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Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
Open accessAbstract
It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes--so-called sporadic or simplex families--we sequenced all coding regions of the genome (the exome) for parent-child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19), for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected β-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.
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In the citing paper
“including that, prima facie , most proteins encoded by ASD risk genes are involved either in synaptic structure and function or chromatin modification and regulation of gene expression 38,46,47,58 (Fig. 3).”
From Autism spectrum disorder (2020) · cites this paper as [38]
Experimental — accuracy not yet measuredIn the citing paper
“CNVs and SNPs have both been reported to play a major role in autism incidence (36–41).”
From Gene × Environment Interactions in Autism Spectrum Disorders: Role of Epigenetic Mechanisms (2014) · cites this paper as [39]
In the citing paper
“An analysis of publicly released whole exome sequence data (Iossifov et al., 2012; O’Roak et al., 2012; Sanders et al., 2012) showed a modest trend towards an excess of biallelic, inherited, rare (MAF<1%), protein-altering variants in cases (8/612 ) compared to control siblings (2/419) (p=0.21, Fisher’s exact test, two-tailed) in at least one of the genes we screened (Table S5).”
From Using Whole-Exome Sequencing to Identify Inherited Causes of Autism (2013) · cites this paper as O’Roak et al., 2012
In the citing paper
“Hypomorphic, biallelic mutations, combined with CNVs and heterozygous stop mutations (Neale et al., 2012; O’Roak et al., 2012; Sanders et al., 2012) which completely inactivate one of two alleles, suggest that a common theme for ASD mutations in general might be partial loss of gene function and/or dosage sensitivity.”
From Using Whole-Exome Sequencing to Identify Inherited Causes of Autism (2013) · cites this paper as O’Roak et al., 2012
In the citing paper
“Together, results from these papers demonstrate a significant role for rare SNVs in genetic liability for ASD”
From Sex differences in autism spectrum disorders (2013) · cites this paper as [49]
In the citing paper
“Exome and whole-genome sequencing studies have estimated at least another ∼6% contribution to ASD7–10,15”
From Convergence of genes and cellular pathways dysregulated in autism spectrum disorders (2014) · cites this paper as [10]
In the citing paper
“and three other recent studies by Sanders et al.8, O’Roak et al.7 and Neale et al.23 (65 genes combined from all three; referred to as ‘SON-exomes’);”
From Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism (2014) · cites this paper as [7]
In the citing paper
“Various genetic approaches have been successful in identifying the causes of more than 1,000 Mendelian, and fewer non-Mendelian, forms of neurodevelopmental disorders: prototypical examples are intellectual disability62–68, autism spectrum disorder (ASD)69–77, epilepsy78,79 and schizophrenia80–82.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [71]
In the citing paper
“Genetic investigations in ASD have constructed seed-based networks with literature-curated PPIs to identify the convergence of ASD risk genes71,73.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [71]
In the citing paper
“This approach was applied to identify a highly interconnected PPI subnetwork among rare de novo variants in ASD71.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [71]
In the citing paper
“Many strong neurobiological candidates have emerged from the genes disrupted by de novo mutations in these studies, including mutations in previously identified ASD/ID genes.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [24]
In the citing paper
“We note that the strongest effects are observed for de novo loss-of-function (or truncating) mutations”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [24]
In the citing paper
“Exome sequencing of ASD/ID families has revealed a significant excess of de novo mutations in probands when compared to unaffected siblings and has identified novel candidate genes contributing to the neurological deficits.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [24]
In the citing paper
“New exome sequencing technology has identified novel rare variants and has found that sporadic cases of ASD/ID are enriched for disruptive de novo mutations.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [24]
In the citing paper
“Another striking candidate is DYRK1A (dual-specificity tyrosine phosphorylation-regulated kinase 1A), for which three truncating mutations have been discovered in autism probands [24,44] and de novo structural variants in ID probands [54,55].”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [24]
In the citing paper
“In summary, only three genes [CHD8, SCN2A, and synaptic Ras GTPase activating protein 1 (SYNGAP1)] had two independent truncating de novo mutations in any single study, and no gene had more than three mutations.”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [24]
In the citing paper
“one de novo frameshift of ARID1B was found in a sporadic ASD case [24]”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [24]
In the citing paper
“In the case of paternal age, one mediating mechanism lies in the increased rate of de novo SNV and CNV with advancing paternal age (22,24,25,43,44).”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [25]
In the citing paper
“TBR1 has been implicated in ASD (21,22,25,26) and ID (73).”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [25]
In the citing paper
“Qualitatively, recent studies of rare variants also find it challenging to distinguish risk variation from the background stochastic noise (12–15).”
From Individual common variants exert weak effects on the risk for autism spectrum disorders (2012) · cites this paper as [13]
In the citing paper
“De novo loss of function mutations in this gene had previously been identified in two patients by WES2 and targeted resequencing16 of patients with ASD. In those studies however, causal relationship did not reach locus-specific significance.”
From A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP (2014) · cites this paper as [2]
In the citing paper
“Albeit rare, de novo mutations have emerged as substantial contributors to ASD risk [83, 165, 166, 254, 261, 309].”
From Autism spectrum disorder: neuropathology and animal models (2017) · cites this paper as [261]
In the citing paper
“Chromodomain helicase DNA-binding protein 8 (CHD8), encoding a chromatin modifying gene on chromosome 14q11.2, is one of the high-penetrance ASD risk genes recently identified by sequencing studies [83, 165, 261, 347].”
From Autism spectrum disorder: neuropathology and animal models (2017) · cites this paper as [261]
In the citing paper
“no truncating coding-sequence variation within SHANK1 and SHANK3”
From Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments (2014) · cites this paper as [36]
In the citing paper
“Recent exome sequencing studies only reported one de novo SHANK2 mutation out of 965 patients [32], [36], [37]”
From Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments (2014) · cites this paper as [36]
In the citing paper
“estimates from de novo exonic mutations (similar to those from SV data) suggest that ASD is highly polygenic (estimates ranged from 400–1000 genes). 84,85”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [85]
In the citing paper
“Three recent papers describe the results from exome sequencing of ~600 trios, and identify roles for de novo exonic mutations in SCN2A, KATNAL2, and CHD8 in the pathogenesis of ASD. 83–85”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [85]
In the citing paper
“Intriguingly, all three studies noted an increased rate of de novo exonic mutations in older parents (with the mutations generally being of paternal origin), 83–85”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [85]
In the citing paper
“However, a central finding from these papers was that only a minority of cases had a de novo putatively functional variant”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [85]
In the citing paper
“Unexpectedly, simplex and multiplex ASD pedigrees show relatively similar de novo mutation rates for SV 80,81 and exonic variation. 83–85”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [85]
In the citing paper
“Projections for ASD and SCZ suggest that variation at hundreds of different genes will ultimately be shown to be involved. 58,80,85”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [85]
In the citing paper
“The published results for ASD 83–85 and unpublished data on SCZ suggest these issues will be important and underscore the need for sequencing studies to have the same emphasis on statistical rigor and large sample sizes that has enabled GWAS to realize success for multiple psychiatric disorders. 154”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [85]
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“This is consistent with evidence from large-scale sequencing and other studies showing that loss-offunction mutations in either Wnt/β-catenin pathway inhibitors (e.g. CHD8, APC)(39, 40) or activators (e.g. CTTNβ1, WNT1)(4, 41, 42) contribute to susceptibility for ASD, as well as identifying differentiating cortical py…”
BackgroundRegulation of neuronal connectivity in the mammalian brain by chromatin remodeling
Goodman, J. V., & Bonni, A. (2019) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2019.04.010 · Cited by 64
Large mosaic copy number variations confer autism risk
Sherman, M. A., Rodin, R. E., Genovese, G., Dias, C., Barton, A. R., Mukamel, R. E., Berger, B., Park, P. J., Walsh, C. A., & Loh, P. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00766-5 · Cited by 56
Desachy, G., Croen, L. A., Torres, A. R., Kharrazi, M., Delorenze, G. N., Windham, G. C., Yoshida, C. K., & Weiss, L. A. (2015) · Molecular Psychiatry · doi:10.1038/mp.2014.179 · Cited by 54
Chuang, H.-C., Huang, T.-N., & Hsueh, Y.-P. (2014) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2014.00280 · Cited by 56
Murdoch, J. D., Gupta, A. R., Sanders, S., Walker, M. F., Keaney, J. F., Fernandez, T. V., Murtha, M. T., Anyanwu, S. I., Ober, G., Raubeson, M. J., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004852 · Cited by 63
“In addition, to date, neither rare de novo [23–26] or compound heterozygous mutations [27, 34, 35] have implicated CNTNAP2 or other Contactin or Contactin Associated Proteins in autism or related phenotypes.”
BackgroundHoms, A., Codina‐Solà, M., Rodríguez‐Santiago, B., Villanueva, C. M., Monk, D., Cuscó, I., & Pérez‐Jurado, L. A. (2016) · Translational Psychiatry · doi:10.1038/tp.2016.120 · Cited by 60
Mahfouz, A. E., Ziats, M. N., Rennert, O. M., Lelieveldt, B. P. F., & Reinders, M. J. T. (2015) · Journal of Molecular Neuroscience · doi:10.1007/s12031-015-0641-3 · Cited by 63
Tilot, A. K., Bebek, G., Niazi, F., Altemus, J. B., Romigh, T., Frazier, T. W., & Eng, C. (2015) · Molecular Psychiatry · doi:10.1038/mp.2015.17 · Cited by 57
Wong, C. T., Ahmad, E., Li, H., & Crawford, D. A. (2014) · Cell Communication and Signaling · doi:10.1186/1478-811x-12-19 · Cited by 65
“Furthermore, de novo mutations of this gene and its relevant network have been ranked significantly as potential autism candidate genes [94,95].”
BackgroundEnriched expression of genes associated with autism spectrum disorders in human inhibitory neurons
Wang, P., Zhao, D., Lachman, H. M., & Zheng, D. (2018) · Translational Psychiatry · doi:10.1038/s41398-017-0058-6 · Cited by 61
Phenotypic and genetic spectrum of epilepsy with myoclonic atonic seizures
Tang, S. S., Addis, L., Smith, A. B., Topp, S. D., Pendziwiat, M., Mei, D., Parker, A. P. J., Agrawal, S., Hughes, E., Lascelles, K., et al. (2020) · Epilepsia · doi:10.1111/epi.16508 · Cited by 61
Molecular mechanisms of synaptogenesis
Qi, C., Luo, L.-D., Feng, I., & Ma, S. (2022) · Frontiers in Synaptic Neuroscience · doi:10.3389/fnsyn.2022.939793 · Cited by 54
Current perspectives in autism spectrum disorder: from genes to therapy
Chahrour, M., O'Roak, B. J., Santini, E., Samaco, R. C., Kleiman, R. J., & Manzini, M. C. (2016) · The Journal of Neuroscience · doi:10.1523/jneurosci.2335-16.2016 · Cited by 54
“…targeted sequencing approaches, 49 different genes no longer merely represent “candidate” ASD genes, but are now mid- to high-confidence genes based on their recurrent disruption by de novo mutations in unrelated probands (O’Roak et al., 2012b, 2014; De Rubeis et al., 2014; Iossifov et al., 2014).”
BackgroundInfluentialSelf-citationSchirer, Y., Malishkevich, A., Ophir, Y., Lewis, J. M., Giladi, E., & Gozes, I. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087383 · Cited by 57
“ADNP-deficiency has been associated with cognitive and social deficits as well as tauopathy and brain cell death in mice [12] and mental retardation [41] as well as autism [42,43] in men.”
BackgroundAdvancing parental age and autism: multifactorial pathways
Lee, B. K., & McGrath, J. J. (2015) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2014.11.005 · Cited by 62
Wang, Q., Lu, Q., & Zhao, H. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00149 · Cited by 62
“Whole-exome sequencing has achieved great success for de novo mutation detection in neurodevelopmental disorders such as autism spectrum disorder (O’Roak et al., 2011, 2012; Iossifov et al., 2012, 2014; Neale et al., 2012; Sanders et al., 2012; Hamilton et al., 2013; De Rubeis et al., 2014;…”
BackgroundThe 16p11.2 homologs fam57ba and doc2a generate certain brain and body phenotypes
McCammon, J. M., Blaker, A. L., Chen, X., & Sive, H. L. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx255 · Cited by 57
“Extensive sequence analysis on large samples from people with autism has not revealed statistically significant variants for any of the 25 single genes from this region (11,12,14,15).”
BackgroundXu, D.-E., Zou, Y., Zhang, W., Liu, H.-Y., Li, X., Zhang, X., Ma, X.-F., Sun, Y., Jiang, S., & Ma, Q. (2017) · Neural Regeneration Research · doi:10.4103/1673-5374.215268 · Cited by 60
“Although little is known regarding the precise functions of the recently identified Caspr3, Caspr4, and Caspr5 proteins, some evidence suggests that Caspr3 is involved in motor control and learning (Peñagarikano et al., 2011; Anderson et al., 2012; O’Roak et al., 2012; Karayannis et al., 2014).”
BackgroundThe effects of male age on sperm DNA damage: an evaluation of 2,178 semen samples
Comar, V. A., Ricci, J., Dieamant, F., Oliveira, J. B. A., Baruffi, R. L. R., & Franco, J. G., Jr. (2018) · JBRA · doi:10.5935/1518-0557.20180047 · Cited by 57
Dinwiddie, D. L., Soden, S. E., Saunders, C., Miller, N., Farrow, E., Smith, L. D., & Kingsmore, S. F. (2013) · BMC Medical Genomics · doi:10.1186/1755-8794-6-32 · Cited by 60
“In addition, new research has implicated de novo mutations in the complex disorders of autism [8-10] and schizophrenia [11,12].”
BackgroundChromodomain Helicase DNA-Binding Proteins in Stem Cells and Human Developmental Diseases
Micucci, J. A., Sperry, E. D., & Martin, D. M. (2015) · Stem Cells and Development · doi:10.1089/scd.2014.0544 · Cited by 56
“In contrast to the rare isolated mutations in these three CHD genes, 13 different recurrent alleles of CHD8 have been observed in individuals with ASD/ID in association with macrocephaly and gastrointestinal disturbance [66,70,75–78].”
Association of genetic variants of GRIN2B with autism
Pan, Y., Chen, J., Guo, H., Ou, J., Peng, Y., Liu, Q., Shen, Y., Shi, L., Liu, Y., Xiong, Z., et al. (2015) · Scientific Reports · doi:10.1038/srep08296 · Cited by 56
Seabury, C. M., Dowd, S. E., Seabury, P. M., Raudsepp, T., Brightsmith, D. J., Liboriussen, P., Halley, Y., Fisher, C. A., Owens, E. K., Viswanathan, G. G., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062415 · Cited by 56
“Application of the same analysis of divergence to a comparison of the scarlet macaw and zebra finch genomes revealed outlier macaw contigs (Figure 4, Table S14) which were predicted to possess coding and noncoding loci that were also characterized according to known function and/or independent human GWAS results (Tabl…”
ResultGilling, M., Rasmussen, H. B., Calløe, K., Sequeira, A. F., Baretto, M., Oliveira, G., Almeida, J., Lauritsen, M. B., Ullmann, R., Boonen, S. E., et al. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2013.00054 · Cited by 55
“Likely explanations are the apparently high degree of locus heterogeneity rendering it difficult to identify mutations in a gene in a convincing number of patients, the pleiotropic effects of many neuronal disease genes making the connection between genotype and phenotype less obvious (Duong et al., 2012; Iossifov et…”
BackgroundInfluentialSETD2 and DNMT3A screen in the Sotos-like syndrome French cohort
Tlemsani, C., Luscan, A., Leulliot, N., Bieth, É., Afenjar, A., Baujat, G., Doco‐Fenzy, M., Goldenberg, A., Lacombe, D., Lambert, L., et al. (2016) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2015-103638 · Cited by 57
Baugh, E. H., Simmons-Edler, R., Müller, C. L., Alford, R. F., Volfovsky, N., Lash, A., & Bonneau, R. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw120 · Cited by 60
Genetic causes of primary aldosteronism
Seidel, E., Schewe, J., & Scholl, U. I. (2019) · Experimental & Molecular Medicine · doi:10.1038/s12276-019-0337-9 · Cited by 56
Increased Ca2+ signaling in NRXN1α+/− neurons derived from ASD induced pluripotent stem cells
Avazzadeh, S., McDonagh, K., Reilly, J., Wang, Y., Boomkamp, S. D., McInerney, V., Krawczyk, J., Fitzgerald, J., Feerick, N., O’Sullivan, M., et al. (2019) · Molecular Autism · doi:10.1186/s13229-019-0303-3 · Cited by 57
Oligodendrocyte dysfunction due to Chd8 mutation gives rise to behavioral deficits in mice
Kawamura, A., Katayama, Y., Nishiyama, M., Shoji, H., Tokuoka, K., Ueta, Y., Miyata, M., Isa, T., Miyakawa, T., Hayashi‐Takagi, A., et al. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa036 · Cited by 58
The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain
Goodman, J. V., Yamada, T., Yang, Y., Kong, L., Wu, D. Y., Zhao, G., Gabel, H. W., & Bonni, A. (2020) · Nature Communications · doi:10.1038/s41467-020-17065-z · Cited by 57
Peters, B. A., Kermani, B. G., Alferov, O., Agarwal, M. R., McElwain, M. A., Gulbahce, N., Hayden, D. M., Tang, Y. T., Zhang, R. Y., Tearle, R. G., et al. (2015) · Genome Research · doi:10.1101/gr.181255.114 · Cited by 57
The G protein-coupled receptor GPR34 – The past 20 years of a grownup
Schöneberg, T., Meister, J., Knierim, A. B., & Schulz, A. (2018) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2018.04.008 · Cited by 54
Díaz‐Caneja, C. M., State, M. W., Hagerman, R. J., Jacquemont, S., Marín, Ó., Bagni, C., Umbricht, D., Simonoff, E. A., Andres-Trelles, F., Kaale, A., et al. (2021) · European Neuropsychopharmacology · doi:10.1016/j.euroneuro.2021.02.020 · Cited by 56
Pintacuda, G., Hsu, Y.-H. H., Tsafou, K., Li, K. W., Martín, J. M., Riseman, J., Biagini, J. C., Ching, J. K. T., Mena, D., Gonzalez‐Lozano, M. A., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2022.100250 · Cited by 53
Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes
Oksenberg, N., Haliburton, G., Eckalbar, W. L., Oren, I., Nishizaki, S. S., Murphy, K. K., Pollard, K. S., Birnbaum, R. Y., & Ahituv, N. (2014) · Translational Psychiatry · doi:10.1038/tp.2014.78 · Cited by 59
Targeted Exon Capture and Sequencing in Sporadic Amyotrophic Lateral Sclerosis
Couthouis, J., Raphael, A. R., Daneshjou, R., & Gitler, A. D. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004704 · Cited by 58
Protection of the Gametes Embryo/Fetus From Prenatal Radiation Exposure
Brent, R. L. (2014) · Health Physics · doi:10.1097/hp.0000000000000235 · Cited by 57
Bonora, E., Graziano, C., Minopoli, F., Bacchelli, E., Magini, P., Diquigiovanni, C., Lomartire, S., Bianco, F., Vargiolu, M., Parchi, P., et al. (2014) · EMBO Molecular Medicine · doi:10.1002/emmm.201303235 · Cited by 54
“Furthermore, large cohorts of trios of ID (Vissers et al , 2010) and ASD (Iossifov et al , 2012; Neale et al , 2012; O’Roak et al , 2012; Sanders et al , 2012) patients filtered for de novo variants (Veltman & Brunner, 2012) could be reassessed in order to verify whether additional maternally…”
Making headway with genetic diagnostics of intellectual disabilities
Willemsen, M. H., & Kleefstra, T. (2013) · Clinical Genetics · doi:10.1111/cge.12244 · Cited by 55
“Both clinical and molecular findings show a remarkable overlap between ‘autism cohorts’ and ‘ID cohorts’ suggesting common biological (etiological) pathways (52, 53).”
BackgroundBacchelli, E., Ceroni, F., Pinto, D., Lomartire, S., Giannandrea, M., D’Adamo, P., Bonora, E., Parchi, P., Tancredi, R., Battaglia, A., et al. (2014) · Journal of Neurodevelopmental Disorders · doi:10.1186/1866-1955-6-17 · Cited by 58
“Previous studies reported common single nucleotide polymorphism (SNP) association [4,5] and the occurrence of rare CNVs intersecting CTNNA3 in ASD cases [18-21].”
BackgroundGhaleiha, A., Alikhani, R., Kazemi, M.-R., Mohammadi, M.-R., Mohammadinejad, P., Zeinoddini, A., Hamedi, M., Shahriari, M., Keshavarzi, Z., & Akhondzadeh, S. (2016) · Journal of Child and Adolescent Psychopharmacology · doi:10.1089/cap.2015.0175 · Cited by 60
“Several mutations in genes encoding subunits of NMDA receptors, mostly de novo , have been reported in patients with ASD (O’Roak et al. 2012a, 2012b; Kenny et al. 2014), which are suspected to alter the function of these receptors and NMDA receptor-dependent plasticity (Lee et al. 2015).”
Ostrowski, P. J., Zachariou, A., Loveday, C., Beleza‐Meireles, A., Bértoli, M., Dean, J., Douglas, A. G. L., Ellis, I., Foster, A. C., Graham, J. M., et al. (2019) · American Journal of Medical Genetics Part C Seminars in Medical Genetics · doi:10.1002/ajmg.c.31749 · Cited by 55
Noh, H. J., Ponting, C. P., Boulding, H. C., Meader, S., Betancur, C., Buxbaum, J. D., Pinto, D., Marshall, C. R., Lionel, A. C., Scherer, S. W., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003523 · Cited by 54
“Recently, two largescale studies examining the exomes of autistic patients also identified an excess of protein-protein interactions between genes harbouring suspected causative mutations, reporting smaller networks with 49 [15] and 45 [14] participating genes of which”
BackgroundMethodPort, R. G., Gajewski, C. R., Krizman, E. N., Dow, H. C., Hirano, S., Brodkin, E. S., Carlson, G. C., Robinson, M. B., Roberts, T. P. L., & Siegel, S. J. (2017) · Neurobiology of Disease · doi:10.1016/j.nbd.2017.08.013 · Cited by 55
“ASD is associatedwith biological alterations affecting neuronal synapses (for review see Port et al., 2014), such as the those involving cell adhesion molecules encoded by the Cadherin/Protocadherin superfamily of genes (Kim et al., 2011; Morrow et al., 2008; O'Roak et al., 2012).”
BackgroundChin, C.-S., Behera, S., Khalak, A., Sedlazeck, F. J., Sudmant, P. H., Wagner, J., & Zook, J. M. (2023) · Nature Methods · doi:10.1038/s41592-023-01914-y · Cited by 61
“7), KATNAL2 (loss of function variant discovered in autistic proband 66,67 ) also has long tandem repeat variations in the HPRC pangenome cohort.”
BackgroundCreating a neural specific chromatin landscape by npBAF and nBAF complexes
Staahl, B. T., & Crabtree, G. R. (2013) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2013.09.003 · Cited by 52
Magen, I., & Gozes, I. (2013) · Neuropeptides · doi:10.1016/j.npep.2013.10.011 · Cited by 52
Point mutations as a source of de novo genetic disease
de Ligt, J., Veltman, J. A., & Vissers, L. E. L. M. (2013) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.01.007 · Cited by 55
“Similarly, based on initial studies in known disease genes, de novo point mutations seem to contribute to ASDs and schizophrenia [20,22,35,37,44,48] albeit at lower impact than for severe ID.”
BackgroundMethodResultInfluentialGenetics of Complex Traits in Psychiatry
Gelernter, J. E. (2014) · Biological Psychiatry · doi:10.1016/j.biopsych.2014.08.005 · Cited by 59
Wu, J., Li, Y., & Jiang, R. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004237 · Cited by 54
“In the literature (O'Roak et al. 2012), 41 mutations were reported as contributing to the risk of autism, based on functional damaging scores, functional evidence, or previous studies.”
BackgroundMethodResultInfluentialPearson, B. L., Corley, M. J., Vasconcellos, A., Blanchard, D. C., & Blanchard, R. J. (2013) · Behavioural Brain Research · doi:10.1016/j.bbr.2012.12.062 · Cited by 54
“A substantial proportion of the 25+ genes regulating HS [51] have been associated with autism: In particular, genes regulating HS synthesis (EXT1, EXT2: [52, 53]), and disaccharide residue sulfation/deacetylation (HS3ST5, HS3ST6, NDST4: [52, 54, 55]) have shown autism related variants.”
BackgroundThe Wnt Signaling Pathway and Related Therapeutic Drugs in Autism Spectrum Disorder
Bae, S. M., & Hong, J. Y. (2018) · Clinical Psychopharmacology and Neuroscience · doi:10.9758/cpn.2018.16.2.129 · Cited by 57
Abnormal mGluR-mediated synaptic plasticity and autism-like behaviours in Gprasp2 mutant mice
Edfawy, M., Guedes, J. R., Pereira, M. I., Laranjo, M., de Carvalho, M. L., Gao, X., Ferreira, P. A., Caldeira, G. L., Franco, L. O., Wang, D., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09382-9 · Cited by 56
Hosokawa, M., Takeuchi, A., Tanihata, J., Iida, K., Takeda, S., & Hagiwara, M. (2019) · iScience · doi:10.1016/j.isci.2019.02.023 · Cited by 54
T‐Brain‐1 – A Potential Master Regulator in Autism Spectrum Disorders
Chuang, H., Huang, T., & Hsueh, Y. (2015) · Autism Research · doi:10.1002/aur.1456 · Cited by 56
“Whole-exome sequencing has been applied to identify hundreds of de novo mutations that potentially cause autism spectrum disorders (ASDs) [Iossifov et al., 2012; Neale et al., 2012; O’Roak et al., 2012b; Sanders et al., 2012; Yu et al., 2013].”
BackgroundMethodInfluentialHaploinsufficiency predictions without study bias
Steinberg, J., Honti, F., Meader, S., & Webber, C. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv474 · Cited by 52
Bridging the Gap between Genotype and Phenotype via Network Approaches
Kim, Y.-A., & Przytycka, T. M. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2012.00227 · Cited by 55
“For example recent large scale studies in sporadic autism showed that 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected β-catenin/chromatin remodeling protein network (O’Roak et al., 2012).”
BackgroundDiscovery of rare variants for complex phenotypes
Kosmicki, J. A., Churchhouse, C. L., Rivas, M. A., & Neale, B. M. (2016) · Human Genetics · doi:10.1007/s00439-016-1679-1 · Cited by 54
“Such information can be incorporated from the sample being analyzed, as proposed in Madsen and Browning (Madsen and Browning 2009), or from a diverse population reference sample.”
BackgroundMethodInfluentialAssessing the reproducibility of exome copy number variations predictions
Hong, C. S., Singh, L. N., Mullikin, J. C., & Biesecker, L. G. (2016) · Genome Medicine · doi:10.1186/s13073-016-0336-6 · Cited by 55
Metadata
- Authors
- O’Roak, B. J., Vives, L., Girirajan, S., Karakoc, E., Krumm, N., Coe, B. P., Levy, R., Ko, A., Lee, C., Smith, J. D., Turner, E. H., Stanaway, I. B., Vernot, B., Malig, M., Baker, C., Reilly, B., Akey, J. M., Borenstein, E., Rieder, M. J., Nickerson, D. A., Bernier, R., Shendure, J., & Eichler, E. E.
- Affiliations
- University of Washington (US)
- Santa Fe Institute (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Shendure, Jay
- Eichler, Evan E.
- ORCID
- Venue
- Nature
- Published
- 2012-04-04
- Volume
- 485
- Issue
- 7397
- Pages
- 246-250
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3350576
- OpenAlex
- W1964444099
- Cited by
- 2,165
- References
- 50
- Citations by year
- 2026: 42 · 2025: 68 · 2024: 85 · 2023: 101 · 2022: 104 · 2021: 137 · 2020: 151 · 2019: 147 · 2018: 143 · 2017: 173 · 2016: 198 · 2015: 219 · 2014: 262 · 2013: 212 · 2012: 118
- FWCI
- 131.12
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Simons Foundation
- University of Washington
- Simons Foundation Autism Research Initiative (137578)
- National Institutes of Health
- National Heart, Lung, and Blood Institute (HL-102924, RC2HL102926, RC2HL102923, UC2HL102924, HL 1029230, R01HL094976, HL094976, RC2HL102924, UC2HL102926, HL-102926)
- National Human Genome Research Institute
- National Institute of Environmental Health Sciences (HHSN273200800010C)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD065285, R01HD065285)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- de novo mutations, paternal age, protein-protein interaction network, β-catenin signaling, chromatin remodeling, CHD8, SCN2A, NTNG1, locus heterogeneity, simplex families, autism risk genes, parent-child trios, unaffected siblings, recurrent mutations, p53 pathway, copy number variation
- MeSH terms
- Netrins, Autistic Disorder, DNA-Binding Proteins, Exons, Humans, Laminin, Nerve Tissue Proteins, Parents, Stochastic Processes, Transcription Factors, Reproducibility of Results, Sodium Channels, Signal Transduction, Tumor Suppressor Protein p53, Receptors, N-Methyl-D-Aspartate, Point Mutation, Genetic Predisposition to Disease, Siblings, beta Catenin, GPI-Linked Proteins, Exome, Protein Interaction Maps, NAV1.1 Voltage-Gated Sodium Channel
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