De Novo Gene Disruptions in Children on the Autistic Spectrum

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
Neuron (Impact Factor: 15.05). 04/2012; 74(2):285-99. DOI: 10.1016/j.neuron.2012.04.009
Source: PubMed


Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point substitutions, which come mostly from the paternal line in an age-dependent manner. We do not see significantly greater numbers of de novo missense mutations in affected versus unaffected children, but gene-disrupting mutations (nonsense, splice site, and frame shifts) are twice as frequent, 59 to 28. Based on this differential and the number of recurrent and total targets of gene disruption found in our and similar studies, we estimate between 350 and 400 autism susceptibility genes. Many of the disrupted genes in these studies are associated with the fragile X protein, FMRP, reinforcing links between autism and synaptic plasticity. We find FMRP-associated genes are under greater purifying selection than the remainder of genes and suggest they are especially dosage-sensitive targets of cognitive disorders.

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    • "The spatiotemporal networks are also significantly enriched in post-synaptic density genes and fragile X mental retardation protein (FMRP) target genes (Table S7), in agreement with previous studies (Fromer et al., 2014; Iossifov et al., 2012). These enrichment results provide independent lines of evidence for disease risk association and suggest that the functional impact of de novo mutations on networks needs further investigation. "
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    ABSTRACT: The psychiatric disorders autism and schizophrenia have a strong genetic component, and copy number variants (CNVs) are firmly implicated. Recurrent deletions and duplications of chromosome 16p11.2 confer a high risk for both diseases, but the pathways disrupted by this CNV are poorly defined. Here we investigate the dynamics of the 16p11.2 network by integrating physical interactions of 16p11.2 proteins with spatiotemporal gene expression from the developing human brain. We observe profound changes in protein interaction networks throughout different stages of brain development and/or in different brain regions. We identify the late mid-fetal period of cortical development as most critical for establishing the connectivity of 16p11.2 proteins with their co-expressed partners. Furthermore, our results suggest that the regulation of the KCTD13-Cul3-RhoA pathway in layer 4 of the inner cortical plate is crucial for controlling brain size and connectivity and that its dysregulation by de novo mutations may be a potential determinant of 16p11.2 CNV deletion and duplication phenotypes. Copyright © 2015 Elsevier Inc. All rights reserved.
    Neuron 02/2015; 85(4):742-54. DOI:10.1016/j.neuron.2015.01.010 · 15.05 Impact Factor
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    • "A sizable fraction (10%–13%) of variants associated with Mendelian disorders are suspected of causing aberrant splicing as they occur in or near exon–intron boundaries [Krawczak et al., 2007]. The clinical importance of this class of variants extends beyond single gene disorders as complex disorders such as autism and psoriasis can also trace their etiology to variants that cause mis-splicing of RNA transcripts [Iossifov et al., 2012; Jordan et al., 2012]. Furthermore, variants near or within exon–intron boundaries are commonly identified in exome sequencing studies of patients with unidentified Mendelian and polygenic diseases [Sanders et al., 2012; Sankaran et al., 2012]. "
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    ABSTRACT: Assessment of the functional consequences of variants near splice sites is a major challenge in the diagnostic laboratory. To address this issue, we created Expression Minigenes (EMGs) to determine the RNA and protein products generated by splice site variants (n = 10) implicated in cystic fibrosis (CF). Experimental results were compared with the splicing predictions of eight in silico tools. EMGs containing the full-length Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) coding sequence and flanking intron sequences generated wild-type transcript and fully processed protein in Human Embryonic Kidney (HEK293) and CF bronchial epithelial (CFBE41o-) cells. Quantification of variant induced aberrant mRNA isoforms was concordant using fragment analysis and pyrosequencing. The splicing patterns of c.1585–1G>A and c.2657+5G>A were comparable to those reported in primary cells from individuals bearing these variants. Bioinformatics predictions were consistent with experimental results for 9/10 variants (MES), 8/10 variants (NNSplice) and 7/10 variants (SSAT and Sroogle). Programs that estimate the consequences of mis-splicing predicted 11/16 (HSF and ASSEDA) and 10/16 (Fsplice and SplicePort) experimentally observed mRNA isoforms. EMGs provide a robust experimental approach for clinical interpretation of splice site variants and refinement of in silico tools.This article is protected by copyright. All rights reserved
    Human Mutation 10/2014; 35(10). DOI:10.1002/humu.22624 · 5.14 Impact Factor
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    • "chr6:64423242 C->T missense Sanders et al., 2012 RIMS1 13162.p1 chr6:72889392 +A frameshift Iossifov et al., 2012 13497.p1 chr6:73102488 +A frameshift Identified herein See also Table S2. "
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    ABSTRACT: Whole-exome sequencing (WES) studies have demonstrated the contribution of de novo loss-of-function single-nucleotide variants (SNVs) to autism spectrum disorder (ASD). However, challenges in the reliable detection of de novo insertions and deletions (indels) have limited inclusion of these variants in prior analyses. By applying a robust indel detection method to WES data from 787 ASD families (2,963 individuals), we demonstrate that de novo frameshift indels contribute to ASD risk (OR = 1.6; 95% CI = 1.0-2.7; p = 0.03), are more common in female probands (p = 0.02), are enriched among genes encoding FMRP targets (p = 6 x 10-9), and arise predominantly on the paternal chromosome (p < 0.001). On the basis of mutation rates in probands versus unaffected siblings, we conclude that de novo frameshift indels contribute to risk in approximately 3% of individuals with ASD. Finally, by observing clustering of mutations in unrelated probands, we uncover two ASD-associated genes: KMT2E (MLL5), a chromatin regulator, and RIMS1, a regulator of synaptic vesicle release.
    Cell Reports 10/2014; 9(1). DOI:10.1016/j.celrep.2014.08.068 · 8.36 Impact Factor
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