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1.
Neuron ; 87(6): 1215-1233, 2015 Sep 23.
Article in English | MEDLINE | ID: mdl-26402605

ABSTRACT

Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex Collection (SSC) (N = 2,591 families) replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci (1q21.1, 3q29, 7q11.23, 16p11.2, 15q11.2-13, and 22q11.2). The addition of published CNV data from the Autism Genome Project (AGP) and exome sequencing data from the SSC and the Autism Sequencing Consortium (ASC) shows that genes within small de novo deletions, but not within large dnCNVs, significantly overlap the high-effect risk genes identified by sequencing. Alternatively, large dnCNVs are found likely to contain multiple modest-effect risk genes. Overall, we find strong evidence that de novo mutations are associated with ASD apart from the risk for intellectual disability. Extending the transmission and de novo association test (TADA) to include small de novo deletions reveals 71 ASD risk loci, including 6 CNV regions (noted above) and 65 risk genes (FDR ≤ 0.1).


Subject(s)
Autism Spectrum Disorder/diagnosis , Autism Spectrum Disorder/genetics , Genetic Loci/genetics , Genetic Variation/genetics , Protein Interaction Maps/genetics , Female , Humans , Male
2.
PLoS Genet ; 11(1): e1004852, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25621974

ABSTRACT

Contactins and Contactin-Associated Proteins, and Contactin-Associated Protein-Like 2 (CNTNAP2) in particular, have been widely cited as autism risk genes based on findings from homozygosity mapping, molecular cytogenetics, copy number variation analyses, and both common and rare single nucleotide association studies. However, data specifically with regard to the contribution of heterozygous single nucleotide variants (SNVs) have been inconsistent. In an effort to clarify the role of rare point mutations in CNTNAP2 and related gene families, we have conducted targeted next-generation sequencing and evaluated existing sequence data in cohorts totaling 2704 cases and 2747 controls. We find no evidence for statistically significant association of rare heterozygous mutations in any of the CNTN or CNTNAP genes, including CNTNAP2, placing marked limits on the scale of their plausible contribution to risk.


Subject(s)
Autistic Disorder/genetics , Contactins/genetics , Genetic Association Studies , Membrane Proteins/genetics , Nerve Tissue Proteins/genetics , Autistic Disorder/pathology , Codon, Nonsense , DNA Copy Number Variations , Genetic Predisposition to Disease , Humans , Point Mutation , Polymorphism, Single Nucleotide , Sequence Analysis, DNA , Sequence Deletion
3.
Biol Psychiatry ; 77(9): 775-84, 2015 May 01.
Article in English | MEDLINE | ID: mdl-25534755

ABSTRACT

BACKGROUND: Phenotypic heterogeneity in autism has long been conjectured to be a major hindrance to the discovery of genetic risk factors, leading to numerous attempts to stratify children based on phenotype to increase power of discovery studies. This approach, however, is based on the hypothesis that phenotypic heterogeneity closely maps to genetic variation, which has not been tested. Our study examines the impact of subphenotyping of a well-characterized autism spectrum disorder (ASD) sample on genetic homogeneity and the ability to discover common genetic variants conferring liability to ASD. METHODS: Genome-wide genotypic data of 2576 families from the Simons Simplex Collection were analyzed in the overall sample and phenotypic subgroups defined on the basis of diagnosis, IQ, and symptom profiles. We conducted a family-based association study, as well as estimating heritability and evaluating allele scores for each phenotypic subgroup. RESULTS: Association analyses revealed no genome-wide significant association signal. Subphenotyping did not increase power substantially. Moreover, allele scores built from the most associated single nucleotide polymorphisms, based on the odds ratio in the full sample, predicted case status in subsets of the sample equally well and heritability estimates were very similar for all subgroups. CONCLUSIONS: In genome-wide association analysis of the Simons Simplex Collection sample, reducing phenotypic heterogeneity had at most a modest impact on genetic homogeneity. Our results are based on a relatively small sample, one with greater homogeneity than the entire population; if they apply more broadly, they imply that analysis of subphenotypes is not a productive path forward for discovering genetic risk variants in ASD.


Subject(s)
Autism Spectrum Disorder/genetics , Autistic Disorder/genetics , Phenotype , Autism Spectrum Disorder/physiopathology , Autism Spectrum Disorder/psychology , Autistic Disorder/physiopathology , Autistic Disorder/psychology , Family , Female , Genetic Predisposition to Disease , Genetic Variation , Genome-Wide Association Study/methods , Humans , Male , Polymorphism, Single Nucleotide
4.
Nature ; 515(7526): 216-21, 2014 Nov 13.
Article in English | MEDLINE | ID: mdl-25363768

ABSTRACT

Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females.


Subject(s)
Child Development Disorders, Pervasive/genetics , Genetic Predisposition to Disease/genetics , Mutation/genetics , Open Reading Frames/genetics , Child , Cluster Analysis , Exome/genetics , Female , Genes , Humans , Intelligence Tests , Male , Reproducibility of Results
5.
Autism Res ; 7(3): 355-62, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24821083

ABSTRACT

The proximal region of chromosome 15 is one of the genomic hotspots for copy number variants (CNVs). Among the rearrangements observed in this region, CNVs from the interval between the common breakpoints 1 and 2 (BP1 and BP2) have been reported cosegregating with autism spectrum disorder (ASD). Although evidence supporting an association between BP1-BP2 CNVs and autism accumulates, the magnitude of the effect of BP1-BP2 CNVs remains elusive, posing a great challenge to recurrence-risk counseling. To gain further insight into their pathogenicity for ASD, we estimated the penetrance of the BP1-BP2 CNVs for ASD as well as their effects on ASD-related phenotypes in a well-characterized ASD sample (n = 2525 families). Transmission disequilibrium test revealed significant preferential transmission only for the duplicated chromosome in probands (20T:9NT). The penetrance of the BP1-BP2 CNVs for ASD was low, conferring additional risks of 0.3% (deletion) and 0.8% (duplication). Stepwise regression analyses suggest a greater effect of the CNVs on ASD-related phenotype in males and when maternally inherited. Taken together, the results are consistent with BP1-BP2 CNVs as risk factors for autism. However, their effect is modest, more akin to that seen for common variants. To be consistent with the current American College of Medical Genetics guidelines for interpretation of postnatal CNV, the BP1-BP2 deletion and duplication CNVs would probably best be classified as variants of uncertain significance (VOUS): they appear to have an impact on risk, but one so modest that these CNVs do not merit pathogenic status.


Subject(s)
Child Development Disorders, Pervasive/genetics , Chromosome Deletion , Chromosomes, Human, Pair 15/genetics , DNA Copy Number Variations/genetics , Genetic Predisposition to Disease/genetics , Adult , Child , Female , Humans , Male
6.
Cell ; 155(5): 997-1007, 2013 Nov 21.
Article in English | MEDLINE | ID: mdl-24267886

ABSTRACT

Autism spectrum disorder (ASD) is a complex developmental syndrome of unknown etiology. Recent studies employing exome- and genome-wide sequencing have identified nine high-confidence ASD (hcASD) genes. Working from the hypothesis that ASD-associated mutations in these biologically pleiotropic genes will disrupt intersecting developmental processes to contribute to a common phenotype, we have attempted to identify time periods, brain regions, and cell types in which these genes converge. We have constructed coexpression networks based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood. By assessing enrichment of an independent set of probable ASD (pASD) genes, derived from the same sequencing studies, we demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons. This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology.


Subject(s)
Brain/metabolism , Child Development Disorders, Pervasive/genetics , Child Development Disorders, Pervasive/physiopathology , Animals , Brain/embryology , Brain/growth & development , Brain/pathology , Child Development Disorders, Pervasive/pathology , Exome , Female , Fetus/metabolism , Fetus/pathology , Gene Expression Profiling , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Male , Mice , Mutation , Neurons/metabolism , Prefrontal Cortex/metabolism , Sequence Analysis, DNA
7.
Am J Hum Genet ; 93(1): 103-9, 2013 Jul 11.
Article in English | MEDLINE | ID: mdl-23830515

ABSTRACT

Intellectual disability (ID), often attributed to autosomal-recessive mutations, occurs in 40% of autism spectrum disorders (ASDs). For this reason, we conducted a genome-wide analysis of runs of homozygosity (ROH) in simplex ASD-affected families consisting of a proband diagnosed with ASD and at least one unaffected sibling. In these families, probands with an IQ ≤ 70 show more ROH than their unaffected siblings, whereas probands with an IQ > 70 do not show this excess. Although ASD is far more common in males than in females, the proportion of females increases with decreasing IQ. Our data do support an association between ROH burden and autism diagnosis in girls; however, we are not able to show that this effect is independent of low IQ. We have also discovered several autism candidate genes on the basis of finding (1) a single gene that is within an ROH interval and that is recurrent in autism or (2) a gene that is within an autism ROH block and that harbors a homozygous, rare deleterious variant upon analysis of exome-sequencing data. In summary, our data suggest a distinct genetic architecture for participants with autism and co-occurring intellectual disability and that this architecture could involve a role for recessively inherited loci for this autism subgroup.


Subject(s)
Child Development Disorders, Pervasive/genetics , Genetic Association Studies/methods , Intellectual Disability/genetics , Child , Chromosomes, Human/genetics , Female , Genetic Diseases, Inborn/genetics , Genetic Predisposition to Disease/genetics , Genetics, Population/methods , Homozygote , Humans , Intelligence Tests , Male , Pedigree , Phenotype , Sex Factors
8.
Biol Psychiatry ; 74(8): 576-84, 2013 Oct 15.
Article in English | MEDLINE | ID: mdl-23746936

ABSTRACT

BACKGROUND: Brain development follows a different trajectory in children with autism spectrum disorders (ASD) than in typically developing children. A proxy for neurodevelopment could be head circumference (HC), but studies assessing HC and its clinical correlates in ASD have been inconsistent. This study investigates HC and clinical correlates in the Simons Simplex Collection cohort. METHODS: We used a mixed linear model to estimate effects of covariates and the deviation from the expected HC given parental HC (genetic deviation). After excluding individuals with incomplete data, 7225 individuals in 1891 families remained for analysis. We examined the relationship between HC/genetic deviation of HC and clinical parameters. RESULTS: Gender, age, height, weight, genetic ancestry, and ASD status were significant predictors of HC (estimate of the ASD effect = .2 cm). HC was approximately normally distributed in probands and unaffected relatives, with only a few outliers. Genetic deviation of HC was also normally distributed, consistent with a random sampling of parental genes. Whereas larger HC than expected was associated with ASD symptom severity and regression, IQ decreased with the absolute value of the genetic deviation of HC. CONCLUSIONS: Measured against expected values derived from covariates of ASD subjects, statistical outliers for HC were uncommon. HC is a strongly heritable trait, and population norms for HC would be far more accurate if covariates including genetic ancestry, height, and age were taken into account. The association of diminishing IQ with absolute deviation from predicted HC values suggests HC could reflect subtle underlying brain development and warrants further investigation.


Subject(s)
Autistic Disorder/pathology , Head/pathology , Quantitative Trait, Heritable , Adult , Autistic Disorder/diagnosis , Autistic Disorder/genetics , Body Weights and Measures , Child , Family , Female , Humans , Intelligence/physiology , Male
9.
Mol Autism ; 3(1): 9, 2012 Oct 15.
Article in English | MEDLINE | ID: mdl-23067556

ABSTRACT

BACKGROUND: Autism spectrum disorders (ASD) are early onset neurodevelopmental syndromes typified by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. While rare and especially de novo genetic variation are known to affect liability, whether common genetic polymorphism plays a substantial role is an open question and the relative contribution of genes and environment is contentious. It is probable that the relative contributions of rare and common variation, as well as environment, differs between ASD families having only a single affected individual (simplex) versus multiplex families who have two or more affected individuals. METHODS: By using quantitative genetics techniques and the contrast of ASD subjects to controls, we estimate what portion of liability can be explained by additive genetic effects, known as narrow-sense heritability. We evaluate relatives of ASD subjects using the same methods to evaluate the assumptions of the additive model and partition families by simplex/multiplex status to determine how heritability changes with status. RESULTS: By analyzing common variation throughout the genome, we show that common genetic polymorphism exerts substantial additive genetic effects on ASD liability and that simplex/multiplex family status has an impact on the identified composition of that risk. As a fraction of the total variation in liability, the estimated narrow-sense heritability exceeds 60% for ASD individuals from multiplex families and is approximately 40% for simplex families. By analyzing parents, unaffected siblings and alleles not transmitted from parents to their affected children, we conclude that the data for simplex ASD families follow the expectation for additive models closely. The data from multiplex families deviate somewhat from an additive model, possibly due to parental assortative mating. CONCLUSIONS: Our results, when viewed in the context of results from genome-wide association studies, demonstrate that a myriad of common variants of very small effect impacts ASD liability.

10.
Nature ; 485(7397): 237-41, 2012 Apr 04.
Article in English | MEDLINE | ID: mdl-22495306

ABSTRACT

Multiple studies have confirmed the contribution of rare de novo copy number variations to the risk for autism spectrum disorders. But whereas de novo single nucleotide variants have been identified in affected individuals, their contribution to risk has yet to be clarified. Specifically, the frequency and distribution of these mutations have not been well characterized in matched unaffected controls, and such data are vital to the interpretation of de novo coding mutations observed in probands. Here we show, using whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with autism spectrum disorders and carry large effects. On the basis of mutation rates in unaffected individuals, we demonstrate that multiple independent de novo single nucleotide variants in the same gene among unrelated probands reliably identifies risk alleles, providing a clear path forward for gene discovery. Among a total of 279 identified de novo coding mutations, there is a single instance in probands, and none in siblings, in which two independent nonsense variants disrupt the same gene, SCN2A (sodium channel, voltage-gated, type II, α subunit), a result that is highly unlikely by chance.


Subject(s)
Autistic Disorder/genetics , Exome/genetics , Exons/genetics , Genetic Predisposition to Disease/genetics , Mutation/genetics , Nerve Tissue Proteins/genetics , Sodium Channels/genetics , Alleles , Codon, Nonsense/genetics , Genetic Heterogeneity , Humans , NAV1.2 Voltage-Gated Sodium Channel , RNA Splice Sites/genetics , Siblings
11.
Hum Mol Genet ; 20(22): 4360-70, 2011 Nov 15.
Article in English | MEDLINE | ID: mdl-21865298

ABSTRACT

Autism is a neurodevelopmental disorder with increasing evidence of heterogeneous genetic etiology including de novo and inherited copy number variants (CNVs). We performed array comparative genomic hybridization using a custom Agilent 1 M oligonucleotide array intended to cover 197 332 unique exons in RefSeq genes; 98% were covered by at least one probe and 95% were covered by three or more probes with the focus on detecting relatively small CNVs that would implicate a single protein-coding gene. The study group included 99 trios from the Simons Simplex Collection. The analysis identified and validated 55 potentially pathogenic CNVs, categorized as de novo autosomal heterozygous, inherited homozygous autosomal, complex autosomal and hemizygous deletions on the X chromosome of probands. Twenty percent (11 of 55) of these CNV calls were rare when compared with the Database of Genomic Variants. Thirty-six percent (20 of 55) of the CNVs were also detected in the same samples in an independent analysis using the 1 M Illumina single-nucleotide polymorphism array. Findings of note included a common and sometimes homozygous 61 bp exonic deletion in SLC38A10, three CNVs found in lymphoblast-derived DNA but not present in whole-blood derived DNA and, most importantly, in a male proband, an exonic deletion of the TMLHE (trimethyllysine hydroxylase epsilon) that encodes the first enzyme in the biosynthesis of carnitine. Data for CNVs present in lymphoblasts but absent in fresh blood DNA suggest that these represent clonal outgrowth of individual B cells with pre-existing somatic mutations rather than artifacts arising in cell culture. GEO accession number GSE23765 (http://www.ncbi.nlm.nih.gov/geo/, date last accessed on 30 August 2011). Genboree accession: http://genboree.org/java-bin/gbrowser.jsp?refSeqId=1868&entryPointId=chr17&from=53496072&to=53694382&isPublic=yes, date last accessed on 30 August 2011.


Subject(s)
Autistic Disorder/genetics , Comparative Genomic Hybridization/methods , DNA Copy Number Variations/genetics , Exons/genetics , Mixed Function Oxygenases/genetics , Female , Humans , Male
12.
Neuron ; 70(5): 863-85, 2011 Jun 09.
Article in English | MEDLINE | ID: mdl-21658581

ABSTRACT

We have undertaken a genome-wide analysis of rare copy-number variation (CNV) in 1124 autism spectrum disorder (ASD) families, each comprised of a single proband, unaffected parents, and, in most kindreds, an unaffected sibling. We find significant association of ASD with de novo duplications of 7q11.23, where the reciprocal deletion causes Williams-Beuren syndrome, characterized by a highly social personality. We identify rare recurrent de novo CNVs at five additional regions, including 16p13.2 (encompassing genes USP7 and C16orf72) and Cadherin 13, and implement a rigorous approach to evaluating the statistical significance of these observations. Overall, large de novo CNVs, particularly those encompassing multiple genes, confer substantial risks (OR = 5.6; CI = 2.6-12.0, p = 2.4 × 10(-7)). We estimate there are 130-234 ASD-related CNV regions in the human genome and present compelling evidence, based on cumulative data, for association of rare de novo events at 7q11.23, 15q11.2-13.1, 16p11.2, and Neurexin 1.


Subject(s)
Child Development Disorders, Pervasive/genetics , Chromosomes, Human, Pair 16/genetics , Chromosomes, Human, Pair 7/genetics , DNA Copy Number Variations/genetics , Family Health , Williams Syndrome/genetics , Adolescent , Cadherins/genetics , Calcium-Binding Proteins , Cell Adhesion Molecules, Neuronal/genetics , Child , Child, Preschool , Chromosomes, Human, X/genetics , Female , Gene Duplication/genetics , Gene Expression Profiling , Genome-Wide Association Study , Genotype , Humans , Male , Nerve Tissue Proteins/genetics , Neural Cell Adhesion Molecules , Oligonucleotide Array Sequence Analysis , Phenotype , Proteins/genetics , Siblings , Ubiquitin Thiolesterase/genetics , Ubiquitin-Specific Peptidase 7
13.
Nat Genet ; 41(12): 1335-40, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19915574

ABSTRACT

The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis are common causes of morbidity in children and young adults in the western world. Here we report the results of a genome-wide association study in early-onset IBD involving 3,426 affected individuals and 11,963 genetically matched controls recruited through international collaborations in Europe and North America, thereby extending the results from a previous study of 1,011 individuals with early-onset IBD. We have identified five new regions associated with early-onset IBD susceptibility, including 16p11 near the cytokine gene IL27 (rs8049439, P = 2.41 x 10(-9)), 22q12 (rs2412973, P = 1.55 x 10(-9)), 10q22 (rs1250550, P = 5.63 x 10(-9)), 2q37 (rs4676410, P = 3.64 x 10(-8)) and 19q13.11 (rs10500264, P = 4.26 x 10(-10)). Our scan also detected associations at 23 of 32 loci previously implicated in adult-onset Crohn's disease and at 8 of 17 loci implicated in adult-onset ulcerative colitis, highlighting the close pathogenetic relationship between early- and adult-onset IBD.


Subject(s)
Genetic Variation , Inflammatory Bowel Diseases/genetics , Age of Onset , Chromosome Mapping , Colitis, Ulcerative/genetics , Genome, Human , Genome-Wide Association Study , Humans , Inflammatory Bowel Diseases/epidemiology
14.
Nat Genet ; 40(8): 955-62, 2008 Aug.
Article in English | MEDLINE | ID: mdl-18587394

ABSTRACT

Several risk factors for Crohn's disease have been identified in recent genome-wide association studies. To advance gene discovery further, we combined data from three studies on Crohn's disease (a total of 3,230 cases and 4,829 controls) and carried out replication in 3,664 independent cases with a mixture of population-based and family-based controls. The results strongly confirm 11 previously reported loci and provide genome-wide significant evidence for 21 additional loci, including the regions containing STAT3, JAK2, ICOSLG, CDKAL1 and ITLN1. The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development.


Subject(s)
Crohn Disease/genetics , Genetic Predisposition to Disease , Genome, Human , Quantitative Trait Loci , Humans
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