Whole-exome sequencing and homozygosity analysis implicate depolarization-regulated neuronal genes in autism.
paper
Cited
Public
- Authors
- Chahrour, Maria H; Yu, Timothy W; Lim, Elaine T; Ataman, Bulent; Coulter, Michael E; Hill, R Sean; Stevens, Christine R; Schubert, Christian R; ARRA Autism Sequencing Collaboration; Greenberg, Michael E; Gabriel, Stacey B; Walsh, Christopher A
- Year
- 2012
- Journal
- PLoS genetics
- PMID
- 22511880
- DOI
- 10.1371/journal.pgen.1002635
- PMCID
- PMC3325173
Although autism has a clear genetic component, the high genetic heterogeneity of the disorder has been a challenge for the identification of causative genes. We used homozygosity analysis to identify probands from nonconsanguineous families that showed evidence of distant shared ancestry, suggesting potentially recessive mutations. Whole-exome sequencing of 16 probands revealed validated homozygous, potentially pathogenic recessive mutations that segregated perfectly with disease in 4/16 families. The candidate genes (UBE3B, CLTCL1, NCKAP5L, ZNF18) encode proteins involved in proteolysis, GTPase-mediated signaling, cytoskeletal organization, and other pathways. Furthermore, neuronal depolarization regulated the transcription of these genes, suggesting potential activity-dependent roles in neurons. We present a multidimensional strategy for filtering whole-exome sequence data to find candidate recessive mutations in autism, which may have broader applicability to other complex, heterogeneous disorders.
Homozygosity analysis in the AGRE collection.(A) A plot of the percent homozygosity in the genome of probands from the entire AGRE collection. All affected individuals with runs of homozygosity (ROHs) >5 cM are plotted. Offspring of first cousin marriages are expected to have 6.25% homozygosity in their genomes, while those of second cousin marriages are expected to have 1.6%. IBD: identity by descent. (B) The average sizes of the ROHs in cM are plotted for each of the 16 AGRE samples that were sequenced. The number of the ROHs is shown in each bar. Values are mean Β± SEM. (C) ROHs containing candidate disease variants are shared by affected individuals and absent from unaffected individuals. Sample names are indicated on the left (Aff.Sib: affected sibling, Unaff.Sib: unaffected sibling). Homozygous SNPs are shown in red or blue and heterozygous SNPs are shown in green. ROHs are enclosed in the dotted box. The candidate autism gene in each family is shown in navy below the ROHs. All other genes in grey did not contain rare, potentially pathogenic variants. No whole genome SNP data is available for individual AU035203, but we genotyped the sample for all homozygous variants identified by the whole exome sequencing of AU035204.
A four-dimensional approach to identifying autism candidate genes.Overview of variant filtration and prioritization of whole exome sequencing data. Results from variant validation and homozygosity analysis were combined with neuronal activity data to identify candidate autism genes from whole exome sequence. 1000G: 1000 Genomes Project, GMCC: genomic mutation consequence calculator, ROHs: runs of homozygosity.
Regulation of four candidate autism genes by neuronal activity.qRT-PCR analysis of total RNA from depolarized mouse cortical neurons stimulated with KCl for 6 hours (the dashed line represents no KCl treatment, values are mean Β± SEM from three independent experiments, each experiment was performed in triplicate, ***P<0.0001, **P<0.004, *P<0.04, t-test).
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| Name | Type |
|---|---|
| 1000 Genomes Project | cohort |
| 1344 control chromosomes local | cohort |
| AFF2 local | gene |
| AFF2 P847A local | variant |
| affected individuals | cohort |
| Affected siblings local | cohort |
| Agilent Technologies local | drug |
| AGRE | cohort |
| Amino aciduria local | phenotype |
| Angelman syndrome | phenotype |
| APV | drug |
| ARC | gene |
| ARHGEF6 | gene |
| ARHGEF6 I444N local | variant |
| ARRA Autism Sequencing Consortium local | cohort |
| ASD candidate genes local | gene |
| autism | phenotype |
| autism genes local | gene |
| Autism Genetic Research Exchange local | cohort |
| autism patients | cohort |
| Autism Sequencing Consortium (ASC) local | cohort |
| autism spectrum disorder | phenotype |
| B27 supplement | drug |
| behavioral abnormalities | phenotype |
| brain | anatomy |
| Broad Institute local | cohort |
| C57BL/6 mouse embryo local | cohort |
| candidate disease variants local | variant |
| Cataract local | phenotype |
| Children's Hospital Boston local | cohort |
| CLTCL1 | gene |
| Cohort of 16 patients local | cohort |
| Compound heterozygous recessive mutations local | variant |
| consanguinity local | phenotype |
| control individuals | cohort |
| control population | cohort |
| Coriell Cell Repositories | cohort |
| cortex | anatomy |
| cortical malformations | phenotype |
| dbSNP130 local | cohort |
| de novo variant | variant |
| DiGeorge syndrome local | phenotype |
| EPHEXIN5 local | gene |
| epilepsy | phenotype |
| facial dysmorphia local | phenotype |
| family members | cohort |
| first cousin parents local | phenotype |
| fragile X syndrome | phenotype |
| genital anomalies local | phenotype |
| genomic DNA | drug |
| glutamine | drug |
| HBSS | drug |
| heterozygous mothers local | cohort |
| homozygosity local | phenotype |
| Homozygous missense changes local | variant |
| Homozygous null mutations local | variant |
| Hydrophthalmia local | phenotype |
| IBS0 local | phenotype |
| IBS1 local | phenotype |
| IBS2* local | phenotype |
| IBS2*_ratio local | phenotype |
| Illumina 550 SNP genotype data local | drug |
| Illumina GA II local | drug |
| intellectual disability | phenotype |
| KCl | drug |
| l-cysteine | drug |
| long slender digits local | phenotype |
| Lowe oculocerebrorenal syndrome local | phenotype |
| male patients | cohort |
| Mendelian recessive diseases local | phenotype |
| Miller syndrome | phenotype |
| Movement or balance problems local | phenotype |
| National Database for Autism Research local | cohort |
| National Institute of Mental Health (NIMH) local | cohort |
| NCKAP5L local | gene |
| NDARCOL0001918 local | cohort |
| neurobasal medium | drug |
| Neurological condition local | phenotype |
| Neurologically normal | phenotype |
| Neuronal depolarization local | drug |
| neuronal depolarization-dependent genes local | gene |
| neurons | phenotype |
| NLGN3 | gene |
| NLGN4X | gene |
| Nonconsanguineous autism cohort local | cohort |
| NRXN1 | gene |
| OCRL local | gene |
| OCRL splice donor site disruption local | variant |
| outlier families local | cohort |
| parental relatedness local | phenotype |
| penicillin | drug |
| percent of informative SNPs local | phenotype |
| Plink | drug |
| poly-ornithine | drug |
| probands | cohort |
| R125C local | variant |
| recessive autism genes local | gene |
| recessive missense mutations local | variant |
| Recessive mutations local | variant |
| Reduced ammonia production local | phenotype |
| Rett syndrome | phenotype |
| Runs of homozygosity local | variant |
| schizophrenia | phenotype |
| SHANK2 | gene |
| SHANK3 | gene |
| siblings | cohort |
| Speech and language impairment local | phenotype |
| streptomycin | drug |
| stress response | phenotype |
| SureSelect Human Exome Kit local | drug |
| SYBR green | drug |
| Trizol | drug |
| trypsin | drug |
| Trypsin inhibitor | drug |
| TTX | drug |
| UBE3A | gene |
| UBE3B local | gene |
| UBE3B R40C local | variant |
| Vitamin D-resistant rickets local | phenotype |
| WDR62 local | gene |
| whole exome sequencing | drug |
| X-linked autism male patients local | cohort |
| Z1 local | phenotype |
| ZNF18 local | gene |
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