Subject(s)
Autism Spectrum Disorder , Autistic Disorder , Mental Retardation, X-Linked , Male , Humans , Siblings , Saudi ArabiaABSTRACT
Comparative analyses have identified genomic regions potentially involved in human evolution but do not directly assess function. Human accelerated regions (HARs) represent conserved genomic loci with elevated divergence in humans. If some HARs regulate human-specific social and behavioral traits, then mutations would likely impact cognitive and social disorders. Strikingly, rare biallelic point mutations-identified by whole-genome and targeted "HAR-ome" sequencing-showed a significant excess in individuals with ASD whose parents share common ancestry compared to familial controls, suggesting a contribution in 5% of consanguineous ASD cases. Using chromatin interaction sequencing, massively parallel reporter assays (MPRA), and transgenic mice, we identified disease-linked, biallelic HAR mutations in active enhancers for CUX1, PTBP2, GPC4, CDKL5, and other genes implicated in neural function, ASD, or both. Our data provide genetic evidence that specific HARs are essential for normal development, consistent with suggestions that their evolutionary changes may have altered social and/or cognitive behavior. PAPERCLIP.
Subject(s)
Autism Spectrum Disorder/genetics , Cognition , Genetic Predisposition to Disease , Neurogenesis/genetics , Point Mutation , Social Behavior , Alleles , Animals , Cerebral Cortex/metabolism , Gene Dosage , Genetic Variation , Genome, Human , Homeodomain Proteins/genetics , Humans , Introns , Mice , Mice, Transgenic , Nuclear Proteins/genetics , Quantitative Trait Loci , Regulatory Elements, Transcriptional , Repressor Proteins/genetics , Transcription FactorsABSTRACT
Despite significant heritability of autism spectrum disorders (ASDs), their extreme genetic heterogeneity has proven challenging for gene discovery. Studies of primarily simplex families have implicated de novo copy number changes and point mutations, but are not optimally designed to identify inherited risk alleles. We apply whole-exome sequencing (WES) to ASD families enriched for inherited causes due to consanguinity and find familial ASD associated with biallelic mutations in disease genes (AMT, PEX7, SYNE1, VPS13B, PAH, and POMGNT1). At least some of these genes show biallelic mutations in nonconsanguineous families as well. These mutations are often only partially disabling or present atypically, with patients lacking diagnostic features of the Mendelian disorders with which these genes are classically associated. Our study shows the utility of WES for identifying specific genetic conditions not clinically suspected and the importance of partial loss of gene function in ASDs.
Subject(s)
Autistic Disorder/diagnosis , Autistic Disorder/genetics , Exome/genetics , Genome-Wide Association Study/methods , Adolescent , Animals , Cells, Cultured , Child , Child, Preschool , Cohort Studies , Female , Humans , Male , Pedigree , Rats , Sequence Analysis, DNA/methods , Young AdultABSTRACT
To find inherited causes of autism-spectrum disorders, we studied families in which parents share ancestors, enhancing the role of inherited factors. We mapped several loci, some containing large, inherited, homozygous deletions that are likely mutations. The largest deletions implicated genes, including PCDH10 (protocadherin 10) and DIA1 (deleted in autism1, or c3orf58), whose level of expression changes in response to neuronal activity, a marker of genes involved in synaptic changes that underlie learning. A subset of genes, including NHE9 (Na+/H+ exchanger 9), showed additional potential mutations in patients with unrelated parents. Our findings highlight the utility of "homozygosity mapping" in heterogeneous disorders like autism but also suggest that defective regulation of gene expression after neural activity may be a mechanism common to seemingly diverse autism mutations.
