Distribution of disease-associated copy number variants across distinct disorders of cognitive development.
- Authors
- Pescosolido, Matthew F; Gamsiz, Ece D; Nagpal, Shailender; Morrow, Eric M
- Year
- 2013
- Journal
- Journal of the American Academy of Child and Adolescent Psychiatry
- PMID
- 23582872
- DOI
- 10.1016/j.jaac.2013.01.003
- PMCID
- PMC3774163
OBJECTIVE: The purpose of the present study was to discover the extent to which distinct DSM disorders share large, highly recurrent copy number variants (CNVs) as susceptibility factors. We also sought to identify gene mechanisms common to groups of diagnoses and/or specific to a given diagnosis based on associations with CNVs. METHOD: Systematic review of 820 PubMed articles on autism spectrum disorder (ASD), intellectual disability (ID), schizophrenia, and epilepsy produced 54 CNVs associated with one or several disorders. Pathway analysis on genes implicated by CNVs in different groupings was conducted. RESULTS: The majority of CNVs were found in ID with the other disorders somewhat subsumed, yet certain CNVs were associated with isolated or groups of disorders. Based on genes implicated by CNVs, ID encompassed 96.8% of genes in ASD, 92.8% of genes in schizophrenia, and 100.0% of genes in epilepsy. Pathway analysis revealed that synapse processes were enriched in ASD, ID, and schizophrenia. Disease-specific processes were identified in ID (actin cytoskeleton processes), schizophrenia (ubiquitin-related processes), and ASD (synaptic vesicle transport and exocytosis). CONCLUSIONS: Intellectual disability may arise from the broadest range of genetic pathways, and specific subsets of these pathways appear to be relevant to other disorders or combinations of these disorders. It is clear that statistically significant CNVs across disorders of cognitive development are highly enriched for biological processes related to the synapse. There are also disorder-specific processes that may aid in understanding the distinct presentations and pathophysiology of these disorders.
Distribution of copy number variants (CNVs) and genes for autism spectrum disorder (ASD), intellectual disability (ID), schizophrenia, and epilepsy. Note: Figure 1A shows the distribution of genes contained within CNVs using strict criteria among all 4 disorders, as well as separates strict gene distribution by deletions (1B) and duplications (1C). Figure 1D shows the distribution of CNVs using strict criteria and is also separated into deletions (1E) and duplications (1F). Figure 1G shows the distribution of genes contained within CNVs for broad criteria, as well as deletions (1H) and duplications (1I). Broad CNV distribution is shown in Figure 1J and also categorized into deletions (1K) and duplications (1L). For Figure 1D, #1β8 represent strict CNV distributions that were analyzed in the pathway analysis (results in Table S4, available online), while in Figure 1J, #1β9 represent broad CNV distributions (results in Table S5, available online).
Figure 2A shows the number of genes per copy number variant (CNV) for all significant CNVs in autism spectrum disorder (ASD), intellectual disability (ID), schizophrenia (SZ), and epilepsy (EP) and is separated into deletions (red) and duplications (blue). Note: The median number of genes per CNV is shown in the center of each box and the whiskers indicate the range. Figure 2B shows the number of CNV categories (e.g. A, B, and C) for all 4 disorders. ID had a greater number of category A CNVs in both ASD (p=.004) and epilepsy (p<.001). Also, ID had a significantly greater number of category C CNVs for ASD (p=.04) and epilepsy (p=.002).
Enriched gene networks of significant pathway analysis results for autism spectrum disorder (ASD) (3A), intellectual disability (ID) (3B), and schizophrenia (3C). Note: ASD processes shown include vesicle and synaptic processes. Synaptic, necrosis factor, and actin filament-based processes are enriched in ID. Significant schizophrenia networks consist of phospholipid, ubiquitin, and synaptic processes.
| Name | Type |
|---|---|
| 15q13.3 local | variant |
| 16p11.2 deletion | variant |
| 16p11.2 duplication | variant |
| 16p13.1 local | variant |
| 1p36 deletion local | variant |
| 1p36 duplication local | variant |
| 7q11.2 deletion local | variant |
| actin cytoskeleton organization local | phenotype |
| actin filament-based process local | phenotype |
| ADHD | phenotype |
| ASD | phenotype |
| ASD CNVs local | variant |
| ASD genes local | gene |
| ASD study local | cohort |
| attentional problems local | phenotype |
| autism | phenotype |
| autism spectrum disorder | phenotype |
| bipolar disorder | phenotype |
| Category A local | cohort |
| Category A CNV local | variant |
| Category A CNVs local | variant |
| Category B local | cohort |
| Category B local | variant |
| Category B CNV local | variant |
| Category B CNVs local | variant |
| Category C local | cohort |
| Category C CNV local | variant |
| Category C CNVs local | variant |
| clinical referrals local | cohort |
| CNV | variant |
| CNV category A local | cohort |
| CNV category B local | cohort |
| CNV category C local | cohort |
| CNV type A local | variant |
| CNV type B local | variant |
| CNV type C local | variant |
| cognitive development disorder local | phenotype |
| Cognitive development disorders local | phenotype |
| copy number variant | variant |
| copy number variation | variant |
| deletion | variant |
| de novo SCN1A mutation local | variant |
| de novo variant | variant |
| developmental disorders | phenotype |
| disorder | phenotype |
| DSM disorders local | cohort |
| duplication | variant |
| epilepsy | phenotype |
| exocytosis | phenotype |
| full sample | cohort |
| Highly recurrent CNVs local | variant |
| ID | phenotype |
| ID CNVs local | variant |
| ID genes local | gene |
| intellectual disability | phenotype |
| large CNV | variant |
| large CNVs | variant |
| large disease cohort local | cohort |
| Large population samples local | cohort |
| large rare CNVs | variant |
| neurodevelopmental disorder | phenotype |
| neuropsychiatric disorders | phenotype |
| NRXN1 | gene |
| NRXN1 deletion local | variant |
| NRXN1 duplication local | variant |
| postsynaptic membrane local | phenotype |
| protein ubiquitination local | phenotype |
| PTEN | gene |
| rare CNVs | variant |
| Ras protein signal transduction local | phenotype |
| regulation of acute inflammatory response local | phenotype |
| regulation of neurotransmitter levels local | phenotype |
| regulation of synaptic transmission local | phenotype |
| research setting local | cohort |
| schizophrenia | phenotype |
| Schizophrenia CNVs local | variant |
| Schizophrenia genes local | gene |
| Schizophrenia-specific CNV local | variant |
| Scn1a | gene |
| second large CNV local | variant |
| single large CNV local | variant |
| synaptic processes | phenotype |
| synaptic vesicle transport local | phenotype |
| TNF | gene |
| tuberous sclerosis | phenotype |
| tumor necrosis factor binding local | phenotype |
| twins cohort with attentional problems local | cohort |
| ubiquitin-protein ligase activity local | phenotype |
| vesicle local | phenotype |
| Williams syndrome local | phenotype |
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