Search

A fundamental question in the biology of sex differences has eluded direct study in humans: How does sex-chromosome dosage (SCD) shape genome function? To address this, we developed a systematic map of SCD effects on gene function by analyzing genome-wide expression data in humans with diverse sex-chromosome aneuploidies (XO, XXX, XXY, XYY, and XXYY). For sex chromosomes, we demonstrate a pattern of obligate dosage sensitivity among evolutionarily preserved X-Y homologs and update prevailing theoretical models for SCD compensation by detecting X-linked genes that increase expression with decreasing X- and/or Y-chromosome dosage. We further show that SCD-sensitive sex-chromosome genes regulate specific coexpression networks of SCD-sensitive autosomal genes with critical cellular functions and a demonstrable potential to mediate previously documented SCD effects on disease. These gene coexpression results converge with analysis of transcription factor binding site enrichment and measures of gene expression in murine knockout models to spotlight the dosage-sensitive X-linked transcription factor ZFX as a key mediator of SCD effects on wider genome expression. Our findings characterize the effects of SCD broadly across the genome, with potential implications for human phenotypic variation.

Children affected by Specific Language Impairment (SLI) fail to acquire age appropriate language skills despite adequate intelligence and opportunity. SLI is highly heritable, but the understanding of underlying genetic mechanisms has proved challenging. In this study, we use molecular genetic techniques to investigate an admixed isolated founder population from the Robinson Crusoe Island (Chile), who are affected by a high incidence of SLI, increasing the power to discover contributory genetic factors. We utilize exome sequencing in selected individuals from this population to identify eight coding variants that are of putative significance. We then apply association analyses across the wider population to highlight a single rare coding variant (rs144169475, Minor Allele Frequency of 4.1% in admixed South American populations) in the NFXL1 gene that confers a nonsynonymous change (N150K) and is significantly associated with language impairment in the Robinson Crusoe population (p = 2.04 × 10-4, 8 variants tested). Subsequent sequencing of NFXL1 in 117 UK SLI cases identified four individuals with heterozygous variants predicted to be of functional consequence. We conclude that coding variants within NFXL1 confer an increased risk of SLI within a complex genetic model.

Altered power of resting-state neurophysiological activity has been associated with autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD), which commonly co-occur. We compared resting-state neurophysiological power in children with ASD, ADHD, co-occurring ASD + ADHD, and typically developing controls. Children with ASD (ASD/ASD + ADHD) showed reduced theta and alpha power compared to children without ASD (controls/ADHD). Children with ADHD (ADHD/ASD + ADHD) displayed decreased delta power compared to children without ADHD (ASD/controls). Children with ASD + ADHD largely presented as an additive co-occurrence with deficits of both disorders, although reduced theta compared to ADHD-only and reduced delta compared to controls suggested some unique markers. Identifying specific neurophysiological profiles in ASD and ADHD may assist in characterising more homogeneous subgroups to inform treatment approaches and aetiological investigations.

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.

Aim: To characterize early changes in developmental ability, language, and adaptive behaviour in infants diagnosed with tuberous sclerosis complex (TSC), and determine whether clinical features of epilepsy influence this pathway. Method: Prospective, longitudinal data were collected within the Early Development in Tuberous Sclerosis (EDiTS) Study to track development of infants with TSC (n = 32) and typically developing infants (n = 33) between 3 and 24 months of age. Questionnaire and observational measures were used at up to seven timepoints to assess infants' adaptive behaviour, developmental ability, language, and epilepsy. Results: A significant group by age interaction effect showed that infants with TSC had lower adaptive functioning at 18 to 24 months old (intercept = 88.12, slope estimate = −0.82, p < 0.001) and lower developmental ability scores from 10 months old (intercept = 83.33, slope estimate = −1.44, p < 0.001) compared to typically developing infants. Early epilepsy severity was a significant predictor of these emerging developmental (R2 = 0.35, p = 0.004, 95% confidence interval [CI] –0.08 to −0.01) and adaptive behaviour delays (R2 = 0.34, p = 0.004, 95% CI –0.05 to −0.01]). Lower vocabulary production (intercept = −1.25, slope = −0.12, p < 0.001) and comprehension scores (intercept = 2.39, slope estimate = −0.05, p < 0.001) in infants with TSC at 24 months old were not associated with epilepsy severity. Interpretation: Divergence of developmental ability and adaptive functioning skills occur in infants with TSC from 10 and 18 months, respectively. Associations between early epilepsy severity and impaired development supports the importance of early intervention to reduce seizure severity. This original article is commented on by Jóźwiak on pages 556–557 of this issue. [ABSTRACT FROM AUTHOR]

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.

Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.

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.

Objective: To chart the emergence of precursors and early signs of autism spectrum disorder (ASD) and autistic traits in the Avon Longitudinal Study of Parents and Children, a prospective longitudinal cohort study of the surviving offspring of 14,541 pregnant women from southwestern England with an expected delivery date between April 1991 and December 1992. Method: Parents' contemporaneous reports of their infant's development (241 questionnaire responses collected up to 30 months of age) were examined in relation to the diagnosis of autism spectrum disorder by age 11 years (n = 86) and a measure of autistic traits, derived by factor analysis. Results: Among the children later diagnosed with ASD, concerns about vision and hearing were more often reported in the first year, and differences in social, communication, and fine motor skills were evident from 6 months of age. Repetitive behaviors and differences in play, imitation, and feeding habits were reported in the second year. Differences in temperament emerged at 24 months of age and bowel habit by 30 months. All of these early signs were strongly associated with the presence of autistic traits in the rest of the population and these differences were often evident in the first year of development. Over the first 30 months of development, the best predictors of both later ASD and autistic traits included the Social Achievement and Communication scores from the Denver Developmental Screening Test, measures of communicative skills (Vocabulary and Combines Words) from the MacArthur Infant Communicative Development Inventories, and a repetitive behavior score. Conclusions: Precursors, early signs, and other developmental differences were reported in the first year of development among children from the general population who later developed autism spectrum disorder and subtler autistic traits. Other differences emerged and unfolded as development progressed. The findings confirm the long-held suspicion that early differences underscore the multifaceted nature of autism spectrum disorder and the broader autism phenotype, and highlight the centrality of impairments in social communication skills. (Contains 16 tables.)

The Childhood Autism Spectrum Test (CAST) (formally known as the Childhood Asperger Screening Test) identifies autism spectrum conditions by measuring social and communication skills. The present study explored the sex distribution of scores. The CAST was distributed to 11,635 children aged 4-9 years in Cambridgeshire primary schools (UK). 3,370 (29%) were returned. The median score was significantly higher in boys (median test, P less than 0.001) (Boys, median = 5 (IQR: 3,8); girls, median = 4 (IQR: 2,6)). There was a predominance of boys (n = 81 (79.4%) over girls (n = 21 (20.6%)) amongst those scoring greater than or equal to 15. Exclusion of children with ASC did not significantly affect the results. We conclude that different profiles of social and communication skills in boys and girls must be taken into account when measuring these skills in the general population.

Background: Impairments in language and communication are core features of autism spectrum disorders (ASDs). The basis for this association is poorly understood. How early language is related to each of the triad of impairments characteristic of ASDs is also in need of clarification. Aims: This is the first study that aims to determine the extent to which shared genetic and environmental factors underlie the association between early language performance and autistic-like traits (ALTs) in middle childhood. Methods & Procedures: Data came from a population-based twin sample (n = 6087 pairs) assessed prospectively at 2, 3, 4 and 8 years. ALTs measured by the Childhood Asperger Syndrome Test (CAST) at 8 years were investigated in relation to language assessed by the MacArthur Communicative Development Inventory (CDI) at 2, 3 and 4 years. Multivariate model fitting techniques were used to analyse the origins of this association. Outcomes & Results: Total CAST scores, as well as Social and Communication subscales, at 8 years were weakly but significantly negatively correlated with language ability at 2, 3 and 4 years. Correlations between language and restrictive and repetitive behaviours and interests (RRBI) were not significant. The phenotypic correlations between language and Social and Communication ALTs were almost entirely mediated by shared genetic influences. There were specific genetic influences on early language that were not shared with ALTs, and specific genetic influences on ALTs not shared with earlier language performance. Conclusions: This is the first study to demonstrate shared genetic influences in relation to language performance as an early antecedent of later ALTs. These results support the idea that the triad of core features in ALTs are aetiologically heterogeneous, with early language relating to social and communication impairments but not RRBIs. (Contains 4 figures and 5 tables.)

Background: Studies of chromosome 15 abnormality have implicated over-expression of paternally imprinted genes in the 15q11-13 region in the aetiology of autism. To test this hypothesis we compared individuals with Prader-Willi syndrome (PWS) due to uniparental disomy (UPD--where paternally imprinted genes are over-expressed) to individuals with the 15q11-13 deletion form of the syndrome (where paternally imprinted genes are not over-expressed). We also tested reports that PWS cases due to the larger type I (TI) form of deletion show differences to cases with the smaller type II (TII) deletion. Method: Ninety-six individuals with PWS were recruited from genetic centres and the PWS association. Forty-nine individuals were confirmed as having maternal UPD of chromosome 15 and were age and sex matched to 47 individuals with a deletion involving 15q11-13 (32 had the shorter (T II) deletion, and 14 had the longer (TI) deletion). Behavioural assessments were carried out blind to genetic status, using the Autism Diagnostic Observation Schedule (ADOS), the Autism Diagnostic Interview (ADI), the Autism Screening Questionnaire (ASQ), the Children's Yale-Brown Obsessive-Compulsive Scale (CY-BOCS), the Vineland Adaptive Behaviour Scales (VABS), and measurements of intellectual ability, including the Wechsler and Mullen Scales and Raven's Matrices. Results: UPD cases exhibited significantly more autistic-like impairments in reciprocal social interaction on questionnaire, interview and standardised observational measures. Comparison of TI and TII deletion cases revealed few differences, but ability levels tended to be lower in the TI deletion cases. Conclusions: Findings from a large study comparing deletion and UPD forms of Prader-Willi syndrome were consistent with other evidence in indicating that paternally imprinted genes in the 15q11-13 region constitute a genetic risk factor for aspects of autistic symptomatology. These genes may therefore play a role in the aetiology of autism. By contrast with another report, there was no clear-cut relationship between the size of the deletion and the form of cognitive and behavioural phenotype.

The Prader-Willi/Angelman Critical Region (PWACR; Chromosome 15q11-13) is of interest as a potential locus for genes conferring susceptibility to autism spectrum disorders (ASD). This report describes a female proband referred for evaluation of a possible ASD. Genetic analyses indicated that the proband, her father and one of her sisters, carried a paternally derived interstitial duplication involving 15q11-13. The proband showed evidence of ASD (PDD-NOS), borderline mental retardation, mild hypotonia and joint laxity. Her father and her sister were of normal intelligence and neither was thought to have an ASD, although speech/language difficulties and some autistic type behaviours were reported to have been present early in the development of the sister. This is one of the first reports of a child with a paternal duplication and an autism spectrum disorder. More research is required to determine whether paternally derived duplications that involve 15q11-13 are associated with developmental impairments.

Tuberous sclerosis is a genetic condition that is strongly associated with the development of an autism spectrum disorder. However, there is marked variability in expression, and only a subset of children with tuberous sclerosis develop autism spectrum disorder. Clarification of the mechanisms that underlie the association and variability in expression will potentially throw light on the biological processes involved in the etiology of idiopathic forms of autism spectrum disorder. Current evidence indicates that the likelihood of a child with tuberous sclerosis developing an autism spectrum disorder is greater if the child has a mutation in the TSC2 gene, although autism can and does develop in children with TSC1 mutations. The likelihood is also greater if the child has early-onset infantile spasms that are difficult to control, especially if there is an epileptiform focus in the temporal lobes. The emerging evidence is consistent with the notion that early onset electrophysiological disturbances within the temporal lobes (and perhaps other locations) has a deleterious effect on the development and establishment of key social cognitive representations concerned with processing social information, perhaps especially from faces. However, alternative mechanisms to account for the findings cannot yet be ruled out. Future research will have to employ prospective longitudinal designs and treatment trials to clarify the processes involved. (Contains 3 tables and 2 figures.)

This study investigated the role of obstetric complications in determining phenotypic manifestations in tuberous sclerosis (TS), a disorder associated with autism spectrum disorders. Comparison of 43 children with TS and 40 unaffected siblings found children with TS experienced more obstetric complications, but these were related to mild rather than severe adversities including autism spectrum disorders and severe mental retardation. (Contains references.) (Author/DB)

The association between attention‐deficit/hyperactivity disorder (ADHD) and tuberous sclerosis complex (TSC) is widely reported, with support for the role of epilepsy, yet the mechanisms underlying the association across development are unclear. The Tuberous Sclerosis 2000 Study is a prospective longitudinal study of TSC. In Phase 1 of the study, baseline measures of epilepsy, cortical tuber load, and mutation were obtained with 125 children ages 0–16 years. In Phase 2, at an average of 8 years later, ADHD symptoms were measured for 81 of the participants. Structural equation modeling revealed an indirect pathway from genetic mutation, to cortical tuber load, to epileptic spasm severity in infancy, to ADHD symptoms in middle childhood and adolescence, in addition to a pathway linking current seizure severity to ADHD symptoms. Findings were retained when intelligence quotient (IQ) was entered as a correlated factor. The findings support a cascading developmental pathway to ADHD symptoms mediated by early‐onset and severe epilepsy in the first 2 years of life. This warrants detailed investigation of seizure characteristics and cognitive and behavioral sequelae associated with ADHD from early in life, to further the understanding of the association between ADHD and early‐onset epilepsy across syndromic and non‐syndromic populations. [ABSTRACT FROM AUTHOR]

Aim: To examine the association between perinatal adversities and neurodevelopmental outcome in tuberous sclerosis complex (TSC). Method: The Tuberous Sclerosis 2000 study is a prospective, longitudinal UK study of TSC. In phase 1, mutation type, TSC family history, tuber characteristics, presence of cardiac rhabdomyomas, seizure characteristics, and intellectual ability were assessed in 125 children affected with TSC (64 females, 61 males; median age 39mo, range 4–254). In phase 2, 88 participants (49 females, 39 males; median age 148mo, range 93–323) were assessed for neurodevelopmental outcomes including intellectual ability, autism spectrum disorder, and attention‐deficit/hyperactivity disorder. Perinatal histories of 88 participants with TSC and 80 unaffected siblings were collected retrospectively using the Obstetric Enquiry Schedule and coded with a modified Gillberg Optimality Scale to measure levels of perinatal adversity. Data were analysed using Mann–Whitney U tests, Spearman's rank correlation, and linear regression with robust standard errors. Results: Children with familial TSC experienced significantly greater perinatal adversity than unaffected siblings. Perinatal adversity was higher in children with TSC‐affected mothers than those with unaffected mothers. There was no significant association between perinatal adversities and neurodevelopmental outcomes after controlling for confounders. Interpretation: Maternal TSC is a significant marker of elevated perinatal risk in addition to risks incurred by fetal genotype. Pregnancies complicated by maternal or fetal TSC require higher vigilance, and mechanisms underlying increased perinatal adversity require further research. What this paper adds: Higher perinatal adversity is associated with familial tuberous sclerosis complex (TSC).Maternal TSC was associated with higher frequencies of several perinatal risk markers.Paternal TSC was not associated with higher levels of perinatal adversity.Perinatal adversity levels in TSC1 and TSC2 subgroups did not differ significantly.Perinatal adversities were not associated with neurodevelopmental outcomes. What this paper adds: Higher perinatal adversity is associated with familial tuberous sclerosis complex (TSC).Maternal TSC was associated with higher frequencies of several perinatal risk markers.Paternal TSC was not associated with higher levels of perinatal adversity.Perinatal adversity levels in TSC1 and TSC2 subgroups did not differ significantly.Perinatal adversities were not associated with neurodevelopmental outcomes. This original article is commented on by Franz on pages 1184–1185 of this issue. [ABSTRACT FROM AUTHOR]

A high-density screen of SLI1region of chromosome 16q associated with phonological short-term memory in the specific language impairment (SLI) developmental disorder is conducted to identify its causative genes. Results suggest that variants in CMIP, a gene encoding c-maf-inducing protein and ATP2C2, a gene encoding calcium-transporting ATPase, type 2C, member2 protein, located in the SLI1 region modulate phonological short-term memory in SLI.

Background: Autism Spectrum Disorder (ASD) and Attention‐Deficit/Hyperactivity Disorder (ADHD) share impairments in top‐down and bottom‐up modulation of attention. However, it is not yet well understood if co‐occurrence of ASD and ADHD reflects a distinct or additive profile of attention deficits. We aimed to characterise alpha oscillatory activity (stimulus‐locked alpha desynchronisation and prestimulus alpha) as an index of integration of top‐down and bottom‐up attentional processes in ASD and ADHD. Methods: Children with ASD, ADHD, comorbid ASD+ADHD, and typically‐developing children completed a fixed‐choice reaction‐time task ('Fast task') while neurophysiological activity was recorded. Outcome measures were derived from source‐decomposed neurophysiological data. Main measures of interest were prestimulus alpha power and alpha desynchronisation (difference between poststimulus and prestimulus alpha). Poststimulus activity linked to attention allocation (P1, P3), attentional control (N2), and cognitive control (theta synchronisation, 100–600 ms) was also examined. ANOVA was used to test differences across diagnostics groups on these measures. Spearman's correlations were used to investigate the relationship between attentional control processes (alpha oscillations), central executive functions (theta synchronisation), early visual processing (P1), and behavioural performance. Results: Children with ADHD (ADHD and ASD+ADHD) showed attenuated alpha desynchronisation, indicating poor integration of top‐down and bottom‐up attentional processes. Children with ADHD showed reduced N2 and P3 amplitudes, while children with ASD (ASD and ASD+ADHD) showed greater N2 amplitude, indicating atypical attentional control and attention allocation across ASD and ADHD. In the ASD group, prestimulus alpha and theta synchronisation were negatively correlated, and alpha desynchronisation and theta synchronisation were positively correlated, suggesting an atypical association between attentional control processes and executive functions. Conclusions: ASD and ADHD are associated with disorder‐specific impairments, while children with ASD+ADHD overall presented an additive profile with attentional deficits of both disorders. Importantly, these findings may inform the improvement of transdiagnostic procedures and optimisation of personalised intervention approaches. [ABSTRACT FROM AUTHOR]