Jennifer Howe

The autism spectrum disorders (ASDs) are a group of conditions typically characterized by repetitive behaviour, severely restricted interests and difficulties with social interactions and communication. ASDs are highly heritable, yet the underlying genetic determinants remain largely unknown. A genome-wide analysis reveals that people with ASDs carry a higher load of rare copy-number variants — segments of DNA for which the copy number differs between individual genomes — which are either inherited or arise de novo. The results implicate several novel genes as ASD candidates and point to the importance of cellular proliferation, projection and motility as well as specific signalling pathways in this disorder. The autistic spectrum disorders (ASDs) are highly heritable, yet the underlying genetic determinants remain largely unknown. Here, a genome-wide analysis of rare copy number variants (CNVs) has been carried out, revealing that ASD sufferers carry a higher load of rare, genic CNVs than do controls. Many of these CNVs are de novo and inherited. The results implicate several novel genes in ASDs, and point to the importance of cellular proliferation, projection and motility, as well as specific signalling pathways, in these disorders. The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours1. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability2. Although ASDs are known to be highly heritable (∼90%)3, the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 × 10-4). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53–PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.

Rare copy-number variation (CNV) is an important source of risk for autism spectrum disorders (ASDs). We analyzed 2,446 ASD-affected families and confirmed an excess of genic deletions and duplications in affected versus control groups (1.41-fold, p = 1.0 × 10(-5)) and an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated with dominant or X-linked ASD and intellectual disability (odds ratio = 12.62, p = 2.7 × 10(-15), ∼3% of ASD subjects). Pathogenic CNVs, often showing variable expressivity, included rare de novo and inherited events at 36 loci, implicating ASD-associated genes (CHD2, HDAC4, and GDI1) previously linked to other neurodevelopmental disorders, as well as other genes such as SETD5, MIR137, and HDAC9. Consistent with hypothesized gender-specific modulators, females with ASD were more likely to have highly penetrant CNVs (p = 0.017) and were also overrepresented among subjects with fragile X syndrome protein targets (p = 0.02). Genes affected by de novo CNVs and/or loss-of-function single-nucleotide variants converged on networks related to neuronal signaling and development, synapse function, and chromatin regulation.

Yuen et al. developed a cloud-based database with 5,205 whole genomes from families with autism spectrum disorder (ASD). They identified 18 new candidate ASD-risk genes and approximately 100 risk genes and copy-number loci, which account for 11% of the cases. They also found that individuals bearing mutations in ASD-risk genes had lower adaptive ability. We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10−4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.

SHANK genes code for scaffold proteins located at the post-synaptic density of glutamatergic synapses. In neurons, SHANK2 and SHANK3 have a positive effect on the induction and maturation of dendritic spines, whereas SHANK1 induces the enlargement of spine heads. Mutations in SHANK genes have been associated with autism spectrum disorders (ASD), but their prevalence and clinical relevance remain to be determined. Here, we performed a new screen and a meta-analysis of SHANK copy-number and coding-sequence variants in ASD. Copy-number variants were analyzed in 5,657 patients and 19,163 controls, coding-sequence variants were ascertained in 760 to 2,147 patients and 492 to 1,090 controls (depending on the gene), and, individuals carrying de novo or truncating SHANK mutations underwent an extensive clinical investigation. Copy-number variants and truncating mutations in SHANK genes were present in ∼1% of patients with ASD: mutations in SHANK1 were rare (0.04%) and present in males with normal IQ and autism; mutations in SHANK2 were present in 0.17% of patients with ASD and mild intellectual disability; mutations in SHANK3 were present in 0.69% of patients with ASD and up to 2.12% of the cases with moderate to profound intellectual disability. In summary, mutations of the SHANK genes were detected in the whole spectrum of autism with a gradient of severity in cognitive impairment. Given the rare frequency of SHANK1 and SHANK2 deleterious mutations, the clinical relevance of these genes remains to be ascertained. In contrast, the frequency and the penetrance of SHANK3 mutations in individuals with ASD and intellectual disability—more than 1 in 50—warrant its consideration for mutation screening in clinical practice.

Autism Spectrum Disorder (ASD) demonstrates high heritability and familial clustering, yet the genetic causes remain only partially understood as a result of extensive clinical and genomic heterogeneity. Whole-genome sequencing (WGS) shows promise as a tool for identifying ASD risk genes as well as unreported mutations in known loci, but an assessment of its full utility in an ASD group has not been performed. We used WGS to examine 32 families with ASD to detect de novo or rare inherited genetic variants predicted to be deleterious (loss-of-function and damaging missense mutations). Among ASD probands, we identified deleterious de novo mutations in six of 32 (19%) families and X-linked or autosomal inherited alterations in ten of 32 (31%) families (some had combinations of mutations). The proportion of families identified with such putative mutations was larger than has been previously reported; this yield was in part due to the comprehensive and uniform coverage afforded by WGS. Deleterious variants were found in four unrecognized, nine known, and eight candidate ASD risk genes. Examples include CAPRIN1 and AFF2 (both linked to FMR1, which is involved in fragile X syndrome), VIP (involved in social-cognitive deficits), and other genes such as SCN2A and KCNQ2 (linked to epilepsy), NRXN1, and CHD7, which causes ASD-associated CHARGE syndrome. Taken together, these results suggest that WGS and thorough bioinformatic analyses for de novo and rare inherited mutations will improve the detection of genetic variants likely to be associated with ASD or its accompanying clinical symptoms.

The use of genome-wide tests to provide molecular diagnosis for individuals with autism spectrum disorder (ASD) requires more study.To perform chromosomal microarray analysis (CMA) and whole-exome sequencing (WES) in a heterogeneous group of children with ASD to determine the molecular diagnostic yield of these tests in a sample typical of a developmental pediatric clinic.The sample consisted of 258 consecutively ascertained unrelated children with ASD who underwent detailed assessments to define morphology scores based on the presence of major congenital abnormalities and minor physical anomalies. The children were recruited between 2008 and 2013 in Newfoundland and Labrador, Canada. The probands were stratified into 3 groups of increasing morphological severity: essential, equivocal, and complex (scores of 0-3, 4-5, and ≥6).All probands underwent CMA, with WES performed for 95 proband-parent trios.The overall molecular diagnostic yield for CMA and WES in a population-based ASD sample stratified in 3 phenotypic groups.Of 258 probands, 24 (9.3%, 95%CI, 6.1%-13.5%) received a molecular diagnosis from CMA and 8 of 95 (8.4%, 95%CI, 3.7%-15.9%) from WES. The yields were statistically different between the morphological groups. Among the children who underwent both CMA and WES testing, the estimated proportion with an identifiable genetic etiology was 15.8% (95%CI, 9.1%-24.7%; 15/95 children). This included 2 children who received molecular diagnoses from both tests. The combined yield was significantly higher in the complex group when compared with the essential group (pairwise comparison, P = .002). [table: see text].Among a heterogeneous sample of children with ASD, the molecular diagnostic yields of CMA and WES were comparable, and the combined molecular diagnostic yield was higher in children with more complex morphological phenotypes in comparison with the children in the essential category. If replicated in additional populations, these findings may inform appropriate selection of molecular diagnostic testing for children affected by ASD.

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear.To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2).In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk.Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level.The SNP that achieves the smallest P-value from secondary analyses is rs1718101.It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD.This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2.In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample.Despite being significant, the variance explained by these allele scores was small (Vm< 1%).Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest.

A high-resolution analysis of copy number variation in patients with ADHD reveals new gene associations, few de novo mutations, and overlap with genes implicated in other disorders such as autism.

De novo mutations (DNMs) are important in Autism Spectrum Disorder (ASD), but so far analyses have mainly been on the ~1.5% of the genome encoding genes. Here, we performed whole genome sequencing (WGS) of 200 ASD parent-child trios and characterized germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from the father, and these increased significantly with paternal age only (p=4.2×10-10). However, when clustered DNMs (those within 20kb) were found in ASD, not only did they mostly originate from the mother (p=7.7×10-13), but they could also be found adjacent to de novo copy number variations (CNVs) where the mutation rate was significantly elevated (p=2.4×10-24). By comparing DNMs detected in controls, we found a significant enrichment of predicted damaging DNMs in ASD cases (p=8.0×10-9; OR=1.84), of which 15.6% (p=4.3×10-3) and 22.5% (p=7.0×10-5) were in the non-coding or genic non-coding, respectively. The non-coding elements most enriched for DNM were untranslated regions of genes, boundaries involved in exon-skipping and DNase I hypersensitive regions. Using microarrays and a novel outlier detection test, we also found aberrant methylation profiles in 2/185 (1.1%) of ASD cases. These same individuals carried independently identified DNMs in the ASD risk- and epigenetic- genes DNMT3A and ADNP. Our data begins to characterize different genome-wide DNMs, and highlight the contribution of non-coding variants, to the etiology of ASD.

Tandem DNA repeats vary in the size and sequence of each unit (motif). When expanded, these tandem DNA repeats have been associated with more than 40 monogenic disorders1. Their involvement in disorders with complex genetics is largely unknown, as is the extent of their heterogeneity. Here we investigated the genome-wide characteristics of tandem repeats that had motifs with a length of 2-20 base pairs in 17,231 genomes of families containing individuals with autism spectrum disorder (ASD)2,3 and population control individuals4. We found extensive polymorphism in the size and sequence of motifs. Many of the tandem repeat loci that we detected correlated with cytogenetic fragile sites. At 2,588 loci, gene-associated expansions of tandem repeats that were rare among population control individuals were significantly more prevalent among individuals with ASD than their siblings without ASD, particularly in exons and near splice junctions, and in genes related to the development of the nervous system and cardiovascular system or muscle. Rare tandem repeat expansions had a prevalence of 23.3% in children with ASD compared with 20.7% in children without ASD, which suggests that tandem repeat expansions make a collective contribution to the risk of ASD of 2.6%. These rare tandem repeat expansions included previously undescribed ASD-linked expansions in DMPK and FXN, which are associated with neuromuscular conditions, and in previously unknown loci such as FGF14 and CACNB1. Rare tandem repeat expansions were associated with lower IQ and adaptive ability. Our results show that tandem DNA repeat expansions contribute strongly to the genetic aetiology and phenotypic complexity of ASD.

Abstract Copy number variations (CNVs) are implicated across many neurodevelopmental disorders (NDDs) and contribute to their shared genetic etiology. Multiple studies have attempted to identify shared etiology among NDDs, but this is the first genome-wide CNV analysis across autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), schizophrenia (SCZ), and obsessive-compulsive disorder (OCD) at once. Using microarray (Affymetrix CytoScan HD), we genotyped 2,691 subjects diagnosed with an NDD (204 SCZ, 1,838 ASD, 427 ADHD and 222 OCD) and 1,769 family members, mainly parents. We identified rare CNVs, defined as those found in &lt;0.1% of 10,851 population control samples. We found clinically relevant CNVs (broadly defined) in 284 (10.5%) of total subjects, including 22 (10.8%) among subjects with SCZ, 209 (11.4%) with ASD, 40 (9.4%) with ADHD, and 13 (5.6%) with OCD. Among all NDD subjects, we identified 17 (0.63%) with aneuploidies and 115 (4.3%) with known genomic disorder variants. We searched further for genes impacted by different CNVs in multiple disorders. Examples of NDD-associated genes linked across more than one disorder (listed in order of occurrence frequency) are NRXN1 , SEH1L , LDLRAD4 , GNAL , GNG13 , MKRN1 , DCTN2, KNDC1 , PCMTD2 , KIF5A , SYNM , and long non-coding RNAs: AK127244 and PTCHD1-AS . We demonstrated that CNVs impacting the same genes could potentially contribute to the etiology of multiple NDDs. The CNVs identified will serve as a useful resource for both research and diagnostic laboratories for prioritization of variants.

Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.

Rare copy number variants (CNVs) disrupting ASTN2 or both ASTN2 and TRIM32 have been reported at 9q33.1 by genome-wide studies in a few individuals with neurodevelopmental disorders (NDDs). The vertebrate-specific astrotactins, ASTN2 and its paralog ASTN1, have key roles in glial-guided neuronal migration during brain development. To determine the prevalence of astrotactin mutations and delineate their associated phenotypic spectrum, we screened ASTN2/TRIM32 and ASTN1 (1q25.2) for exonic CNVs in clinical microarray data from 89 985 individuals across 10 sites, including 64 114 NDD subjects. In this clinical dataset, we identified 46 deletions and 12 duplications affecting ASTN2. Deletions of ASTN1 were much rarer. Deletions near the 3' terminus of ASTN2, which would disrupt all transcript isoforms (a subset of these deletions also included TRIM32), were significantly enriched in the NDD subjects (P = 0.002) compared with 44 085 population-based controls. Frequent phenotypes observed in individuals with such deletions include autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), speech delay, anxiety and obsessive compulsive disorder (OCD). The 3'-terminal ASTN2 deletions were significantly enriched compared with controls in males with NDDs, but not in females. Upon quantifying ASTN2 human brain RNA, we observed shorter isoforms expressed from an alternative transcription start site of recent evolutionary origin near the 3' end. Spatiotemporal expression profiling in the human brain revealed consistently high ASTN1 expression while ASTN2 expression peaked in the early embryonic neocortex and postnatal cerebellar cortex. Our findings shed new light on the role of the astrotactins in psychopathology and their interplay in human neurodevelopment.

Autism spectrum disorder (ASD) is phenotypically and genetically heterogeneous. We present a CRISPR gene editing strategy to insert a protein tag and premature termination sites creating an induced pluripotent stem cell (iPSC) knockout resource for functional studies of ten ASD-relevant genes (AFF2/FMR2, ANOS1, ASTN2, ATRX, CACNA1C, CHD8, DLGAP2, KCNQ2, SCN2A, TENM1). Neurogenin 2 (NGN2)-directed induction of iPSCs allowed production of excitatory neurons, and mutant proteins were not detectable. RNA sequencing revealed convergence of several neuronal networks. Using both patch-clamp and multi-electrode array approaches, the electrophysiological deficits measured were distinct for different mutations. However, they culminated in a consistent reduction in synaptic activity, including reduced spontaneous excitatory postsynaptic current frequencies in AFF2/FMR2-, ASTN2-, ATRX-, KCNQ2-, and SCN2A-null neurons. Despite ASD susceptibility genes belonging to different gene ontologies, isogenic stem cell resources can reveal common functional phenotypes, such as reduced functional connectivity.

Autism spectrum disorder (ASD) is often grouped with other brain-related phenotypes into a broader category of neurodevelopmental disorders (NDDs). In clinical practice, providers need to decide which genes to test in individuals with ASD phenotypes, which requires an understanding of the level of evidence for individual NDD genes that supports an association with ASD. Consensus is currently lacking about which NDD genes have sufficient evidence to support a relationship to ASD. Estimates of the number of genes relevant to ASD differ greatly among research groups and clinical sequencing panels, varying from a few to several hundred. This Roadmap discusses important considerations necessary to provide an evidence-based framework for the curation of NDD genes based on the level of information supporting a clinically relevant relationship between a given gene and ASD. A curated list of genes that are relevant to autism spectrum disorder (ASD) would greatly benefit clinical genetic testing. This Roadmap discusses the need for an evidence-based framework for gene curation that is based on the level of information supporting a clinically relevant relationship between a given gene and ASD.

Induced pluripotent stem cell (iPSC)-derived neurons are increasingly used to model Autism Spectrum Disorder (ASD), which is clinically and genetically heterogeneous. To study the complex relationship of penetrant and weaker polygenic risk variants to ASD, 'isogenic' iPSC-derived neurons are critical. We developed a set of procedures to control for heterogeneity in reprogramming and differentiation, and generated 53 different iPSC-derived glutamatergic neuronal lines from 25 participants from 12 unrelated families with ASD. Heterozygous de novo and rare-inherited presumed-damaging variants were characterized in ASD risk genes/loci. Combinations of putative etiologic variants (GLI3/KIF21A or EHMT2/UBE2I) in separate families were modeled. We used a multi-electrode array, with patch-clamp recordings, to determine a reproducible synaptic phenotype in 25% of the individuals with ASD (other relevant data on the remaining lines was collected). Our most compelling new results revealed a consistent spontaneous network hyperactivity in neurons deficient for CNTN5 or EHMT2. The biobank of iPSC-derived neurons and accompanying genomic data are available to accelerate ASD research.This article has been through an editorial process in which authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

Abstract We report detailed functional analyses and genotype-phenotype correlations in 392 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel Nav1.6, with the aim of describing clinical phenotypes related to functional effects. Six different clinical subgroups were identified: Group 1, benign familial infantile epilepsy (n = 15, normal cognition, treatable seizures); Group 2, intermediate epilepsy (n = 33, mild intellectual disability, partially pharmaco-responsive); Group 3, developmental and epileptic encephalopathy (n = 177, severe intellectual disability, majority pharmaco-resistant); Group 4, generalized epilepsy (n = 20, mild to moderate intellectual disability, frequently with absence seizures); Group 5, unclassifiable epilepsy (n = 127); and Group 6, neurodevelopmental disorder without epilepsy (n = 20, mild to moderate intellectual disability). Those in Groups 1–3 presented with focal or multifocal seizures (median age of onset: 4 months) and focal epileptiform discharges, whereas the onset of seizures in patients with generalized epilepsy was later (median: 42 months) with generalized epileptiform discharges. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin-insensitive human Nav1.6 channels and whole-cell patch-clamping. Two variants causing developmental and epileptic encephalopathy showed a strong gain-of-function (hyperpolarizing shift of steady-state activation, strongly increased neuronal firing rate) and one variant causing benign familial infantile epilepsy or intermediate epilepsy showed a mild gain-of-function (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (reduced current amplitudes, depolarizing shift of steady-state activation, reduced neuronal firing). Functional effects were known for 170 individuals. All 136 individuals carrying a functionally tested gain-of-function variant had either focal (n = 97, Groups 1–3) or unclassifiable (n = 39) epilepsy, whereas 34 individuals with a loss-of-function variant had either generalized (n = 14), no (n = 11) or unclassifiable (n = 6) epilepsy; only three had developmental and epileptic encephalopathy. Computational modelling in the gain-of-function group revealed a significant correlation between the severity of the electrophysiological and clinical phenotypes. Gain-of-function variant carriers responded significantly better to sodium channel blockers than to other anti-seizure medications, and the same applied for all individuals in Groups 1–3. In conclusion, our data reveal clear genotype-phenotype correlations between age at seizure onset, type of epilepsy and gain- or loss-of-function effects of SCN8A variants. Generalized epilepsy with absence seizures is the main epilepsy phenotype of loss-of-function variant carriers and the extent of the electrophysiological dysfunction of the gain-of-function variants is a main determinant of the severity of the clinical phenotype in focal epilepsies. Our pharmacological data indicate that sodium channel blockers present a treatment option in SCN8A-related focal epilepsy with onset in the first year of life.

The 5'-terminal sequences of the virion protein mRNAs of ononis yellow mosaic and kennedya yellow mosaic tymoviruses were determined, and also the positions in the genomes of the transcription initiation sites of those mRNAs. Comparisons of the available genomic sequences of tymoviruses revealed two conserved regions, one at the initiation site and another longer sequence of sixteen nucleotides to the 5' side of it. The longer sequence, which we call the tymobox, was tested as a target for a designed ribozyme, which cleaved appropriate genomic fragments of three tymoviruses. A synthetic oligonucleotide with sequence complementary to the tymobox was shown to be a tymovirus-specific probe for diagnosing and identifying tymoviruses, except for wild cucumber mosaic tymovirus. The tymobox sequence was also used as a primer for the second strand DNA synthesis of dsDNA representing the virion protein gene of cacao yellow mosaic tymovirus, a tymovirus with unknown sequence. Thus, the tymobox is a useful tool in molecular studies of tymoviruses.

The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers.Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant.Whole genome sequencing of the first 56 participants identified 207 662 805 sequence variants and 27 494 copy number variations. We analyzed a prioritized disease-associated data set (n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants - associated with cancer, cardiac or neurodegenerative phenotypes - remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual.Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care.

Autism spectrum disorder (ASD) is a collection of neurodevelopmental disorders characterized by deficits in social communication and restricted, repetitive patterns of behavior or interests. ASD is highly heritable, but genetically and phenotypically heterogeneous, reducing the power to identify causative genes. We performed whole genome sequencing (WGS) in an ASD cohort of 68 individuals from 22 families enriched for recent shared ancestry. We identified an average of 3.07 million variants per genome, of which an average of 112,512 were rare. We mapped runs of homozygosity (ROHs) in affected individuals and found an average genomic homozygosity of 9.65%, consistent with expectations for multiple generations of consanguineous unions. We identified potentially pathogenic rare exonic or splice site variants in 12 known (including KMT2C, SCN1A, SPTBN1, SYNE1, ZNF292) and 12 candidate (including CHD5, GRB10, PPP1R13B) ASD genes. Furthermore, we annotated noncoding variants in ROHs with brain-specific regulatory elements and identified putative disease-causing variants within brain-specific promoters and enhancers for 5 known ASD and neurodevelopmental disease genes (ACTG1, AUTS2, CTNND2, CNTNAP4, SPTBN4). We also identified copy number variants in two known ASD and neurodevelopmental disease loci in two affected individuals. In total we identified potentially etiological variants in known ASD or neurodevelopmental disease genes for ~61% (14/23) of affected individuals. We combined WGS with homozygosity mapping and regulatory element annotations to identify candidate ASD variants. Our analyses add to the growing number of ASD genes and variants and emphasize the importance of leveraging recent shared ancestry to map disease variants in complex neurodevelopmental disorders.

Autism spectrum disorder (ASD), a developmental disorder of early childhood onset, affects males four times more frequently than females, suggesting a role for the sex chromosomes. In this study, we describe a family with ASD in which a predicted pathogenic nonsense mutation in the X-chromosome gene RAB39B segregates with ASD phenotype.Clinical phenotyping, microarray, and whole genome sequencing (WGS) were performed on the five members of this family. Maternal and female sibling X inactivation ratio was calculated, and phase was investigated. Mutant-induced pluripotent stem cells engineered for an exon 2 nonsense mutation were generated and differentiated into cortical neurons for expression and pathway analyses.Two males with an inherited RAB39B mutation both presented with macrocephaly, intellectual disability (ID), and ASD. Their female sibling with the same mutation presented with ID and a broad autism phenotype. In contrast, their transmitting mother has no neurodevelopmental diagnosis. Our investigation of phase indicated maternal preferential inactivation of the mutated allele, with no such bias observed in the female sibling. We offer the explanation that this bias in X inactivation may explain the absence of a neurocognitive phenotype in the mother. Our cellular knockout model of RAB39B revealed an impact on expression in differentiated neurons for several genes implicated in brain development and function, supported by our pathway enrichment analysis.Penetrance for ASD is high among males but more variable among females with RAB39B mutations. A critical role for this gene in brain development and function is demonstrated.

Abstract We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health and cognition in a community sample of 7100 unrelated children and youth of European or East Asian ancestry (Spit for Science). Clinically significant or susceptibility CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of attention-deficit/hyperactivity disorder (ADHD) traits (P = 5.0 × 10−3), longer response inhibition (a cognitive deficit found in several mental health and neurodevelopmental disorders; P = 1.0 × 10−2) and increased prevalence of mental health diagnoses (P = 1.9 × 10−6, odds ratio: 3.09), specifically ADHD, autism spectrum disorder anxiety and learning problems/learning disorder (P’s &amp;lt; 0.01). There was an increased burden of rare deletions in gene-sets related to brain function or expression in brain associated with more ADHD traits. With the current mental health crisis, our data established a baseline for delineating genetic contributors in pediatric-onset conditions.

Autism Spectrum Disorder (ASD) is a developmental condition of early childhood onset, which impacts socio-communicative functioning and is principally genetic in etiology. Currently, more than 50 genomic loci are deemed to be associated with susceptibility to ASD, showing de novo and inherited unbalanced copy number variants (CNVs) and smaller insertions and deletions (indels), more complex structural variants (SVs), as well as single nucleotide variants (SNVs) deemed of pathological significance. However, the phenotypes associated with many of these genes are variable, and penetrance is largely unelaborated in clinical descriptions. This case report describes a family harboring two CNV microdeletions, which affect regions of NRXN1 and MBD5 - each well-established in association with risk of ASD and other neurodevelopmental disorders. Although each CNV would likely be categorized as pathologically significant, both genomic alterations are transmitted in this family from an unaffected father to the proband, and shared by an unaffected sibling. This family case illustrates the importance of recognizing that phenotype can vary among exon overlapping variants of the same gene, and the need to evaluate penetrance of such variants in order to properly inform on risks.

Abstract Identification of genetic biomarkers associated with autism spectrum disorders (ASDs) could improve recurrence prediction for families with a child with ASD. Here, we describe clinical microarray findings for 253 longitudinally phenotyped ASD families from the Baby Siblings Research Consortium (BSRC), encompassing 288 infant siblings. By age 3, 103 siblings (35.8%) were diagnosed with ASD and 54 (18.8%) were developing atypically. Thirteen siblings have copy number variants (CNVs) involving ASD-relevant genes: 6 with ASD, 5 atypically developing, and 2 typically developing. Within these families, an ASD-related CNV in a sibling has a positive predictive value (PPV) for ASD or atypical development of 0.83; the Simons Simplex Collection of ASD families shows similar PPVs. Polygenic risk analyses suggest that common genetic variants may also contribute to ASD. CNV findings would have been pre-symptomatically predictive of ASD or atypical development in 11 (7%) of the 157 BSRC siblings who were eventually diagnosed clinically.

In recent years, several hundred autism spectrum disorder (ASD) implicated genes have been discovered impacting a wide range of molecular pathways. However, the molecular underpinning of ASD, particularly from the point of view of 'brain to behaviour' pathogenic mechanisms, remains largely unknown.We undertook a study to investigate patterns of spatiotemporal and cell type expression of ASD-implicated genes by integrating large-scale brain single-cell transcriptomes (> million cells) and de novo loss-of-function (LOF) ASD variants (impacting 852 genes from 40,122 cases).We identified multiple single-cell clusters from three distinct developmental human brain regions (anterior cingulate cortex, middle temporal gyrus and primary visual cortex) that evidenced high evolutionary constraint through enrichment for brain critical exons and high pLI genes. These clusters also showed significant enrichment with ASD loss-of-function variant genes (p < 5.23 × 10-11) that are transcriptionally highly active in prenatal brain regions (visual cortex and dorsolateral prefrontal cortex). Mapping ASD de novo LOF variant genes into large-scale human and mouse brain single-cell transcriptome analysis demonstrate enrichment of such genes into neuronal subtypes and are also enriched for subtype of non-neuronal glial cell types (astrocyte, p < 6.40 × 10-11, oligodendrocyte, p < 1.31 × 10-09).Among the ASD genes enriched with pathogenic de novo LOF variants (i.e. KANK1, PLXNB1), a subgroup has restricted transcriptional regulation in non-neuronal cell types that are evolutionarily conserved. This association strongly suggests the involvement of subtype of non-neuronal glial cells in the pathogenesis of ASD and the need to explore other biological pathways for this disorder.

The X-linked PTCHD1 locus is strongly associated with autism spectrum disorder (ASD). Males who carry chromosome microdeletions of PTCHD1 antisense long non-coding RNA (PTCHD1-AS)/DEAD-box helicase 53 (DDX53) have ASD, or a sub-clinical form called Broader Autism Phenotype. If the deletion extends beyond PTCHD1-AS/DDX53 to the next gene, PTCHD1, which is protein-coding, the individuals typically have ASD and intellectual disability (ID). Three male siblings with a 90 kb deletion that affects only PTCHD1-AS (and not including DDX53) have ASD. We performed a functional analysis of DDX53 to examine its role in NGN2 neurons.We used the clustered regularly interspaced short palindromic repeats (CRISPR) gene editing strategy to knock out DDX53 protein by inserting 3 termination codons (3TCs) into two different induced pluripotent stem cell (iPSC) lines. DDX53 CRISPR-edited iPSCs were differentiated into cortical excitatory neurons by Neurogenin 2 (NGN-2) directed differentiation. The functional differences of DDX53-3TC neurons compared to isogenic control neurons with molecular and electrophysiological approaches were assessed.Isogenic iPSC-derived control neurons exhibited low levels of DDX53 transcripts. Transcriptional analysis revealed the generation of excitatory cortical neurons and DDX53 protein was not detected in iPSC-derived control neurons by western blot. Control lines and DDX53-3TC neurons were active in the multi-electrode array, but no overt electrophysiological phenotype in either isogenic line was observed.DDX53-3TC mutation does not alter NGN2 neuronal function in these experiments, suggesting that synaptic deficits causing ASD are unlikely in this cell type.

De novo variants are a leading cause of neurodevelopmental disorders (NDDs), but because every monogenic NDD is different and usually extremely rare, it remains a major challenge to understand the complete phenotype and genotype spectrum of any morbid gene. According to OMIM, heterozygous variants in KDM6B cause "neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities." Here, by examining the molecular and clinical spectrum of 85 reported individuals with mostly de novo (likely) pathogenic KDM6B variants, we demonstrate that this description is inaccurate and potentially misleading. Cognitive deficits are seen consistently in all individuals, but the overall phenotype is highly variable. Notably, coarse facies and distal skeletal anomalies, as defined by OMIM, are rare in this expanded cohort while other features are unexpectedly common (e.g., hypotonia, psychosis, etc.). Using 3D protein structure analysis and an innovative dual Drosophila gain-of-function assay, we demonstrated a disruptive effect of 11 missense/in-frame indels located in or near the enzymatic JmJC or Zn-containing domain of KDM6B. Consistent with the role of KDM6B in human cognition, we demonstrated a role for the Drosophila KDM6B ortholog in memory and behavior. Taken together, we accurately define the broad clinical spectrum of the KDM6B-related NDD, introduce an innovative functional testing paradigm for the assessment of KDM6B variants, and demonstrate a conserved role for KDM6B in cognition and behavior. Our study demonstrates the critical importance of international collaboration, sharing of clinical data, and rigorous functional analysis of genetic variants to ensure correct disease diagnosis for rare disorders.

Induced pluripotent stem cells (iPSC) derived from healthy individuals are important controls for disease-modeling studies. Here we apply precision health to create a high-quality resource of control iPSCs. Footprint-free lines were reprogrammed from four volunteers of the Personal Genome Project Canada (PGPC). Multilineage-directed differentiation efficiently produced functional cortical neurons, cardiomyocytes and hepatocytes. Pilot users demonstrated versatility by generating kidney organoids, T lymphocytes, and sensory neurons. A frameshift knockout was introduced into MYBPC3 and these cardiomyocytes exhibited the expected hypertrophic phenotype. Whole-genome sequencing-based annotation of PGPC lines revealed on average 20 coding variants. Importantly, nearly all annotated PGPC and HipSci lines harbored at least one pre-existing or acquired variant with cardiac, neurological, or other disease associations. Overall, PGPC lines were efficiently differentiated by multiple users into cells from six tissues for disease modeling, and variant-preferred healthy control lines were identified for specific disease settings.

Abstract The Per family of genes functions as a primary circadian rhythm maintenance in the brain. Mutations in PER2 are associated with familial advanced sleep‐phase syndrome 1 (FASPS1), and recently suggested in delayed sleep phase syndrome and idiopathic hypersomnia. The detection of PER2 variants in individuals with autism spectrum disorder (ASD) and without reported sleep disorders, has suggested a role of circadian‐relevant genes in the pathophysiology of ASD. It remains unclear whether these individuals may have, in addition to ASD, an undiagnosed circadian rhythm sleep disorder. The MSSNG database was used to screen whole genome sequencing data of 5,102 individuals with ASD for putative mutations in PER2 . Families identified were invited to complete sleep phenotyping consisting of a structured interview and two standardized sleep questionnaires: the Pittsburgh Sleep Quality Index and the Morningness‐Eveningness Questionnaire. From 5,102 individuals with ASD, two nonsense, one frameshift, and one de novo missense PER2 variants were identified (0.08%). Of these four, none had a diagnosed sleep disorder. Three reported either a history of, or ongoing sleep disturbances, and one had symptoms highly suggestive of FASPS1 (as did a mutation carrier father without ASD). The individual with the missense variant did not report sleep concerns. The ASD and cognitive profiles of these individuals varied in severity and symptoms. The results support a possible role of PER2 ‐related circadian rhythm disturbances in the dysregulation of sleep overall and sometimes FASPS1. The relationship between dysregulated sleep and the pathophysiology of ASD require further exploration.

Autism Spectrum Disorder (ASD) is characterized by impaired social communication, restricted interests, and repetitive and stereotyped behaviors. The TRPC6 (transient receptor potential channel 6) represents an ASD candidate gene under an oligogenic/multifactorial model based on the initial description and cellular characterization of an individual with ASD bearing a de novo heterozygous mutation disrupting TRPC6, together with the enrichment of disruptive TRPC6 variants in ASD cases as compared to controls. Here, we perform a clinical re-evaluation of the initial non-verbal patient, and also present eight newly reported individuals ascertained for ASD and bearing predicted loss-of-function mutations in TRPC6. In order to understand the consequences of mutations in TRPC6 on nervous system function, we used the fruit fly, Drosophila melanogaster, to show that null mutations in transient receptor gamma (trpγ; the fly gene most similar to TRPC6), cause a number of behavioral defects that mirror features seen in ASD patients, including deficits in social interactions (based on courtship behavior), impaired sleep homeostasis (without affecting the circadian control of sleep), hyperactivity in both young and old flies, and defects in learning and memory. Some defects, most notably in sleep, differed in severity between males and females and became normal with age. Interestingly, hyperforin, a TRPC6 agonist and the primary active component of the St. John's wort antidepressant, attenuated many of the deficits expressed by trpγ mutant flies. In summary, our results provide further evidence that the TRPC6 gene is a risk factor for ASD. In addition, they show that the behavioral defects caused by mutations in TRPC6 can be modeled in Drosophila, thereby establishing a paradigm to examine the impact of mutations in other candidate genes.

Abstract We describe an autosomal dominant disorder associated with loss-of-function variants in the Cell cycle associated protein 1 (CAPRIN1; MIM*601178). CAPRIN1 encodes a ubiquitous protein that regulates the transport and translation of neuronal mRNAs critical for synaptic plasticity, as well as mRNAs encoding proteins important for cell proliferation and migration in multiple cell types. We identified 12 cases with loss-of-function CAPRIN1 variants, and a neurodevelopmental phenotype characterized by language impairment/speech delay (100%), intellectual disability (83%), attention deficit hyperactivity disorder (82%) and autism spectrum disorder (67%). Affected individuals also had respiratory problems (50%), limb/skeletal anomalies (50%), developmental delay (42%) feeding difficulties (33%), seizures (33%) and ophthalmologic problems (33%). In patient-derived lymphoblasts and fibroblasts, we showed a monoallelic expression of the wild-type allele, and a reduction of the transcript and protein compatible with a half dose. To further study pathogenic mechanisms, we generated sCAPRIN1+/− human induced pluripotent stem cells via CRISPR–Cas9 mutagenesis and differentiated them into neuronal progenitor cells and cortical neurons. CAPRIN1 loss caused reduced neuronal processes, overall disruption of the neuronal organization and an increased neuronal degeneration. We also observed an alteration of mRNA translation in CAPRIN1+/− neurons, compatible with its suggested function as translational inhibitor. CAPRIN1+/− neurons also showed an impaired calcium signalling and increased oxidative stress, two mechanisms that may directly affect neuronal networks development, maintenance and function. According to what was previously observed in the mouse model, measurements of activity in CAPRIN1+/− neurons via micro-electrode arrays indicated lower spike rates and bursts, with an overall reduced activity. In conclusion, we demonstrate that CAPRIN1 haploinsufficiency causes a novel autosomal dominant neurodevelopmental disorder and identify morphological and functional alterations associated with this disorder in human neuronal models.

Copy number variations (CNVs) are associated with psychiatric and neurodevelopmental disorders (NDDs), and most, including the recurrent 15q13.3 microdeletion disorder, have unknown disease mechanisms. We used a heterozygous 15q13.3 microdeletion mouse model and patient iPSC-derived neurons to reveal developmental defects in neuronal maturation and network activity. To identify the underlying molecular dysfunction, we developed a neuron-specific proximity-labeling proteomics (BioID2) pipeline, combined with patient mutations, to target the 15q13.3 CNV genetic driver OTUD7A. OTUD7A is an emerging independent NDD risk gene with no known function in the brain, but has putative deubiquitinase function. The OTUD7A protein-protein interaction network included synaptic, axonal, and cytoskeletal proteins and was enriched for ASD and epilepsy risk genes (Ank3, Ank2, SPTAN1, SPTBN1). The interactions between OTUD7A and Ankyrin-G (Ank3) and Ankyrin-B (Ank2) were disrupted by an epilepsy-associated OTUD7A L233F variant. Further investigation of Ankyrin-G in mouse and human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed protein instability, increased polyubiquitination, and decreased levels in the axon initial segment, while structured illumination microscopy identified reduced Ankyrin-G nanodomains in dendritic spines. Functional analysis of human 15q13.3 microdeletion and OTUD7AL233F/L233F models revealed shared and distinct impairments to axonal growth and intrinsic excitability. Importantly, restoring OTUD7A or Ankyrin-G expression in 15q13.3 microdeletion neurons led to a reversal of abnormalities. These data reveal a critical OTUD7A-Ankyrin pathway in neuronal development, which is impaired in the 15q13.3 microdeletion syndrome, leading to neuronal dysfunction. Furthermore, our study highlights the utility of targeting CNV genes using cell type-specific proteomics to identify shared and unexplored disease mechanisms across NDDs.

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills, restricted interests, and repetitive behaviors. The prevalence of ASD among children in Qatar was recently estimated to be 1.1%, though the genetic architecture underlying ASD both in Qatar and the greater Middle East has been largely unexplored. Here, we describe the first genomic data release from the BARAKA-Qatar Study-a nationwide program building a broadly consented biorepository of individuals with ASD and their families available for sample and data sharing and multi-omics research.In this first release, we present a comprehensive analysis of whole-genome sequencing (WGS) data of the first 100 families (372 individuals), investigating the genetic architecture, including single-nucleotide variants (SNVs), copy number variants (CNVs), tandem repeat expansions (TREs), as well as mitochondrial DNA variants (mtDNA) segregating with ASD in local families.Overall, we identify potentially pathogenic variants in known genes or regions in 27 out of 100 families (27%), of which 11 variants (40.7%) were classified as pathogenic or likely-pathogenic based on American College of Medical Genetics (ACMG) guidelines. Dominant variants, including de novo and inherited, contributed to 15 (55.6%) of these families, consisting of SNVs/indels (66.7%), CNVs (13.3%), TREs (13.3%), and mtDNA variants (6.7%). Moreover, homozygous variants were found in 7 families (25.9%), with a sixfold increase in homozygous burden in consanguineous versus non-consanguineous families (13.6% and 1.8%, respectively). Furthermore, 28 novel ASD candidate genes were identified in 20 families, 23 of which had recurrent hits in MSSNG and SSC cohorts.This study illustrates the value of ASD studies in under-represented populations and the importance of WGS as a comprehensive tool for establishing a molecular diagnosis for families with ASD. Moreover, it uncovers a significant role for recessive variation in ASD architecture in consanguineous settings and provides a unique resource of Middle Eastern genomes for future research to the global ASD community.

Objective: To describe and analyze utilization of preventive care services and their effect on cardiovascular outcomes in the United States. Methods: Data from the 2007 Medical Expenditure Panel Survey (MEPS) were used to analyze utilization of preventive care services and their effect on cardiovascular outcomes. Recommendations by the Seventh Report of the Joint Committee on Prevention, Detection, Evaluation and Treatment of High Blood Pressure and the National Cholesterol Education Program were used to determine appropriate levels of preventive care utilization. Utilization of blood pressure screening and cholesterol checkup services were used as the dependent variable, while age, gender, race, ethnicity, insurance status, and perceived health status were used as independent variables. Since guidelines differ for people with elevated blood pressure, respondents with elevated blood pressure were identified in the MEPS database by self-reported diagnosis. Descriptive statistics were used to describe the population, while a multivariate logistic regression model was built to predict odds of utilizing appropriate levels of preventive services. Results: Total number of adult respondents for which data were available for blood pressure checkup and cholesterol checkup was 20,523 and 15,784, respectively. Overall, MEPS respondents were found to adhere to guideline recommendations for preventive care utilization. Multivariate logistic regression showed that odds of utilization of preventive care services were higher for elderly patients (age >65 years) for blood pressure (odds ratio [OR] = 2.39, 95% confidence interval [CI]: 1.92–2.97) and cholesterol (OR = 3.05, 95% CI: 2.18–4.27) preventive services compared with younger population (age 18–54 years). Males had much lower odds of getting blood pressure (OR = 0.33, 95% CI: 0.30–0.37) and cholesterol (OR = 0.59, 95% CI: 0.50–0.70) checks done compared with females. Odds of utilization were nearly similar for all races. Uninsured had lower odds for blood pressure (OR = 0.26, 95% CI: 0.23–0.30) and cholesterol (OR = 0.30, 95% CI: 0.24–0.39) checks compared with privately insured people. Asians had lower odds of getting blood pressure checkups compared to Whites (OR = 0.49, 95% CI: 0.39–0.63). Similar trends were recorded for other covariates such as race and perceived health status. Conclusion: The study was successful in identifying existing age, race, income, and insurance-status related disparities in preventive care utilization within a US population. Keywords: guidelines, prevention/screening, gender differences in health and health care, racial/ethnic differences in health and health care

Although several genetic variants for autism spectrum disorder (ASD) have now been identified, these largely occur sporadically or are de novo. Much less progress has been made in identifying inherited variants, even though the disorder itself is familial in the majority of cases. The objective of this study was to identify chromosomal regions that harbor inherited variants increasing the risk for ASD using an approach that examined both ASD and the broad autism phenotype (BAP) among a unique sample of extended pedigrees. ASD and BAP were assessed using standardized tools in 28 pedigrees from Canada and the USA, each with at least three ASD-diagnosed individuals from two nuclear families. Genome-wide linkage analysis was performed using the posterior probability of linkage (PPL) statistic, a quasi-Bayesian method that provides strength of evidence for or against linkage in an essentially model-free manner, with outcomes on the probability scale. The results confirm appreciable interfamilial heterogeneity as well as a high level of intrafamilial heterogeneity. Both ASD and combined ASD/BAP specific loci are apparent. Inclusion of subclinical phenotypes such as BAP should be more widely employed in genetic studies of ASD as a way of identifying inherited genetic variants for the disorder. Moreover, the results underscore the need for approaches to identifying genetic risk factors in extended pedigrees that are robust to high levels of inter/intrafamilial locus and allelic heterogeneity.

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.

Cerebral organoids have emerged as robust models for neurodevelopmental and pathological processes, as well as a powerful discovery platform for less-characterized neurobiological programs. Toward this prospect, we leverage mass-spectrometry-based proteomics to molecularly profile precursor and neuronal compartments of both human-derived organoids and mid-gestation fetal brain tissue to define overlapping programs. Our analysis includes recovery of precursor-enriched transcriptional regulatory proteins not found to be differentially expressed in previous transcriptomic datasets. To highlight the discovery potential of this resource, we show that RUVBL2 is preferentially expressed in the SOX2-positive compartment of organoids and that chemical inactivation leads to precursor cell displacement and apoptosis. To explore clinicopathological correlates of this cytoarchitectural disruption, we interrogate clinical datasets and identify rare de novo genetic variants involving RUVBL2 in patients with neurodevelopmental impairments. Together, our findings demonstrate how cell-type-specific profiling of organoids can help nominate previously unappreciated genes in neurodevelopment and disease.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas nucleases and human induced pluripotent stem cell (iPSC) technology can reveal deep insight into the genetic and molecular bases of human biology and disease. Undesired editing outcomes, both on-target (at the edited locus) and off-target (at other genomic loci) hinder the application of CRISPR-Cas nucleases. We developed Off-flow, a Nextflow-coded bioinformatic workflow that takes a specific guide sequence and Cas protein input to call four separate off-target prediction programs (CHOPCHOP, Cas-Offinder, CRISPRitz, CRISPR-Offinder) to output a comprehensive list of predicted off-target sites. We applied it to whole genome sequencing (WGS) data to investigate the occurrence of unintended effects in human iPSCs that underwent repair or insertion of disease-related variants by homology-directed repair. Off-flow identified a 3-base-pair-substitution and a mono-allelic genomic deletion at the target loci, KCNQ2, in 2 clones. Unbiased WGS analysis further identified off-target missense variants and a mono-allelic genomic deletion at the targeted locus, GNAQ, in 10 clones. On-target substitution and deletions had escaped standard PCR and Sanger sequencing analysis, while missense variants at other genomic loci were not detected by Off-flow. We used these results to filter out iPSC clones for subsequent functional experiments. Off-flow, which we make publicly available, works for human and mouse genomes currently and can be adapted for other genomes. Off-flow and WGS analysis can improve the integrity of studies using CRISPR/Cas-edited cells and animal models.

The human PLAA gene encodes Phospholipase-A2-Activating-Protein (PLAA) involved in trafficking of membrane proteins. Through its PUL domain (PLAP, Ufd3p, and Lub1p), PLAA interacts with p97/VCP modulating synaptic vesicles recycling. Although few families carrying biallelic PLAA variants were reported with progressive neurodegeneration, consequences of monoallelic PLAA variants have not been elucidated. Using exome or genome sequencing we identified PLAA de-novo missense variants, affecting conserved residues within the PUL domain, in children affected with neurodevelopmental disorders (NDDs), including psychomotor regression, intellectual disability (ID) and autism spectrum disorders (ASDs). Computational and in-vitro studies of the identified variants revealed abnormal chain arrangements at C-terminal and reduced PLAA-p97/VCP interaction, respectively. These findings expand both allelic and phenotypic heterogeneity associated to PLAA-related neurological disorders, highlighting perturbed vesicle recycling as a potential disease mechanism in NDDs due to genetic defects of PLAA.

Abstract Mendelian and early-onset severe psychiatric phenotypes often involve genetic variants having a large effect, offering opportunities for genetic discoveries and early therapeutic interventions. Here, the index case is an 18-year-old boy, who at 14 years of age had a decline in cognitive functioning over the course of a year and subsequently presented with catatonia, auditory and visual hallucinations, paranoia, aggression, mood dysregulation, and disorganized thoughts. Exome sequencing revealed a stop-gain mutation in RCL1 (NM_005772.4:c.370 C &gt; T, p.Gln124Ter), encoding an RNA 3′-terminal phosphate cyclase-like protein that is highly conserved across eukaryotic species. Subsequent investigations across two academic medical centers identified eleven additional cases of RCL1 copy number variations (CNVs) with varying neurodevelopmental or psychiatric phenotypes. These findings suggest that dosage variation of RCL1 contributes to a range of neurological and clinical phenotypes.

Human MutationVolume 43, Issue 4 p. 461-470 BRIEF REPORT Delineation of a novel neurodevelopmental syndrome associated with PAX5 haploinsufficiency Yoel Gofin, Yoel Gofin orcid.org/0000-0003-3233-258X Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USASearch for more papers by this authorTianyun Wang, Tianyun Wang orcid.org/0000-0002-5179-087X Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USASearch for more papers by this authorMadelyn A. Gillentine, Madelyn A. Gillentine orcid.org/0000-0002-8989-2214 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA Seattle Children's Hospital, Seattle, Washington, USASearch for more papers by this authorTiana M. Scott, Tiana M. Scott orcid.org/0000-0002-6209-8301 Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, Utah, USASearch for more papers by this authorAliska M. Berry, Aliska M. Berry Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USASearch for more papers by this authorMahshid S. Azamian, Mahshid S. Azamian orcid.org/0000-0002-8543-8284 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USASearch for more papers by this authorCasie Genetti, Casie Genetti orcid.org/0000-0003-4173-9947 Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USASearch for more papers by this authorPankaj B. Agrawal, Pankaj B. Agrawal Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Department of Pediatrics, Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USASearch for more papers by this authorJonathan Picker, Jonathan Picker Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USASearch for more papers by this authorMonica H. Wojcik, Monica H. Wojcik orcid.org/0000-0002-8162-5031 Department of Pediatrics, Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Department of Pediatrics, Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USASearch for more papers by this authorMauricio R. Delgado, Mauricio R. Delgado Department of Neurology, University of Texas Southwestern, Dallas, Texas, USA Scottish Rite for Children, Dallas, Texas, USASearch for more papers by this authorSally A. Lynch, Sally A. Lynch orcid.org/0000-0003-3540-1333 Clinical Genetics, Dublin 1, IrelandSearch for more papers by this authorStephen W. Scherer, Stephen W. Scherer orcid.org/0000-0002-8326-1999 Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, Ontario, CanadaSearch for more papers by this authorJennifer L. Howe, Jennifer L. Howe Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, CanadaSearch for more papers by this authorCarlos A. Bacino, Carlos A. Bacino orcid.org/0000-0002-4342-5012 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USASearch for more papers by this authorStephanie DiTroia, Stephanie DiTroia orcid.org/0000-0002-6847-6780 Department of Pediatrics, Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USASearch for more papers by this authorGrace E. VanNoy, Grace E. VanNoy orcid.org/0000-0003-1257-9702 Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USASearch for more papers by this authorAnne O'Donnell-Luria, Anne O'Donnell-Luria orcid.org/0000-0001-6418-9592 Department of Pediatrics, Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USASearch for more papers by this authorSeema R. Lalani, Seema R. Lalani Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USASearch for more papers by this authorWilliam D. Graf, William D. Graf orcid.org/0000-0003-0460-4605 Department of Pediatrics, Division of Neurology, Connecticut Children's, University of Connecticut, Farmington, Connecticut, USASearch for more papers by this authorJill A. Rosenfeld, Jill A. Rosenfeld orcid.org/0000-0001-5664-7987 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Baylor Genetics Laboratory, Houston, Texas, USASearch for more papers by this authorEvan E. Eichler, Evan E. Eichler orcid.org/0000-0002-8246-4014 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USASearch for more papers by this authorRachel K. Earl, Rachel K. Earl Center on Human Development and Disability, University of Washington, Seattle, Washington, USA Seattle Children's Autism Center, Seattle, Washington, USA Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USASearch for more papers by this authorDaryl A. Scott, Corresponding Author Daryl A. Scott dscott@bcm.edu orcid.org/0000-0003-1460-5169 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USA Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA Correspondence Daryl A. Scott, Department of Molecular and Human Genetics, Baylor College of Medicine, R813, One Baylor Plaza, BCM225, Houston, TX 770303, USA. Email: dscott@bcm.eduSearch for more papers by this author Yoel Gofin, Yoel Gofin orcid.org/0000-0003-3233-258X Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USASearch for more papers by this authorTianyun Wang, Tianyun Wang orcid.org/0000-0002-5179-087X Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USASearch for more papers by this authorMadelyn A. Gillentine, Madelyn A. Gillentine orcid.org/0000-0002-8989-2214 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA Seattle Children's Hospital, Seattle, Washington, USASearch for more papers by this authorTiana M. Scott, Tiana M. Scott orcid.org/0000-0002-6209-8301 Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, Utah, USASearch for more papers by this authorAliska M. Berry, Aliska M. Berry Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USASearch for more papers by this authorMahshid S. Azamian, Mahshid S. Azamian orcid.org/0000-0002-8543-8284 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USASearch for more papers by this authorCasie Genetti, Casie Genetti orcid.org/0000-0003-4173-9947 Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USASearch for more papers by this authorPankaj B. Agrawal, Pankaj B. Agrawal Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Department of Pediatrics, Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USASearch for more papers by this authorJonathan Picker, Jonathan Picker Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USASearch for more papers by this authorMonica H. Wojcik, Monica H. Wojcik orcid.org/0000-0002-8162-5031 Department of Pediatrics, Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Department of Pediatrics, Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USASearch for more papers by this authorMauricio R. Delgado, Mauricio R. Delgado Department of Neurology, University of Texas Southwestern, Dallas, Texas, USA Scottish Rite for Children, Dallas, Texas, USASearch for more papers by this authorSally A. Lynch, Sally A. Lynch orcid.org/0000-0003-3540-1333 Clinical Genetics, Dublin 1, IrelandSearch for more papers by this authorStephen W. Scherer, Stephen W. Scherer orcid.org/0000-0002-8326-1999 Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, Ontario, CanadaSearch for more papers by this authorJennifer L. Howe, Jennifer L. Howe Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, CanadaSearch for more papers by this authorCarlos A. Bacino, Carlos A. Bacino orcid.org/0000-0002-4342-5012 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USASearch for more papers by this authorStephanie DiTroia, Stephanie DiTroia orcid.org/0000-0002-6847-6780 Department of Pediatrics, Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USASearch for more papers by this authorGrace E. VanNoy, Grace E. VanNoy orcid.org/0000-0003-1257-9702 Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USASearch for more papers by this authorAnne O'Donnell-Luria, Anne O'Donnell-Luria orcid.org/0000-0001-6418-9592 Department of Pediatrics, Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USASearch for more papers by this authorSeema R. Lalani, Seema R. Lalani Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USASearch for more papers by this authorWilliam D. Graf, William D. Graf orcid.org/0000-0003-0460-4605 Department of Pediatrics, Division of Neurology, Connecticut Children's, University of Connecticut, Farmington, Connecticut, USASearch for more papers by this authorJill A. Rosenfeld, Jill A. Rosenfeld orcid.org/0000-0001-5664-7987 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Baylor Genetics Laboratory, Houston, Texas, USASearch for more papers by this authorEvan E. Eichler, Evan E. Eichler orcid.org/0000-0002-8246-4014 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USASearch for more papers by this authorRachel K. Earl, Rachel K. Earl Center on Human Development and Disability, University of Washington, Seattle, Washington, USA Seattle Children's Autism Center, Seattle, Washington, USA Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USASearch for more papers by this authorDaryl A. Scott, Corresponding Author Daryl A. Scott dscott@bcm.edu orcid.org/0000-0003-1460-5169 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA Texas Children's Hospital, Houston, Texas, USA Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA Correspondence Daryl A. Scott, Department of Molecular and Human Genetics, Baylor College of Medicine, R813, One Baylor Plaza, BCM225, Houston, TX 770303, USA. Email: dscott@bcm.eduSearch for more papers by this author First published: 18 January 2022 https://doi.org/10.1002/humu.24332Citations: 1Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Abstract PAX5 is a transcription factor associated with abnormal posterior midbrain and cerebellum development in mice. PAX5 is highly loss-of-function intolerant and missense constrained, and has been identified as a candidate gene for autism spectrum disorder (ASD). We describe 16 individuals from 12 families who carry deletions involving PAX5 and surrounding genes, de novo frameshift variants that are likely to trigger nonsense-mediated mRNA decay, a rare stop-gain variant, or missense variants that affect conserved amino acid residues. Four of these individuals were published previously but without detailed clinical descriptions. All these individuals have been diagnosed with one or more neurodevelopmental phenotypes including delayed developmental milestones (DD), intellectual disability (ID), and/or ASD. Seizures were documented in four individuals. No recurrent patterns of brain magnetic resonance imaging (MRI) findings, structural birth defects, or dysmorphic features were observed. Our findings suggest that PAX5 haploinsufficiency causes a neurodevelopmental disorder whose cardinal features include DD, variable ID, and/or ASD. Open Research DATA AVAILABILITY STATEMENT All previously unreported variants described in this manuscript have been submitted to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/). Citing Literature Supporting Information Filename Description humu24332-sup-0001-Supp_Mat.pdf160.2 KB Supporting information. humu24332-sup-0002-Supplement_Table_1_11_10_2021.xlsx17.5 KB Supporting information. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. Volume43, Issue4April 2022Pages 461-470 RelatedInformation

Autism Spectrum Disorder (ASD) is genetically complex with ~100 copy number variants and genes involved. To try to establish more definitive genotype and phenotype correlations in ASD, we searched genome sequence data, and the literature, for recurrent predicted damaging sequence-level variants affecting single genes. We identified 18 individuals from 16 unrelated families carrying a heterozygous guanine duplication (c.3679dup; p.Ala1227Glyfs*69) occurring within a string of 8 guanines (genomic location [hg38]g.50,721,512dup) affecting SHANK3, a prototypical ASD gene (0.08% of ASD-affected individuals carried the predicted p.Ala1227Glyfs*69 frameshift variant). Most probands carried de novo mutations, but five individuals in three families inherited it through somatic mosaicism. We scrutinized the phenotype of p.Ala1227Glyfs*69 carriers, and while everyone (17/17) formally tested for ASD carried a diagnosis, there was the variable expression of core ASD features both within and between families. Defining such recurrent mutational mechanisms underlying an ASD outcome is important for genetic counseling and early intervention.

(Stem Cell Reports 11, 1211–1225; January 13, 2018) The original representative trace of excitatory post-synaptic current (EPSC) for AFF2−/y was used twice by mistake to generate the ASTN2−/y cropped trace on the top panel of Figure 5A. However, we confirm that the original data was not a duplicate; only the image file was cropped incorrectly as a display figure for the trace. We have made a new Figure 5 with the correct ASTN2 trace cropped in Figure 5A. None of the original data or interpretation of the data was impacted.Figure 5Electrophysiological Phenotyping of KO iPSC-Derived Neurons (original)View Large Image Figure ViewerDownload Hi-res image Download (PPT) Complete Disruption of Autism-Susceptibility Genes by Gene Editing Predominantly Reduces Functional Connectivity of Isogenic Human NeuronsDeneault et al.Stem Cell ReportsNovember 1, 2018In BriefIn this article, Scherer and colleagues present a human induced pluripotent stem cell (iPSC) knockout resource for functional studies of ten genes associated with autism spectrum disorder. They also show that some of these genes, pertaining to diverse functional categories, can underlie common phenotypes in CRISPR-isogenic iPSC-derived glutamatergic neurons. Full-Text PDF Open Access

The clinical integration of chromosomal microarray testing promises improvements in diagnostic yields in Autism Spectrum Disorder (ASD). While the impact on clinical management is promising for some families, the utility perceived by families, including the majority for whom results are negative, is unclear. With next generation genomic sequencing technologies poised for integration, along with promising ASD biomarkers being developed, there is a need to understand the extent to which genomic and other biological testing would have utility for the target recipients of these tests and their families. The purpose of the present cross-sectional study was to examine the predictors of perceived utility of biological testing among parents of a child with ASD. The Perceived Utility of Biotesting (PUB) Questionnaire was developed based on literature review and integrating family review. Following their child's diagnosis, families participating in an ongoing prospective study completed the PUB questionnaire along with self-reported measures of parent stress, child and family functioning, and family-centered care prior to undergoing genetic testing for both clinical and research purposes. Based on n = 85 families, psychometric properties of the Perceived Utility of Biotesting questionnaire suggest a reliable and valid instrument. A stepwise regression analysis reveals that lower levels of child emotional and behavioural functioning and higher levels of family functioning correlated with higher perceived utility for biological testing. A main limitation in the study is the participation rate of 50 %, thus the possibility of self-selection bias cannot be ruled out. We also chose to assess perceived utility among parents rather than the individuals with ASD themselves: modifying the questionnaire to capture perceived utility from autistic individuals across the lifespan would prove essential in future studies. Finally, ongoing validation of the PUB by assessing the PUB's discriminant and convergent validity is still needed. We conclude that the utility of biological testing perceived by families whose child is undergoing genetic testing around ASD diagnosis depends on their unique child and family characteristics. This signifies that engaging families in biomarker discovery for improving the impact of research and care requires systematic input from a representative sample of families.

To characterize a novel neurodevelopmental syndrome due to loss-of-function (LoF) variants in Ankyrin 2 (ANK2), and to explore the effects on neuronal network dynamics and homeostatic plasticity in human-induced pluripotent stem cell-derived neurons.We collected clinical and molecular data of 12 individuals with heterozygous de novo LoF variants in ANK2. We generated a heterozygous LoF allele of ANK2 using CRISPR/Cas9 in human-induced pluripotent stem cells (hiPSCs). HiPSCs were differentiated into excitatory neurons, and we measured their spontaneous electrophysiological responses using micro-electrode arrays (MEAs). We also characterized their somatodendritic morphology and axon initial segment (AIS) structure and plasticity.We found a broad neurodevelopmental disorder (NDD), comprising intellectual disability, autism spectrum disorders and early onset epilepsy. Using MEAs, we found that hiPSC-derived neurons with heterozygous LoF of ANK2 show a hyperactive and desynchronized neuronal network. ANK2-deficient neurons also showed increased somatodendritic structures and altered AIS structure of which its plasticity is impaired upon activity-dependent modulation.Phenotypic characterization of patients with de novo ANK2 LoF variants defines a novel NDD with early onset epilepsy. Our functional in vitro data of ANK2-deficient human neurons show a specific neuronal phenotype in which reduced ANKB expression leads to hyperactive and desynchronized neuronal network activity, increased somatodendritic complexity and AIS structure and impaired activity-dependent plasticity of the AIS.

Background We present genomic and phenotypic findings of a transgenerational family consisting of three male offspring, each with a maternally inherited distal 220 kb deletion at locus 16p11.2 (BP2–BP3). Genomic analysis of all family members was prompted by a diagnosis of autism spectrum disorder (ASD) in the eldest child, who also presented with a low body mass index. Methods All male offspring underwent extensive neuropsychiatric evaluation. Both parents were also assessed for social functioning and cognition. The family underwent whole-genome sequencing. Further data curation was undertaken from samples ascertained for neurodevelopmental disorders and congenital abnormalities. Results On medical examination, both the second and third-born male offspring presented with obesity. The second-born male offspring met research diagnostic criteria for ASD at 8 years of age and presented with mild attention deficits. The third-born male offspring was only noted as having motor deficits and received a diagnosis of developmental coordination disorder. Other than the 16p11.2 distal deletion, no additional contributing variants of clinical significance were observed. The mother was clinically evaluated and noted as having a broader autism phenotype. Conclusion In this family, the phenotypes observed are most likely caused by the 16p11.2 distal deletion. The lack of other overt pathogenic mutations identified by genomic sequencing reinforces the variable expressivity that should be heeded in a clinical setting. Importantly, distal 16p11.2 deletions can present with a highly variable phenotype even within a single family. Our additional data curation provides further evidence on the variable clinical presentation among those with pathogenetic 16p11.2 (BP2–BP3) mutations.

Autism Spectrum Disorder (ASD) exhibits an ~4:1 male-to-female sex bias and is characterized by early-onset impairment of social/communication skills, restricted interests, and stereotyped behaviors. Disruption of the Xp22.11 locus has been associated with ASD in males. This locus includes the three-exon PTCHD1 gene, an adjacent multi-isoform long noncoding RNA (lncRNA) named PTCHD1-AS (spanning ~1Mb), and a poorly characterized single-exon RNA helicase named DDX53 that is intronic to PTCHD1-AS. While the relationship between PTCHD1/PTCHD1-AS and ASD is being studied, the role of DDX53 has not been examined, in part because there is no apparent functional murine orthologue. Through clinical testing, here, we identified 6 males and 1 female with ASD from 6 unrelated families carrying rare, predicted-damaging or loss-of-function variants in DDX53. Then, we examined databases, including the Autism Speaks MSSNG and Simons Foundation Autism Research Initiative, as well as population controls. We identified 24 additional individuals with ASD harboring rare, damaging DDX53 variations, including the same variants detected in two families from the original clinical analysis. In this extended cohort of 31 participants with ASD (28 male, 3 female), we identified 25 mostly maternally-inherited variations in DDX53, including 18 missense changes, 2 truncating variants, 2 in-frame variants, 2 deletions in the 3' UTR and 1 copy number deletion. Our findings in humans support a direct link between DDX53 and ASD, which will be important in clinical genetic testing. These same autism-related findings, coupled with the observation that a functional orthologous gene is not found in mouse, may also influence the design and interpretation of murine-modelling of ASD.

Abstract Autism spectrum disorder (ASD) is a relatively common childhood onset neurodevelopmental disorder with a complex genetic etiology. While progress has been made in identifying the de novo mutational landscape of ASD, the genetic factors that underpin the ASD's tendency to run in families are not well understood. In this study, nine extended pedigrees each with three or more individuals with ASD, and others with a lesser autism phenotype, were phenotyped and genotyped in an attempt to identify heritable copy number variants (CNVs). Although these families have previously generated linkage signals, no rare CNV segregated with these signals in any family. A small number of clinically relevant CNVs were identified. Only one CNV was identified that segregated with ASD phenotype; namely, a duplication overlapping DLGAP2 in three male offspring each with an ASD diagnosis. This gene encodes a synaptic scaffolding protein, part of a group of proteins known to be pathologically implicated in ASD. On the whole, however, the heritable nature of ASD in the families studied remains poorly understood.

Understanding the overall utility of biological testing for autism spectrum disorder (ASD) is essential for the development and integration of biomarkers into routine care. One measure related to the overall utility of biological testing is the knowledge that a person has about the condition he/she suffers from. However, a major gap towards understanding the role of knowledge in overall utility is the absence of studies that have assessed knowledge of autism along with its predictors within a representative sample of families within the context of routine care. The objective of this study was to measure knowledge of ASD among families within the routine care pathway for biological testing in ASD by examining the association between knowledge with potential correlates of knowledge namely sociodemographic factors, parental stress and distress, and time since diagnosis among parents whose child with ASD is undergoing clinical genetic testing. Parents of a child diagnosed with ASD (n = 85, Mage = 39.0, SD = 7.7) participating in an ongoing prospective genomics study completed the ASD Quiz prior to undergoing genetic testing for clinical and research purposes. Parents also completed self-reported measures of stress and distress. Parent stress and distress was each independently correlated with knowledge of ASD, rs ≥ 0.26, ps < 0.05. Stepwise regression analysis revealed a significant model accounting for 7.8% of the variance in knowledge, F (1, 82) = 8.02, p = 0.006. The only factor significantly associated with knowledge was parental distress, β = 0.30, p = 0.006. Parental stress, time since diagnosis, and sociodemographic factors were not significant predictors in this model. We concluded that families require tailored support prior to undergoing genetic testing to address either knowledge gaps or high distress. Ongoing appraisal of the testing process among families of diverse backgrounds is essential in offering optimal care for families undergoing genetic testing.

The genetics care pathway experienced by families affected by autism spectrum disorder (ASD) around the time of diagnosis is currently uncharacterized and potentially variable across contexts. The lack of consensus on outcome measures to capture the impact of genetic services for these families shows a gap in understanding and optimizing this genetics care pathway. The Genetic Counseling Outcome Scale (GCOS-24) is a validated outcome measure of clinical genetics services. The current study aims to adapt and validate the GCOS-24 as an outcome measure in the context routine genetic testing in ASD and related conditions. Families seen for their child's developmental evaluation for ASD and related conditions were invited to participate in a genomics cohort between 2016 and 2018. Families (n = 111) completed the mGCOS-24 (modified GCOS-24), adapted from the original GCOS-24 by clinicians working in the target population's routine care pathway. The mGCOS-24 has acceptable internal consistency (Cronbach's α = 0.84) and high test-retest reliability (ICC = 0.88). It also inversely correlates with stress as measured by Perceived Stress Scale (PSS-10) and distress, as measured by the Distress Thermometer, rs ≥ 0.39, ps < 0.001. The mGCOS-24 had adequate readability, as supported by cognitive interviews completed by a sub-sample of five mothers of a child with ASD. Together, our findings show that the mGCOS-24 has good validity for the target population. Preliminary characterization of the genetics care pathway in this population revealed remarkable variability in pre-test counseling and limited post-test counseling. The use of the mGCOS-24 as an outcome measure is useful in filling some of these gaps by offering a way to assess, and in the future, optimize the genetics care pathway for families affected by autism and related neurodevelopmental conditions.

Abstract We report detailed functional analyses and genotype-phenotype correlations in 433 individuals carrying disease-causing variants in SCN8A , encoding the voltage-gated Na + channel Na V 1.6. Five different clinical subgroups could be identified: 1) Benign familial infantile epilepsy (BFIE) (n=17, normal cognition, treatable seizures), 2) intermediate epilepsy (n=36, mild ID, partially pharmacoresponsive), 3) developmental and epileptic encephalopathy (DEE, n=191, severe ID, majority pharmacoresistant), 4) generalized epilepsy (n=21, mild to moderate ID, frequently with absence seizures), and 5) affected individuals without epilepsy (n=25, mild to moderate ID). Groups 1-3 presented with early-onset (median: four months) focal or multifocal seizures and epileptic discharges, whereas the onset of seizures in group 4 was later (median: 39 months) with generalized epileptic discharges. The epilepsy was not classifiable in 143 individuals. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin insensitive human Na V 1.6 channels and whole-cell patch clamping. Two variants causing DEE showed a strong gain-of-function (GOF, hyperpolarising shift of steady-state activation, strongly increased neuronal firing rate), and one variant causing BFIE or intermediate epilepsy showed a mild GOF (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (LOF, reduced current amplitudes, depolarising shift of steady-state activation, reduced neuronal firing). Including previous studies, functional effects were known for 165 individuals. All 133 individuals carrying GOF variants had either focal (76, groups 1-3), or unclassifiable epilepsy (37), whereas 32 with LOF variants had either generalized (14), no (11) or unclassifiable (5) epilepsy; only two had DEE. Computational modeling in the GOF group revealed a significant correlation between the severity of the electrophysiological and clinical phenotypes. GOF variant carriers responded significantly better to sodium channel blockers (SCBs) than to other anti-seizure medications, and the same applied for all individuals of groups 1-3. In conclusion, our data reveal clear genotype-phenotype correlations between age at seizure onset, type of epilepsy and gain- or loss-of-function effects of SCN8A variants. Generalized epilepsy with absence seizures is the main epilepsy phenotype of LOF variant carriers and the extent of the electrophysiological dysfunction of the GOF variants is a main determinant of the severity of the clinical phenotype in focal epilepsies. Our pharmacological data indicate that SCBs present a therapeutic treatment option in early onset SCN8A -related focal epilepsy.

Summary Autism Spectrum Disorder is phenotypically and genetically heterogeneous, but genomic analyses have identified candidate susceptibility genes. We present a CRISPR gene editing strategy to insert a protein tag and premature termination sites creating an induced pluripotent stem cell (iPSC) knockout resource for functional studies of 10 ASD-relevant genes ( AFF2/FMR2, ANOS1, ASTN2, ATRX , CACNA1C , CHD8, DLGAP2, KCNQ2 , SCN2A , TENM1 ). Neurogenin 2 (NEUROG2)-directed differentiation of iPSCs allowed production of cortical excitatory neurons, and mutant proteins were not detectable. RNAseq revealed convergence of several neuronal networks. Using both patch-clamp and multi-electrode array approaches, the electrophysiological deficits measured were distinct for different mutations. However, they culminated in a consistent reduction in synaptic activity, including reduced spontaneous excitatory post-synaptic current frequencies in AFF2/FMR2- , ASTN2-, ATRX -, KCNQ2 - and SCN2A -null neurons. Despite ASD susceptibility genes belonging to different gene ontologies, isogenic stem cell resources can reveal common functional phenotypes, such as reduced functional connectivity.

International Journal of Developmental NeuroscienceVolume 47, Issue Part_A p. 76-76 Article ISDN2014_0253: High resolution genomic analyses of a clinically defined autism spectrum disorder cohort Kristiina Tammimies, Corresponding Author Kristiina Tammimies n/a@.dne The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorBridget A. Fernandez, Bridget A. Fernandez Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John's, Canada Provincial Medical Genetic Program, Eastern Health, St. John's, CanadaSearch for more papers by this authorSusan Walker, Susan Walker The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorBhooma Thiruvahindrapuram, Bhooma Thiruvahindrapuram The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorGaganjot Kaur, Gaganjot Kaur The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorAnath C. Lionel, Anath C. Lionel The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorWendy Roberts, Wendy Roberts The Autism Research Unit, Hospital for Sick Children, Toronto, Ontario, CanadaSearch for more papers by this authorRosanna Weksberg, Rosanna Weksberg Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorJennifer L. Howe, Jennifer L. Howe The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorMohammed Uddin, Mohammed Uddin The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorRyan K.C. Yuen, Ryan K.C. Yuen The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorZhuozhi Wang, Zhuozhi Wang The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorPeter Szatmari, Peter Szatmari Centre for Addiction and Mental Health, University of Toronto, Toronto, CanadaSearch for more papers by this authorKathy Whitten, Kathy Whitten Child Health Program, Eastern Health, St. John's, NL, Canada Discipline of Pediatrics, Memorial University of Newfoundland, St John's, CanadaSearch for more papers by this authorCathy Vardy, Cathy Vardy Child Health Program, Eastern Health, St. John's, NL, CanadaSearch for more papers by this authorVictoria Crosbie, Victoria Crosbie Discipline of Pediatrics, Memorial University of Newfoundland, St John's, CanadaSearch for more papers by this authorSandra Luscombe, Sandra Luscombe Child Health Program, Eastern Health, St. John's, NL, CanadaSearch for more papers by this authorTyna Doyle, Tyna Doyle Child Health Program, Eastern Health, St. John's, NL, CanadaSearch for more papers by this authorSusan Stuckless, Susan Stuckless Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John's, CanadaSearch for more papers by this authorDaniele Merico, Daniele Merico The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorChristian R. Marshall, Christian R. Marshall Molecular Genetics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorStephen W. Scherer, Stephen W. Scherer The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, CanadaSearch for more papers by this author Kristiina Tammimies, Corresponding Author Kristiina Tammimies n/a@.dne The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorBridget A. Fernandez, Bridget A. Fernandez Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John's, Canada Provincial Medical Genetic Program, Eastern Health, St. John's, CanadaSearch for more papers by this authorSusan Walker, Susan Walker The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorBhooma Thiruvahindrapuram, Bhooma Thiruvahindrapuram The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorGaganjot Kaur, Gaganjot Kaur The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorAnath C. Lionel, Anath C. Lionel The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorWendy Roberts, Wendy Roberts The Autism Research Unit, Hospital for Sick Children, Toronto, Ontario, CanadaSearch for more papers by this authorRosanna Weksberg, Rosanna Weksberg Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorJennifer L. Howe, Jennifer L. Howe The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorMohammed Uddin, Mohammed Uddin The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorRyan K.C. Yuen, Ryan K.C. Yuen The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorZhuozhi Wang, Zhuozhi Wang The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorPeter Szatmari, Peter Szatmari Centre for Addiction and Mental Health, University of Toronto, Toronto, CanadaSearch for more papers by this authorKathy Whitten, Kathy Whitten Child Health Program, Eastern Health, St. John's, NL, Canada Discipline of Pediatrics, Memorial University of Newfoundland, St John's, CanadaSearch for more papers by this authorCathy Vardy, Cathy Vardy Child Health Program, Eastern Health, St. John's, NL, CanadaSearch for more papers by this authorVictoria Crosbie, Victoria Crosbie Discipline of Pediatrics, Memorial University of Newfoundland, St John's, CanadaSearch for more papers by this authorSandra Luscombe, Sandra Luscombe Child Health Program, Eastern Health, St. John's, NL, CanadaSearch for more papers by this authorTyna Doyle, Tyna Doyle Child Health Program, Eastern Health, St. John's, NL, CanadaSearch for more papers by this authorSusan Stuckless, Susan Stuckless Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John's, CanadaSearch for more papers by this authorDaniele Merico, Daniele Merico The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorChristian R. Marshall, Christian R. Marshall Molecular Genetics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, CanadaSearch for more papers by this authorStephen W. Scherer, Stephen W. Scherer The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada Department of Molecular Genetics, McLaughlin Centre, University of Toronto, Toronto, CanadaSearch for more papers by this author First published: 05 November 2015 https://doi.org/10.1016/j.ijdevneu.2015.04.208Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume47, IssuePart_AISDN 2014 AbstractsDecember 2015Pages 76-76 RelatedInformation

<h3>Objective:</h3> To capture the full extent of genomic contributions to cerebral palsy (CP) in an unselected cohort. <h3>Background:</h3> CP is the most common childhood physical disability. It is increasingly recognized that genomic changes can contribute to at least some of the clinical features and phenotypes of individuals with CP . The uncovering of rare variants can result in a degree of diagnostic confusion, with some known disorders labeled as CP “mimics”. This has led to debate about the validity of a clinical diagnosis of CP in individuals with a “genetic diagnosis”. Resolution of these discussions will be made easier by the comprehensive understanding of the full range of genomic factors contributing to CP features and phenotypes in a large, prospectively collected cohort, with analysis of parental samples to assist in identification of inherited and <i>de novo</i> variation, and paired with thorough clinical phenotype assessments. <h3>Design/Methods:</h3> We report on whole genome sequencing in 327 unselected children with cerebral palsy (CP) and their biologic parents recruited from CP-NET and the Canadian CP Registry. <h3>Results:</h3> We identified clinically relevant variants in 29.1 % (95/327) with 11.3% classified as pathogenic/likely pathogenic (P/LP) and 17.8% as variants of unknown significance. Multiple classes of rare variants included copy number variations (16.5%), damaging single nucleotide variants (SNV) and indels (12.5%), mitochondrial variants (1.5%) and structural variants (0.6%). <i>COL4A1</i>, a gene that encodes the alpha-1 subunit of collagen type IV, was the most frequent SNV (4 cases). Mitochondrial variants were associated with mitochondrial phenotypes including mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). A burden analysis demonstrated associations between <i>de novo</i> damaging variants and genes related to neuro-functions, nervous system and FMR1 target genes. <h3>Conclusions:</h3> A multifactorial CP risk profile and high rate of P/LP variants (11.3%) combine to support genomic testing, including mitochondrial variants, in the diagnostic work-up across all CP phenotypes. <b>Disclosure:</b> Dr. Oskoui has received personal compensation in the range of $500-$4,999 for serving as an officer or member of the Board of Directors for the Association des Neurologues du Quebec. The institution of Dr. Oskoui has received research support from Biogen. The institution of Dr. Oskoui has received research support from Roche Genetech. The institution of Dr. Oskoui has received research support from Muscular Dystrophy Canada. The institution of Dr. Oskoui has received research support from Canadian Institutes of Health Research. Dr. Oskoui has received personal compensation in the range of $50,000-$99,999 for serving as a Methodologist with American Academy of Neurology. Dr. Oskoui has a non-compensated relationship as a Member of the Medical and Scientific Advisory Committee with Muscular Dystrophy Canada that is relevant to AAN interests or activities. Dr. Zarrei has nothing to disclose. Dr. Engchuan has nothing to disclose. Dr. Sondheimer has received personal compensation for serving as an employee of Synlogic. Dr. Sondheimer has received personal compensation in the range of $5,000-$9,999 for serving as an Editor, Associate Editor, or Editorial Advisory Board Member for Science Advances. Ms. Thiruv has nothing to disclose. Mr. Higginbotham has nothing to disclose. Dr. Thapa has stock in Alibaba Group Holding Limited,Exro Technologies Inc, Drone Delivery Canada Corp, Vanguard S&amp;P 500 ETF, Nokia Corp. Dr. Behlim has nothing to disclose. Ms. Aimola has nothing to disclose. Dr. Wei has nothing to disclose. Mrs. Danthi has nothing to disclose. Dr. Pellecchia has nothing to disclose. Karen Ho, MD has nothing to disclose. Miss De Rijke has nothing to disclose. Ms. Howe has nothing to disclose. Mr. Nalpathamkalam has nothing to disclose. Dr. Manshaei has nothing to disclose. Mr. Whitney has nothing to disclose. Mr. Patel has nothing to disclose. Mr. Hamdan has nothing to disclose. Miss Shaath has nothing to disclose. Dr. Knights has nothing to disclose. Dr. Trost has nothing to disclose. Dr. Samdup has nothing to disclose. The institution of Dr. MCCORMICK has received research support from Ontario Brain Institute. The institution of Dr. MCCORMICK has received research support from Brain Canada . Dr. Hunt has received personal compensation in the range of $10,000-$49,999 for serving as an Expert Witness for Borden Ladner Gervais. Dr. Kirton has received personal compensation in the range of $10,000-$49,999 for serving as an Expert Witness for Multiple. The institution of Dr. Kirton has received research support from Multiple. Dr. Kawamura has nothing to disclose. Dr. Mesterman has nothing to disclose. Dr. Gorter has received personal compensation in the range of $5,000-$9,999 for serving as an Editor, Associate Editor, or Editorial Advisory Board Member for Wiley. Dr. Gorter has received research support from McMaster University. Dr. Dlamini has nothing to disclose. Dr. Merico has received personal compensation for serving as an employee of Deep Genomics. Dr. Merico has stock in Deep Genomics. Ryan Yuen has nothing to disclose. Dr. Shevell has nothing to disclose. James Stavropoulos has stock in Phenotips. James Stavropoulos has received intellectual property interests from a discovery or technology relating to health care. Dr. Wintle has nothing to disclose. The institution of Darcy L. Fehlings has received research support from Ontario Brain Institute. The institution of Darcy L. Fehlings has received research support from Kids Brain Health Network. The institution of Darcy L. Fehlings has received research support from CHILD BRIGHT. Darcy L. Fehlings has received personal compensation in the range of $500-$4,999 for serving as a Member of the Selection Committee for the Elsass Foundation CP Research Prize with Elsass Foundation . Dr. Scherer has received personal compensation in the range of $500-$4,999 for serving on a Scientific Advisory or Data Safety Monitoring board for Population Bio. Dr. Scherer has received personal compensation in the range of $5,000-$9,999 for serving as an Editor, Associate Editor, or Editorial Advisory Board Member for Nature-Springer. The institution of Dr. Scherer has received research support from Autism Speaks. The institution of Dr. Scherer has received research support from Genome Canada. The institution of Dr. Scherer has received research support from SFARI. The institution of Dr. Scherer has received research support from CIHR. The institution of Dr. Scherer has received research support from NIH. The institution of Dr. Scherer has received research support from Qatar National Research Fund. The institution of Dr. Scherer has received research support from Ontario Brain Institute. The institution of Dr. Scherer has received research support from Canada’s Digital Technology Supercluster. The institution of Dr. Scherer has received research support from Canada Foundation for Innovation. The institution of Dr. Scherer has received research support from Ontario Research Fund. Dr. Scherer has received intellectual property interests from a discovery or technology relating to health care. Dr. Scherer has received personal compensation in the range of $10,000-$49,999 for serving as a Highly Cited Academic Research Program with King Abdullaziz University.

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

Additional file 1. Supplementary tables.

SUMMARY SCN2A is an autism spectrum disorder (ASD) risk gene and encodes a voltage-gated sodium channel. However, the impact of autism-associated SCN2A de novo variants on human neuron development is unknown. We studied SCN2A using isogenic SCN2A -/- induced pluripotent stem cells (iPSCs), and patient-derived iPSCs harboring a p.R607* or a C-terminal p.G1744* de novo truncating variant. We used Neurogenin2 to generate excitatory glutamatergic neurons and found that SCN2A +/ p . R607 * and SCN2A -/- neurons displayed a reduction in synapse formation and excitatory synaptic activity using multielectrode arrays and electrophysiology. However, the p.G1744* variant, which leads to early-onset seizures in addition to ASD, altered action-potential dynamics but not synaptic activity. Proteomic and functional analysis of SCN2A +/ p . R607 * neurons revealed defects in neuronal morphology and bioenergetic pathways, which were not present in SCN2A +/ p . G1744 * neurons. Our study reveals that SCN2A de novo variants can have differential impact on human neuron function and signaling. HIGHTLIGHTS - Isogenic SCN2A -/- neurons display intrinsic hyperexcitability and impaired excitatory synapse function - SCN2A +/ p . R607 * variant reduces excitatory synapse function in patient neurons - C-terminal SCN2A +/ p . G1744 * variant enhances action potential properties but not synaptic transmission in patient neurons - SCN2A +/ p . R607 * variant display impacts on morphological and bioenergetic signaling networks through proteomic and functional analysis eTOC - Brown et al. examined Autism-associated SCN2A variants using patient-derived iPSC NGN2-neurons. They discover that genetic variants differentially impact neuronal development and synaptic function, and highlight neuronal and bioenergetic signaling networks underlying SCN2A loss-of-function.

There is limited empirical data quantifying the utility of genetic testing for families of children with autism spectrum disorder (ASD) or related neurodevelopmental disorders (NDD). We assessed the utility of clinical chromosomal microarray analysis (CMA), defined by diagnostic yield and parental empowerment, in population-based sample of parents of affected children; and explored child, family, and health services factors predictive of empowerment.Participants were families of children undergoing diagnostic assessments, between 2016 and 2019. Diagnostic yield of CMA in affected children was determined. Parental empowerment was measured through adapted version of the Genetics Counseling Outcome Scale-24. Parents completed questionnaires to capture child, family, and health service factors.The diagnostic yield of CMA was 2.8% for pathogenic variants. Parental empowerment was significantly correlated with family functioning and aspects of perceived family-centeredness of care. The model accounted for 49.8% of the variation in parental empowerment, F (10,37) = 3.67, p = 0.002. After accounting for other predictors, parental perception of the provision of general information remained significantly associated with empowerment.The informational needs of families play an important role in their empowerment during genetic testing. Meeting these needs and monitoring empowerment can aid genomic technologies integration in personalized healthcare for ASD/NDD.

ABSTRACT Copy number variations (CNV) are associated with psychiatric and neurodevelopmental disorders (NDDs), and most, including the recurrent 15q13.3 microdeletion disorder, have unknown disease mechanisms. We used a heterozygous 15q13.3 microdeletion mouse model and patient iPSC-derived neurons to reveal developmental defects in neuronal maturation and network activity. To identify the underlying molecular dysfunction, we developed a neuron-specific proximity-labeling proteomics (BioID2) pipeline, combined with patient mutations, to target the 15q13.3 CNV genetic driver OTUD7A . OTUD7A is an emerging independent NDD risk gene with no known function in the brain, but has putative deubiquitinase (DUB) function. The OTUD7A protein-protein interaction (PPI) network revealed interactions with synaptic, axonal, and cytoskeletal proteins and was enriched for known ASD and epilepsy risk genes. The interactions between OTUD7A and the NDD risk genes Ankyrin-G ( Ank3 ) and Ankyrin-B ( Ank2 ) were disrupted by an epilepsy-associated OTUD7A L233F variant. Further investigation of Ankyrin-G in mouse and human 15q13.3 microdeletion and OTUD7A L233F/L233F models revealed protein instability, increased polyubiquitination, and decreased levels in the axon initial segment (AIS), while structured illumination microscopy identified reduced Ankyrin-G nanodomains in dendritic spines. Functional analysis of human 15q13.3 microdeletion and OTUD7A L233F/L233F models revealed shared and distinct impairments to axonal growth and intrinsic excitability. Importantly, restoring OTUD7A or Ankyrin-G expression in 15q13.3 microdeletion neurons led to a reversal of abnormalities. These data reveal a critical OTUD7A-Ankyrin pathway in neuronal development, which is impaired in the 15q13.3 microdeletion syndrome, leading to neuronal dysfunction. Further, our study highlights the utility of targeting CNV genes using cell-type specific proteomics to identify shared and unexplored disease mechanisms across NDDs.

Abstract Fully understanding the genetic factors involved in Autism Spectrum Disorder (ASD) requires whole-genome sequencing (WGS), which theoretically allows the detection of all types of genetic variants. With the aim of generating an unprecedented resource for resolving the genomic architecture underlying ASD, we analyzed genome sequences and phenotypic data from 5,100 individuals with ASD and 6,212 additional parents and siblings (total n=11,312) in the Autism Speaks MSSNG Project, as well as additional individuals from other WGS cohorts. WGS data and autism phenotyping were based on high-quality short-read sequencing (&gt;30x coverage) and clinically accepted diagnostic measures for ASD, respectively. For initial discovery of ASD-associated genes, we used exonic sequence-level variants from MSSNG as well as whole-exome sequencing-based ASD data from SPARK and the Autism Sequencing Consortium (&gt;18,000 trios plus additional cases and controls), identifying 135 ASD-associated protein-coding genes with false discovery rate &lt;10%. Combined with ASD-associated genes curated from the literature, this list was used to guide the interpretation of all other variant types in WGS data from MSSNG and the Simons Simplex Collection (SSC; n=9,205). We identified ASD-associated rare variants in 789/5,100 individuals with ASD from MSSNG (15%) and 421/2,419 from SSC (17%). Considering the genomic architecture, 57% of ASD-associated rare variants were nuclear sequence-level variants, 41% were nuclear structural variants (SVs) (mainly copy number variants, but also including inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Several of the ASD-associated SVs would have been difficult to detect without WGS, including an inversion disrupting SCN2A and a nuclear mitochondrial insertion impacting SYNGAP1 . Polygenic risk scores did not differ between children with ASD in multiplex families versus simplex, and rare, damaging recessive events were significantly depleted in multiplex families, collectively suggesting that rare, dominant variation plays a predominant role in multiplex ASD. Our study provides a guidebook for exploring genotype-phenotype correlations in the 15-20% of ASD families who carry ASD-associated rare variants, as well as an entry point to the larger and more diverse studies that will be required to dissect the etiology in the &gt;80% of the ASD population that remains idiopathic. All data resulting from this study are available to the medical genomics research community in an open but protected manner.

Summary Induced Pluripotent Stem Cells (iPSC) derived from healthy individuals are important controls for disease modeling studies. To create a resource of genetically annotated iPSCs, we reprogrammed footprint-free lines from four volunteers in the Personal Genome Project Canada (PGPC). Multilineage directed differentiation efficiently produced functional cortical neurons, cardiomyocytes and hepatocytes. Pilot users further demonstrated line versatility by generating kidney organoids, T-lymphocytes and sensory neurons. A frameshift knockout was introduced into MYBPC3 and these cardiomyocytes exhibited the expected hypertrophic phenotype. Whole genome sequencing (WGS) based annotation of PGPC lines revealed on average 20 coding variants. Importantly, nearly all annotated PGPC and HipSci lines harboured at least one pre-existing or acquired variant with cardiac, neurological or other disease associations. Overall, PGPC lines were efficiently differentiated by multiple users into cell types found in six tissues for disease modeling, and clinical annotation highlighted variant-preferred lines for use as unaffected controls in specific disease settings.

In March 2003, The Cincinnati Art Museum will celebrate the opening of the Cincinnati Wing: eighteen thousand square feet of handsomely renovated gallery space devoted to the museum's renowned collections of painting, sculpture, furniture, ceramics, and metalwork by Cincinnati artists. The museum is the first in the country to reinterpret its American art collections with a regional emphasis, fostering civic pride and drawing attention to the achievements of the city's artists. In conjunction with the celebration, Ohio University Press is proud to publish The Cincinnati Wing: The Story of Art in the Queen City, showcasing one of America's foremost art centers of the nineteenth and early twentieth centuries. The authors of this collection trace the thematic arrangement of the Cincinnati Wing galleries, situating the artwork in the context of the city's history as it progressed from a frontier river town to an industrial powerhouse. The Cincinnati Wing provides a vivid picture of the fertile social and cultural climate that produced such prominent figures in the history of American art as sculptor Hiram Powers and painters Robert S. Duncanson, Frank Duveneck, and John H. Twachtman. Cincinnati's contributions to the decorative arts are exemplified by the stunning ceramics of the celebrated Rookwood Pottery Company, the nation's leading art pottery firm, and by the city's lesser-known yet equally significant Aesthetic Movement furniture. One hundred fifty-one color plates highlight the beauty and diversity of the Cincinnati Art Museum's collections and illuminate the Queen City's great artistic legacy.

To evaluate the antimicrobial activity of propolis samples collected from different regions of Algeria and their chemical composition.The antibacterial activity of ethanolic extract of Algerian propolis against Bacillus cereus (IPA), Staphylococcus aureus (ATCC25923R), Escherichia coli (ATCC25922) and Pseudomonas aeruginosa (ATCC27893R) was evaluated by the disc diffusion method and determined as an equivalent of the inhibition zones diameters after incubation of the cultures at 37 °C for 24 h. The investigation of the polyphenol and flavonoid contents was done spectrophotometrically.The ethanolic extract of Algerian propolis samples inhibited the growth of all examined microorganisms with the highest antimicrobial activity against the Gram-positive bacteria. Polyphenol and flavonoids contents were variable, depending on the propolis samples and a positive correlation between antimicrobial activity and chemical composition was observed.Antimicrobial activity, polyphenol and flavonoid contents were variable, depending on the propolis sample. The strong antimicrobial activity of Algerian propolis may be due to high total phenolic and flavonoid contents and this study suggests potential use of propolis in foods.

Previous articleNext article No AccessWOMEN DESIGNERS IN THE USA, 1900-2000Breaking the Mold: The Metalwork of Maria Longworth StorerJENNIFER HOWEJENNIFER HOWE Search for more articles by this author PDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by Volume 8, Number 1FALL-WINTER 2000-2001 Article DOIhttps://doi.org/10.1086/studdecoarts.8.1.40662759 Views: 5Total views on this site Journal History This article was published in Studies in the Decorative Arts (1993-2009), which is continued by West 86th (2011-present). Copyright 2000 The Bard Graduate Center for Studies in the Decorative Arts, Design, and CulturePDF download Crossref reports no articles citing this article.

enrichment_RAB39B4_vs_Controls6.txt (GO terms associated with differentially expressed genes) (TXT 484 kb)

RAB39B4_vs_Controls6_RPKM_Filt.txt (differential expression analysis results) (TXT 4721 kb)

human_GO_15_800_PATH_10_500.gmt (filtered gene-set definitions) (GMT 4425Â kb)

Previous articleNext article No AccessBook Reviews Carol Boram‐Hays. Bringing Modernism Home: Ohio Decorative Arts, 1890–1960. Athens: Ohio University Press, 2005. 241 pp.; 120 illustrations, bibliography, index. $40.00.Jennifer HoweJennifer HoweArt Academy of Cincinnati and independent curator Search for more articles by this author Art Academy of Cincinnati and independent curatorPDFPDF PLUSFull Text Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by Winterthur Portfolio Volume 42, Number 4Winter 2008 Published for the Henry Francis du Pont Winterthur Museum, Inc. Article DOIhttps://doi.org/10.1086/592795 Views: 3Total views on this site © 2008 by The Henry Francis du Pont Winterthur Museum, Inc. All rights reserved. For permission to reuse, please contact [email protected]PDF download Crossref reports no articles citing this article.

Abstract BACKGROUND AND AIMS Calciphylaxis is a rare but devastating disorder predominantly affecting patients with end-stage kidney disease [1]. Patients with calciphylaxis present with painful ischemic skin lesions caused by microvascular occlusion secondary to calcification, intimal hyperplasia, and thrombosis. In experimental models and in genetic disorders of mineralization, deficiency of pyrophosphate (PPi) results in vascular calcification and neointimal formation [2–4]. We investigated the role of PPi deficiency in the development of calciphylaxis and explored whether PPi levels predict outcomes among patients with calciphylaxis. METHOD As part of the ongoing national-level calciphylaxis registry work (ClinicalTrials.gov Identifier: NCT03032835) [5], we prospectively enrolled 14 dialysis-dependent patients with calciphylaxis (cases) and 7 dialysis-dependent patients without calciphylaxis (controls) matched for age, sex and race. Clinical data and blood samples were collected at enrolment. PPi levels were measured using an ATP Sulfurylase/Luminescence-Based Method for the quantification of inorganic PPi in human plasma and were compared between cases and controls using the Kruskal–Wallis test. Associations between PPi levels and clinical outcomes (ulcer formation, number of skin lesions and 1-year mortality) were explored. RESULTS The average age of calciphylaxis cases and controls was 62 and 61 years, respectively; 53% were women and 53% were Caucasian. The prevalence of diabetes mellitus, obesity, coronary artery disease and peripheral arterial disease were 71%, 23%, 29% and 53%, respectively and comparable between cases and controls. Warfarin exposure was present in 19% of cases. Most patients with calciphylaxis had ulcerated skin lesions involving abdominal wall and/or thighs. Median number of calciphylaxis skin lesions was 2 [interquartile range (IQR) 1–4]. Serum levels of calcium, phosphate, intact parathyroid hormone, 25-OH vitamin D and alkaline phosphatase were similar between cases and controls. Compared with controls, however, patients with calciphylaxis had lower plasma PPi levels [0.32 μM (IQR 0.19–0.70) versus 0.64 μM (IQR 0.46–1.08); P = 0.03]. Plasma PPi levels demonstrated a modest correlation with skin lesion count (r = –0.35) but were similar between patients with and without ulcer formation. Lower plasma PPi levels predicted 1-year mortality (Fig. 1). CONCLUSION In this pilot study, dialysis-dependent patients with calciphylaxis had lower levels of plasma PPi compared with controls. Plasma PPi levels predicted 1-year mortality among patients with calciphylaxis. Additional data from a larger study and longitudinal assessments of PPi levels are needed to support future clinical intervention trials targeting the PPi pathway in calciphylaxis.

Abstract We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health, and cognitive biomarkers in a community sample of 7,100 unrelated European, and East Asian children and youth (Spit for Science). Diagnoses of mental health disorders were found in 17.5% of participants and 27.6% scored in the highest 10% on either or both ADHD and OCD trait measures. Clinically relevant CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of ADHD ( p =5.0×10 −3 ), on a cognitive biomarker of mental health (response inhibition ( p =1.0×10 −2 )), and on prevalence of mental disorders ( p =1.9×10 −6 , odds ratio: 3.09). With a rise of mental illness, our data establishes a baseline for delineating genetic contributors in paediatric-onset conditions. One Sentence Summary Copy number variation predicts neurodevelopmental and mental health phenotypes in the general population.

Abstract Induced pluripotent stem cell (iPSC)-derived cortical neurons are increasingly used as a model to study developmental aspects of Autism Spectrum Disorder (ASD), which is clinically and genetically heterogeneous. To study the complex relationship of rare (penetrant) variant(s) and common (weaker) polygenic risk variant(s) to ASD, “isogenic” iPSC-derived neurons from probands and family-based controls, for modeling, is critical. We developed a standardized set of procedures, designed to control for heterogeneity in reprogramming and differentiation, and generated 53 different iPSC-derived glutamatergic neuronal lines from 25 participants from 12 unrelated families with ASD (14 ASD-affected individuals, 3 unaffected siblings, 8 unaffected parents). Heterozygous de novo (7 families; 16p11.2, NRXN1 , DLGAP2 , CAPRIN1 , VIP , ANOS1 , THRA ) and rare-inherited (2 families; CNTN5 , AGBL4 ) presumed-damaging variants were characterized in ASD risk genes/loci. In three additional families, functional candidates for ASD ( SET ), and combinations of putative etiologic variants ( GLI3/KIF21A and EHMT2/UBE2I combinations in separate families), were modeled. We used a large-scale multi-electrode array (MEA) as our primary high-throughput phenotyping assay, followed by patch clamp recordings. Our most compelling new results revealed a consistent spontaneous network hyperactivity in neurons deficient for CNTN5 or EHMT2. Our biobank of iPSC-derived neurons and accompanying genomic data are available to accelerate ASD research.

The upper and middle Eden valley is an example of a region in which agriculture is the major economic activity. Although sparsely populated, regions such as this are of fundamental importance in the economy of the country as a whole. This study was undertaken in order to assess the importance of geographical factors in the evolution and present characteristics of the economy and pattern of settlement. In part I and examination is made of the relief and drainage, climate and soils. The region is a distinctive physical region, having clearly defined upland areas as its boundaries. Following the discussion of the relief and drainage in the region as a whole, a more detailed study is made of the four physical regions. Because the region is a lowland flanked by uplands, there are differences in climatic conditions. Temperatures are most extreme in the lowlands. The incidence and duration of rainfall and snowfall increase rapidly with altitude. In addition, the higher areas suffer from exposure to the wind and look of sunshine. Although a comprehensive survey of soils, based on a study of soil profiles, has not been carried out in the area, information is available on soil texture and this is discussed in Chapter 3. In part II an assessment is made of the influence of these physical factors on the economy and pattern of settlement. The natural resources of the region are limited and farming has always been the major activity. In accordance with the contrasts in the physical environment, farming varies considerably within the region. After discussing the general characteristics of farming, the region is divided into three agricultural regions and to illustrate these, eight specimen farms are analysed in detail. Mining quarrying are of some importance in the region and the economy is further diversified by the processing of the raw materials. The pattern of settlement has evolved to serve the needs of this predominantly agricultural area. Detailed fieldwork was carried out in order to asses the functions of the elements in the modern pattern. Because so much of the area is above 750 feet and because the region is bounded by uplands, communications within, and into other regions, are limited. At the present time road transport plays a much more significant role in the economy than railways. The planned extension to the M6 passes through the western part of the area. In Chapter 6 the population trends since 1851 are first discussed. The most significant point to emerge is that there has been overall decline in population of 20%. Following the analysis of the distribution of population, is a study of population structure. This latter study reveals that most of the people leaving the area are in the vital age groups of 15 - 39.The greatest problem in the upper and middle 2den valley is depopulation. In order to alleviate this, the area's first need is more processing industries. One asset the area possesses is that the cost of building land is lower than in many areas of the country. Secondly, the planned extension to the N6 will give the region more efficient links with the rest of the country. The Motorway could help the upper and middle Eden valley to achieve a more balanced economy and thus, a more stable population.

Previous articleNext article No AccessBook ReviewsRookwood and the Industry of Art: Women, Culture, and Commerce, 1880-1913. Nancy E. Owen Jennifer HoweJennifer Howe Search for more articles by this author PDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by Volume 10, Number 2SPRING-SUMMER 2003 Article DOIhttps://doi.org/10.1086/studdecoarts.10.2.40663052 Views: 2Total views on this site Journal History This article was published in Studies in the Decorative Arts (1993-2009), which is continued by West 86th (2011-present). Copyright 2003 The Bard Graduate Center for Studies in the Decorative Arts, Design, and CulturePDF download Crossref reports no articles citing this article.

Abstract Autism Spectrum Disorder (ASD) is genetically complex, but specific copy number variants (CNVs; e.g., 1q21.1, 16p11.2) and genes (e.g., NRXN1, NLGN4 ) have been identified as penetrant susceptibility factors, and all of these demonstrate pleiotropy. Many ASD-associated CNVs are, in fact, genomic disorder loci where flanking segmental duplications lead to recurrent deletion and duplication events of the same region in unrelated individuals, but these lesions are large and involve multiple genes. To identify opportunities to establish a more specific genotype and phenotype correlation in ASD, we searched genomic data, and the literature, for recurrent predicted damaging sequence-level variants affecting single genes. We identified 17 individuals from 15 unrelated families carrying a heterozygous guanine duplication (rs797044936; NM_033517.1; c.3679dup; p.Ala1227Glyfs*69) occurring within a string of 8 guanines (at genomic location [hg38]g.50,721,512dup) affecting SHANK3 , a prototypical ASD gene (6/7,521 or 0.08% of ASD-affected individuals studied by whole genome sequencing carried the p.Ala1227Glyfs*69 variant). This variant, which is predicted to cause a frameshift leading to a premature stop codon truncating the C-terminal region of the corresponding protein, was not reproducibly found in any of the control groups we analyzed. All probands identified carried de novo mutations with the exception of five individuals in three families who inherited it through somatic mosaicism. This same heterozygous variant in published mouse models leads to an ASD-like phenotype. We scrutinized the phenotype of p.Ala1227Glyfs*69 carriers, and while everyone (16/16) formally tested for ASD carried a diagnosis, there was variable expression of core ASD features both within families and between families, underscoring the impact of as yet unknown modifiable factors affecting expressivity in autism.

Abstract 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 categorized 325 Canadian children with ASD into dysmorphic and nondysmorphic subgroups. We developed 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 had a significantly higher GRVS compared to those with nondysmorphic ASD ( P = 0.027). Using the polygenic transmission disequilibrium test, we observed an over-transmission of ASD-associated common variants in nondysmorphic ASD probands ( P = 2.9×10 −3 ). These findings replicated 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.

Abstract Background In recent years, several hundred autism spectrum disorder (ASD) implicated genes have been discovered impacting a wide range of molecular pathways. However, the molecular underpinning of ASD, particularly from the point of view of ‘brain to behaviour’ pathogenic mechanisms, remains largely unknown. Methods We undertook a study to investigate patterns of spatiotemporal and cell type expression of ASD-implicated genes by integrating large-scale brain single cell transcriptomes (&gt; million cells) and de novo loss of function (LOF) ASD mutations (impacting 852 genes from 40122 cases). Results We identified multiple single cell clusters from three distinct developmental human brain regions (anterior cingulate cortex, middle temporal gyrus and primary visual cortex) that evidenced high evolutionary constraint through enrichment for brain critical exons and high PLi genes. These clusters also showed significant enrichment with ASD loss of function mutation genes (p &lt; 5.23 x 10 − 11 ) that are transcriptionally highly active in prenatal brain regions (visual cortex and dorsolateral prefrontal cortex). Mapping ASD de novo LOF mutated genes into large scale human and mouse brain single cell transcriptome analysis demonstrate enrichment of such genes into neuronal subtypes and are also enriched for subtype of non-neuronal glial cell types (astrocyte, p &lt; 6.40 x 10 − 11 ; oligodendrocyte, p &lt; 1.31 x 10 − 09 ). Conclusion Among the ASD genes enriched with pathogenic de novo LOF mutations (i.e., KANK1, PLXNB1), a subgroup has restricted transcriptional regulation in non-neuronal cell types that are evolutionarily conserved. This association strongly suggests the involvement of subtype of non-neuronal glial cells in the pathogenesis of ASD, and the need to explore other biological pathways for this disorder.

Additional file 2. Supplementary Tables - 1, 2, 3, 5, 6.

Additional file 4. Supplementary Tables - 7, 8, 9, 11, 12.

Additional file 6. Supplementary Table - 16.

Additional file 5. Supplementary Table - 15.