diagnostic and treatment opportunities.

Development and validation of a measure of dysmorphology: useful for autism subgroup classification.

Autism spectrum disorders (ASD) comprise a class of neurodevelopmental disorders that can originate from a variety of genetic and environmental causes. To delineate autism's heterogeneity we have looked for biologically-based phenotypes found in consistent proportions of ASD individuals. One informative phenotype is that of generalized dysmorphology, based on whole body examinations by medical geneticists trained in the nuances of anomalous embryologic development. We identified a need for a dysmorphology measure that could be completed by medical clinicians not extensively trained in dysmorphology that would still retain the level of sensitivity and specificity of the comprehensive dysmorphology examination. Based on expert-derived consensus dysmorphology designation of 222 autism patients and a classification validation study of 30 subjects by four dysmorphologists, we determined that dysmorphology designations based on body areas provided superior inter-rater reliability. Using 34 body area designations, we performed a classification and regression tree (CART) analysis to construct a scoring algorithm. Compared to the consensus classification, the model performed with 81% sensitivity and 99% specificity, and classification of a replication dataset of 31 ASD individuals performed well, with 82% sensitivity and 95% specificity. The autism dysmorphology measure (ADM) directs the clinician to score 12 body areas sequentially to arrive at a determination of "dysmorphic" or "nondysmorphic." We anticipate the ADM will permit clinicians to differentiate accurately between dysmorphic and nondysmorphic individuals-allowing better diagnostic classification, prognostication, recurrence risk assessment, and laboratory analysis decisions-and research scientists to better define more homogeneous autism subtypes.

Defining autism subgroups: a taxometric solution.

The purpose of the present study was to determine which behavioral and physical phenotypes would be most likely to divide the ASD population into discrete subgroups. The taxometric methods of Maximum Covariance (MAXCOV) and Minus Mean Below A Cut (MAMBAC) were employed to test for categorical versus continuous variation of each phenotype across the ASD population. Data was retrieved from the Autism Genetic Resource Exchange and the University of Missouri Autism Database. The results of our analyses support subgrouping subjects based on variation in social interaction/communication, intelligence, and essential/complex phenotype; in contrast, subjects varied continuously in insistence on sameness, repetitive sensory motor actions, language acquisition, and, tentatively, adaptive functioning. Stratifying ASD samples based on taxometric results should increase power in gene-finding studies and aid in treatment efficacy research.

Atypical pupillary light reflex in 2-6-year-old children with autism spectrum disorders.

The purpose of this study was to investigate pupillary light reflex (PLR) in 2-6-years-old children with autism spectrum disorders (ASD). A total of 117 medication-free 2-6-year-old boys participated in this study. Sixty participants were diagnosed with ASD (the "ASD group") and the other 57 were in the control group of typical development (the "TD group"). A questionnaire was completed by the parent/guardian for assessing potential dysfunctions in the autonomic nervous system (ANS). The base pupil radius, PLR latency, and constriction time showed a significant age-related trend in both the ASD and TD groups. The base pupil size increased with age in the typically developing children, but not in the ASD group. The ASD group showed more symptoms related to ANS dysfunctions. An association between abnormal sweating with base pupil radius and PLR constriction was observed in the TD group but not the ASD group. The different association of PLR parameters with ANS dysfunction may suggest disrupted autonomic controls in children with ASD. Autism Res 2017, 10: 829-838. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.

Catatonia in Down syndrome; a treatable cause of regression.

OBJECTIVE: The main aim of this case series report is to alert physicians to the occurrence of catatonia in Down syndrome (DS). A second aim is to stimulate the study of regression in DS and of catatonia. A subset of individuals with DS is noted to experience unexplained regression in behavior, mood, activities of daily living, motor activities, and intellectual functioning during adolescence or young adulthood. Depression, early onset Alzheimer's, or just "the Down syndrome" are often blamed after general medical causes have been ruled out. Clinicians are generally unaware that catatonia, which can cause these symptoms, may occur in DS. STUDY DESIGN: Four DS adolescents who experienced regression are reported. Laboratory tests intended to rule out causes of motor and cognitive regression were within normal limits. Based on the presence of multiple motor disturbances (slowing and/or increased motor activity, grimacing, posturing), the individuals were diagnosed with unspecified catatonia and treated with anti-catatonic treatments (benzodiazepines and electroconvulsive therapy [ECT]). RESULTS: All four cases were treated with a benzodiazepine combined with ECT and recovered their baseline functioning. CONCLUSION: We suspect catatonia is a common cause of unexplained deterioration in adolescents and young adults with DS. Moreover, pediatricians and others who care for individuals with DS are generally unfamiliar with the catatonia diagnosis outside schizophrenia, resulting in misdiagnosis and years of morbidity. Alerting physicians to catatonia in DS is essential to prompt diagnosis, appropriate treatment, and identification of the frequency and course of this disorder.

Facial structure analysis separates autism spectrum disorders into meaningful clinical subgroups.

Varied cluster analysis were applied to facial surface measurements from 62 prepubertal boys with essential autism to determine whether facial morphology constitutes viable biomarker for delineation of discrete Autism Spectrum Disorders (ASD) subgroups. Earlier study indicated utility of facial morphology for autism subgrouping (Aldridge et al. in Mol Autism 2(1):15, 2011). Geodesic distances between standardized facial landmarks were measured from three-dimensional stereo-photogrammetric images. Subjects were evaluated for autism-related symptoms, neurologic, cognitive, familial, and phenotypic variants. The most compact cluster is clinically characterized by severe ASD, significant cognitive impairment and language regression. This verifies utility of facially-based ASD subtypes and validates Aldridge et al.'s severe ASD subgroup, notwithstanding different techniques. It suggests that language regression may define a unique ASD subgroup with potential etiologic differences.

Autism families with a high incidence of alcoholism.

To determine the significance of neuropsychiatric disorders in autism families, we analyzed 167 pedigrees ascertained through an autistic child; 39% had alcoholism in patterns consistent with transmission of a genetic trait. Children from high alcoholism families were more likely to have the onset of their autistic behavior occur with a loss of language (52.5% vs. 35.8%, p = 0.04). This occurred primarily in families where the mother was alcoholic (80% vs. 40%, p = 0.05), suggesting an association between maternal alcoholism and regressive onset autism. Children from high alcoholism families were less likely to be macrocephalic (14.7% vs. 40.6%, p = 0.0006). Children from high alcohol and low alcohol families did not differ in dysmorphology status, IQ, sex ratio or sib recurrence risk.

19q13.32 microdeletion syndrome: three new cases.

A previous report described a unique phenotype associated with an apparently de novo 732 kb 19q13.32 microdeletion, consisting of intellectual disability, facial asymmetry, ptosis, oculomotor abnormalities, orofacial clefts, cardiac defects, scoliosis and chronic constipation. We report three unrelated patients with developmental delay and dysmorphic features, who were all found to have interstitial 19q13.32 microdeletions of varying sizes. Both the previously reported patient and our Patient 1 with a larger, 1.3-Mb deletion have distinctive dysmorphic features and medical problems, allowing us to define a recognizable 19q13.32 microdeletion syndrome. Patient 1 was hypotonic and dysmorphic at birth, with aplasia of the posterior corpus callosum, bilateral ptosis, oculomotor paralysis, down-slanting palpebral fissures, facial asymmetry, submucosal cleft palate, micrognathia, wide-spaced nipples, right-sided aortic arch, hypospadias, bilateral inguinal hernias, double toenail of the left second toe, partial 2-3 toe syndactyly, kyphoscoliosis and colonic atony. Therefore, the common features of the 19q13.32 microdeletion syndrome include facial asymmetry, ptosis, oculomotor paralysis, orofacial clefting, micrognathia, kyphoscoliosis, aortic defects and colonic atony. These findings are probably related to a deletion of some combination of the 20-23 genes in common between these two patients, especially NPAS1, NAPA, ARHGAP35, SLC8A2, DHX34, MEIS3, and ZNF541. These candidate genes are expressed in the brain parenchyma, glia, heart, gastrointestinal tract and musculoskeletal system and likely play a fundamental role in the expression of this phenotype. This report delineates the phenotypic spectrum associated with the haploinsufficiency of genes found in 19q13.32.