Functional impact of global rare copy number variation in autism spectrum 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 behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), 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 x 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.

Mapping autism risk loci using genetic linkage and chromosomal rearrangements.

Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,181 [corrected] families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.

Individual common variants exert weak effects on the risk for autism spectrum disorders.

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 genome-wide scan for common alleles affecting risk for autism.

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.

A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder.

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.

Etiologies of autism in a case-series from Tanzania.

Most autism has a genetic cause although post-encephalitis cases are reported. In a case-series (N = 20) from Tanzania, 14 met research criteria for autism. Three (M:F = 1:2) had normal development to age 22, 35, and 42 months, with onset of autism upon recovery from severe malaria, attended by prolonged high fever, convulsions, and in one case prolonged loss of consciousness. In four other cases (M:F = 3:1), the temporal relationship between onset of autism and severe infection was close, but possibly spurious since malaria is common in Tanzania and there were indications of abnormal development in the child or a family member. In seven cases, (M:F = 6:1) autism onset was unrelated to malaria. The excess of non-verbal cases (N = 10) is related local diagnostic practice.

Comorbid psychiatric disorders in children with autism: interview development and rates of disorders.

The Kiddie Schedule for Affective Disorders and Schizophrenia was modified for use in children and adolescents with autism by developing additional screening questions and coding options that reflect the presentation of psychiatric disorders in autism spectrum disorders. The modified instrument, the Autism Comorbidity Interview-Present and Lifetime Version (ACI-PL), was piloted and frequently diagnosed disorders, depression, ADHD, and OCD, were tested for reliability and validity. The ACI-PL provides reliable DSM diagnoses that are valid based on clinical psychiatric diagnosis and treatment history. The sample demonstrated a high prevalence of specific phobia, obsessive compulsive disorder, and ADHD. The rates of psychiatric disorder in autism are high and are associated with functional impairment.

Genome-wide and Ordered-Subset linkage analyses provide support for autism loci on 17q and 19p with evidence of phenotypic and interlocus genetic correlates.

BACKGROUND: Autism is a neurobehavioral spectrum of phenotypes characterized by deficits in the development of language and social relationships and patterns of repetitive, rigid and compulsive behaviors. Twin and family studies point to a significant genetic etiology, and several groups have performed genomic linkage screens to identify susceptibility loci. METHODS: We performed a genome-wide linkage screen in 158 combined Tufts, Vanderbilt and AGRE (Autism Genetics Research Exchange) multiplex autism families using parametric and nonparametric methods with a categorical autism diagnosis to identify loci of main effect. Hypothesizing interdependence of genetic risk factors prompted us to perform exploratory studies applying the Ordered-Subset Analysis (OSA) approach using LOD scores as the trait covariate for ranking families. We employed OSA to test for interlocus correlations between loci with LOD scores > or =1.5, and empirically determined significance of linkage in optimal OSA subsets using permutation testing. Exploring phenotypic correlates as the basis for linkage increases involved comparison of mean scores for quantitative trait-based subsets of autism between optimal subsets and the remaining families. RESULTS: A genome-wide screen for autism loci identified the best evidence for linkage to 17q11.2 and 19p13, with maximum multipoint heterogeneity LOD scores of 2.9 and 2.6, respectively. Suggestive linkage (LOD scores > or =1.5) at other loci included 3p, 6q, 7q, 12p, and 16p. OSA revealed positive correlations of linkage between the 19p locus and 17q, between 19p and 6q, and between 7q and 5p. While potential phenotypic correlates for these findings were not identified for the chromosome 7/5 combination, differences indicating more rapid achievement of "developmental milestones" was apparent in the chromosome 19 OSA-defined subsets for 17q and 6q. OSA was used to test the hypothesis that 19p linkage involved more rapid achievement of these milestones and it revealed significantly increased LOD* scores at 19p13. CONCLUSIONS: Our results further support 19p13 as harboring an autism susceptibility locus, confirm other linkage findings at 17q11.2, and demonstrate the need to analyze more discreet trait-based subsets of complex phenotypes to improve ability to detect genetic effects.

Diagnostic reliability of bipolar II disorder.

BACKGROUND: Although the diagnostic reliability of major depression and mania has been well established, that of hypomania and bipolar II (BPII) disorder has not. This remains an important issue for clinicians, especially for those undertaking genetic studies of BP disorder since bipolar I (BPI) and BPII disorders often cluster in the same families. We have assessed our diagnostic reliability of BP disorders, recurrent unipolar disorder, and their constituent episodes (major depression, mania, and hypomania) using interview and best-estimate diagnostic procedures used in a genetic study of families with BPI disorder. METHODS: Reliability was assessed for (1) co-rated Schedule for Affective Disorders and Schizophrenia-Lifetime version interviews of 37 subjects including 15 with BP disorders; (2) test-retest Schedule for Affective Disorders and Schizophrenia-Lifetime version interviews of 26 subjects including 13 with BP disorders; and (3) best-estimate diagnoses made by 2 noninterviewing psychiatrists on 524 subjects in a genetic linkage study of BPI disorder. Diagnoses were based on Research Diagnostic Criteria for a Selected Group of Functional Disorders, except that recurrent major depression as well as hypomania was required for a diagnosis of BPII disorder. RESULTS: On co-rated interviews, we observed complete agreement between interviewers for diagnosing major depressive, manic, and hypomanic episodes. For test-retest interviews, the Cohen kappa coefficients were 0.83 for manic, 0.72 for hypomanic, and 1.0 for major depressive episodes. At the best-estimate level, the Cohen kappa coefficients were 0.99 for BPI, 0.99 for BPII, and 0.98 for recurrent unipolar disorder. CONCLUSION: Good interrater reliability for BPII can be achieved when the interviews and best-estimate diagnoses are done by experienced psychiatrists.

Examination of NRCAM, LRRN3, KIAA0716, and LAMB1 as autism candidate genes.

BACKGROUND: A substantial body of research supports a genetic involvement in autism. Furthermore, results from various genomic screens implicate a region on chromosome 7q31 as harboring an autism susceptibility variant. We previously narrowed this 34 cM region to a 3 cM critical region (located between D7S496 and D7S2418) using the Collaborative Linkage Study of Autism (CLSA) chromosome 7 linked families. This interval encompasses about 4.5 Mb of genomic DNA and encodes over fifty known and predicted genes. Four candidate genes (NRCAM, LRRN3, KIAA0716, and LAMB1) in this region were chosen for examination based on their proximity to the marker most consistently cosegregating with autism in these families (D7S1817), their tissue expression patterns, and likely biological relevance to autism. METHODS: Thirty-six intronic and exonic single nucleotide polymorphisms (SNPs) and one microsatellite marker within and around these four candidate genes were genotyped in 30 chromosome 7q31 linked families. Multiple SNPs were used to provide as complete coverage as possible since linkage disequilibrium can vary dramatically across even very short distances within a gene. Analyses of these data used the Pedigree Disequilibrium Test for single markers and a multilocus likelihood ratio test. RESULTS: As expected, linkage disequilibrium occurred within each of these genes but we did not observe significant LD across genes. None of the polymorphisms in NRCAM, LRRN3, or KIAA0716 gave p < 0.05 suggesting that none of these genes is associated with autism susceptibility in this subset of chromosome 7-linked families. However, with LAMB1, the allelic association analysis revealed suggestive evidence for a positive association, including one individual SNP (p = 0.02) and three separate two-SNP haplotypes across the gene (p = 0.007, 0.012, and 0.012). CONCLUSIONS: NRCAM, LRRN3, KIAA0716 are unlikely to be involved in autism. There is some evidence that variation in or near the LAMB1 gene may be involved in autism.

Evaluation of FOXP2 as an autism susceptibility gene.

A mutation in the gene FOXP2 was recently identified as being responsible for a complicated speech and language phenotype in a single large extended pedigree. This gene is of interest to autism because it lies in one of the most consistently linked autism chromosomal regions of interest. We therefore tested this gene for its involvement in autism in a large sample of autism families. We completely sequenced the exon containing the mutation, screened the remaining coding sequence using SSCP technology, and identified and genotyped two novel intronic tetranucleotide repeat polymorphisms that were then analyzed for evidence of linkage and linkage disequilibrium (LD). We identified two families in which heterozygous deletions of a small number of glutamines in a long poly-glutamine stretch were found in one parent and the autistic probands; no other non-conservative coding sequence changes were identified. Linkage and LD analyses were performed in 75 affected sibling pair families and in two subgroups of this sample defined by the presence/absence of severe language impairment. One allele appeared to have an opposite pattern of transmission in the language based subgroups, but otherwise the linkage and LD analyses were negative. We conclude that FOXP2 is unlikely to contribute significantly to autism susceptibility.

How might genetic mechanisms operate in autism?

Twin and family studies provide strong evidence that autism has a largely genetic aetiology. The pattern of familial aggregation suggests that in individual families, a small number of genes act together to cause the phenotype. However, it is unlikely that the same genes act in all families. Thus, the total number of genes involved could be large. One key to finding genes for disorders with considerable locus heterogeneity is to detect genetically more homogeneous subsamples. There exist several traits in families who have a child with autism--biochemical, physical, or behavioural--that are likely to reflect underlying genetic heterogeneity and can thus be used to divide families into more homogeneous subsets. These traits (1) show variation in autism samples; (2) are found in non-autistic family members more often than controls; (3) aggregate in particular autism families; and (4) result in increased signals when used in linkage analysis to define 'affected'.

Exploratory subsetting of autism families based on savant skills improves evidence of genetic linkage to 15q11-q13.

OBJECTIVE: Autism displays a remarkably high heritability but a complex genetic etiology. One approach to identifying susceptibility loci under these conditions is to define more homogeneous subsets of families on the basis of genetically relevant phenotypic or biological characteristics that vary from case to case. METHOD: The authors performed a principal components analysis, using items from the Autism Diagnostic Interview, which resulted in six clusters of variables, five of which showed significant sib-sib correlation. The utility of these phenotypic subsets was tested in an exploratory genetic analysis of the autism candidate region on chromosome 15q11-q13. RESULTS: When the Collaborative Linkage Study of Autism sample was divided, on the basis of mean proband score for the "savant skills" cluster, the heterogeneity logarithm of the odds under a recessive model at D15S511, within the GABRB3 gene, increased from 0.6 to 2.6 in the subset of families in which probands had greater savant skills. CONCLUSIONS: These data are consistent with the genetic contribution of a 15q locus to autism susceptibility in a subset of affected individuals exhibiting savant skills. Similar types of skills have been noted in individuals with Prader-Willi syndrome, which results from deletions of this chromosomal region.

A principal components analysis of the Autism Diagnostic Interview-Revised.

OBJECTIVE: To develop factors based on the Autism Diagnostic Interview-Revised (ADI-R) that index separate components of the autism phenotype that are genetically relevant and validated against standard measures of the constructs. METHOD: ADIs and ADI-Rs of 292 individuals with autism were subjected to a principal components analysis using VARCLUS. The resulting variable clusters were validated against standard measures. RESULTS: Six clusters of variables emerged: spoken language, social intent, compulsions, developmental milestones, savant skills and sensory aversions. Five of the factors were significantly correlated with the validating measures and had good internal consistency, face validity, and discriminant and construct validity. Most intraclass correlations between siblings were adequate for use in genetic studies. CONCLUSION: The ADI-R contains correlated clusters of variables that are valid, genetically relevant, and that can be used in a variety of studies.

Autism-related language, personality, and cognition in people with absolute pitch: results of a preliminary study.

Reports of a relatively high prevalence of absolute pitch (AP) in autistic disorder suggest that AP is associated with some of the distinctive cognitive and social characteristics seen in autism spectrum disorders. Accordingly we examined cognition, personality, social behavior, and language in 13 musicians with strictly defined AP (APS) and 33 musician controls (MC) without AP using standardized interviews and tests previously applied to identify the broad autism phenotype seen in the relatives of autistic probands. These included the Pragmatic Rating Scale (PRS) (social aspects of language) the Personality Assessment Schedule (PAS) (rigidity, aloofness, anxiety/worry, hypersensitivity), and WAIS performance subtests (PIQ). On the basis of their behavior in the interviews, subjects were classified as socially eccentric, somewhat eccentric, or not eccentric. Forty-six percent of the APS, but only 15% of the MC, were classified as socially eccentric (p < .03). APS but not MC showed higher scores on block design than on the other PIQ tests (p < .06), a PIQ pattern seen in autism spectrum disorders. Although APS and MC did not differ significantly on other measures it is of note that APS mean scores on the PRS and PAS (5.69, 4.92) were almost twice as high as those for the MC (3.03, 2.45). Thus, musicians with AP show some of the personality, language, and cognitive features associated with autism. Piecemeal information processing, of which AP is an extreme and rare example, is characteristic of autism and may be associated as well with subclinical variants in language and behavior. We speculate that the gene or genes that underlie AP may be among the genes that contribute to autism.

Language and reading abilities of children with autism spectrum disorders and specific language impairment and their first-degree relatives.

Autism spectrum disorder (ASD) and specific language impairment (SLI) are developmental disorders exhibiting language deficits, but it is unclear whether they arise from similar etiologies. Language impairments have been described in family members of children with ASD and SLI, but few studies have quantified them. In this study, we examined IQ, language, and reading abilities of ASD and SLI children and their first-degree relatives to address whether the language difficulties observed in some children with ASD are familial and to better understand the degree of overlap between these disorders and their broader phenotypes. Participants were 52 autistic children, 36 children with SLI, their siblings, and their parents. The ASD group was divided into those with (ALI, n=32) and without (ALN, n=20) language impairment. Relationships between ASD severity and language performance were also examined in the ASD probands. ALI and SLI probands performed similarly on most measures while ALN probands scored higher. ALN and ALI probands' language scores were not related to Autism Diagnostic Interview-Revised and Autism Diagnostic Observation Schedule algorithm scores. SLI relatives scored lowest on all measures, and while scores were not in the impaired range, relatives of ALI children scored lower than relatives of ALN children on some measures, though not those showing highest heritability in SLI. Given that ALI relatives performed better than SLI relatives across the language measures, the hypothesis that ALI and SLI families share similar genetic loading for language is not strongly supported.

Overrepresentation of mood and anxiety disorders in adults with autism and their first-degree relatives: what does it mean?

Research indicates that relatives of individuals with autism have higher rates of affective disorders than both the general population and families of children with other developmental disabilities. In addition, individuals with autism have high rates of co-morbid mood and anxiety disorders. This study sought to identify possible reasons for these previous findings by documenting the presence of affective disorders in both probands (the individuals with autism) and their family members. A sub-sample of 17 adults with autism and their first-degree relatives from the Baltimore Family Study of Autism completed a structured psychiatric interview. The results indicated that the rates of mood and anxiety disorders were 35 and 77%, respectively, for probands, and these disorders were present in at least one first-degree relative at rates of 71 and 29%, respectively. Exploring patterns within families revealed that 80% of probands with a mother who had a mood disorder history also had a mood disorder themselves, compared to only 16% of probands whose mothers did not have a mood disorder history. The results must be considered preliminary given the small sample size. Replicating these findings in a larger sample would help clarify whether a true increased risk of mood disorder exists, which would have potential implications for prevention efforts and understanding possible genetic mechanisms.

Overlap between autism and specific language impairment: comparison of Autism Diagnostic Interview and Autism Diagnostic Observation Schedule scores.

Autism and specific language impairment (SLI) are developmental disorders that, although distinct by definition, have in common some features of both language and social behavior. The goal of this study was to further explore the extent to which specific clinical features of autism are seen in SLI. The children with the two disorders, matched for non-verbal IQ, were compared on the Autism Diagnostic Interview-Revised (ADI-R) and the Autism Diagnostic Observation Schedule (ADOS). In the SLI group, 41% met autism or autism spectrum cut-offs for social or communication domains either on the ADI or ADOS or both. No relationship was found between the language deficits exhibited by the children with SLI and their scores on the ADI and ADOS. These findings contribute to evidence that there is some overlap in social and communicative deficits between autism and SLI, supporting the view that autism and SLI share etiologic factors. This continuum of pathology between SLI and autism appears to range from structural language abnormalities as seen in individuals with SLI to individuals with SLI with both structural and social abnormalities to individuals with autism with pragmatic impairment and language abnormalities.

Allelic heterogeneity at the serotonin transporter locus (SLC6A4) confers susceptibility to autism and rigid-compulsive behaviors.

Autism is a spectrum of neurodevelopmental disorders with a primarily genetic etiology exhibiting deficits in (1) development of language and (2) social relationships and (3) patterns of repetitive, restricted behaviors or interests and resistance to change. Elevated platelet serotonin (5-HT) in 20%-25% of cases and efficacy of selective 5-HT reuptake inhibitors (SSRIs) in treating anxiety, depression, and repetitive behaviors points to the 5-HT transporter (5-HTT; SERT) as a strong candidate gene. Association studies involving the functional insertion/deletion polymorphism in the promoter (5-HTTLPR) and a polymorphism in intron 2 are inconclusive, possibly because of phenotypic heterogeneity. Nonetheless, mounting evidence for genetic linkage of autism to the chromosome 17q11.2 region that harbors the SERT locus (SLC6A4) supports a genetic effect at or near this gene. We confirm recent reports of sex-biased genetic effects in 17q by showing highly significant linkage driven by families with only affected males. Association with common alleles fails to explain observed linkage; therefore, we hypothesized that preferential transmission of multiple alleles does explain it. From 120 families, most contributing to linkage at 17q11.2, we found four coding substitutions at highly conserved positions and 15 other variants in 5' noncoding and other intronic regions transmitted in families exhibiting increased rigid-compulsive behaviors. In the aggregate, these variants show significant linkage to and association with autism. Our data provide strong support for a collection of multiple, often rare, alleles at SLC6A4 as imposing risk of autism.

A linkage disequilibrium map of the 1-Mb 15q12 GABA(A) receptor subunit cluster and association to autism.

Autism is a complex genetic neuropsychiatric condition characterized by deficits in social interaction and language and patterns of repetitive or stereotyped behaviors and restricted interests. Chromosome 15q11.2-q13 is a candidate region for autism susceptibility based on observations of chromosomal duplications in a small percentage of affected individuals and findings of linkage and association. We performed linkage disequilibrium (LD) mapping across a 1-Mb interval containing a cluster of GABA(A) receptor subunit genes (GABRB3, GABRA5, and GABRG3) which are good positional and functional candidates. Intermarker LD was measured for 59 single nucleotide polymorphism (SNP) markers spanning this region, corresponding to an average marker spacing of 17.7 kb(-1). We identified haplotype blocks, and characterized these blocks for common (>5%) haplotypes present in the study population. At this marker resolution, haplotype blocks comprise <50% of the DNA in this region, consistent with a high local recombination rate. Identification of haplotype tag SNPs reduces the overall number of markers necessary to detect all common alleles by only 12%. Individual SNPs and multi-SNP haplotypes were examined for evidence of allelic association to autism, using a dataset of 123 multiplex autism families. Six markers individually, across GABRB3 and GABRA5, and several haplotypes inclusive of those markers, demonstrated nominally significant association. These results are positively correlated with the position of observed linkage. These studies support the existence of one or more autism risk alleles in the GABA(A) receptor subunit cluster on 15q12 and have implications for analysis of LD and association in regions with high local recombination.