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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
“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]
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Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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 measuredThe cited source says what the claim attributes to it.
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
“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
“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
“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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“Integrin alpha 6 is a receptor for laminin in epithelial cells and laminin (the LAMC3 gene) has been suggested as a candidate gene for autism [86].”
BackgroundEpigenetic Mechanisms in Autism Spectrum Disorder
Zhubi, A., Cook, E. H., Guidotti, A., & Grayson, D. R. (2014) · International review of neurobiology · doi:10.1016/b978-0-12-801311-3.00006-8 · Cited by 56
Behavioral phenotype in five individuals with de novo mutations within the GRIN2B gene
Freunscht, I., Popp, B., Blank, R., Endele, S. U., Moog, U., Petri, H., Prott, E., Reis, A., Rübo, J., Zabel, B., et al. (2013) · Behavioral and Brain Functions · doi:10.1186/1744-9081-9-20 · Cited by 53
“All other reports dealing with GRIN2B mutations also focused on other aspects [7,10-14,17].”
BackgroundThe Yin and Yang of Autism Genetics: How Rare De Novo and Common Variations Affect Liability
Chaste, P., Roeder, K., & Devlin, B. (2017) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022647 · Cited by 54
“dnLoF mutations of chromodomain helicase DNA binding protein 8 (CHD8) increase ASD liability, as evidenced by their recurrence in dozens of independent probands (13, 101, 103, 121).”
BackgroundResultGayet‐Primo, J., Yaeger, D. B., Khanjian, R., & Puthussery, T. (2018) · Journal of Neuroscience · doi:10.1523/jneurosci.2440-17.2018 · Cited by 49
Citrigno, L., Muglia, M., Qualtieri, A., Spadafora, P., Cavalcanti, F., Pioggia, G., & Cerasa, A. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21165785 · Cited by 51
“These studies also show that the genetic vulnerability is not specific for ASD but it is shared with other neurodevelopmental conditions, further increasing the complexity [4,7] and suggesting the convergence on common dysfunctional pathways of the neuronal channel activity [8,9], neuronal communication [10,11], synap…”
BackgroundThe mechanisms of action of chromatin remodelers and implications in development and disease
Sahu, R. K., Singh, S., & Tomar, R. S. (2020) · Biochemical Pharmacology · doi:10.1016/j.bcp.2020.114200 · Cited by 50
Wei, H., Zhu, Y., Wang, T., Zhang, X., Zhang, K., & Zhang, Z. (2021) · Journal of Neural Transmission · doi:10.1007/s00702-021-02360-w · Cited by 53
Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network
Honti, F., Meader, S., & Webber, C. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003815 · Cited by 46
“Genes with de novo substitutions in patients with the same disorder [6–9,16–18] showed a tendency to be more interconnected Author Summary”
BackgroundMethodInfluentialFanale, D., Iovanna, J., Calvo, E. L., Berthézène, P., Belleau, P., Dagorn, J. C., Bronte, G., Cicero, G., Bazan, V., Rolfo, C. D., et al. (2014) · Expert Opinion on Therapeutic Targets · doi:10.1517/14728222.2014.920324 · Cited by 49
“Furthermore, rare mutations in the YTHDC2 gene have been identified in individuals with autism spectrum disorders [30].”
BackgroundA case of autism spectrum disorder arising from a de novo missense mutation in POGZ
Fukai, R., Hiraki, Y., Yofune, H., Tsurusaki, Y., Nakashima, M., Saitsu, H., Tanaka, F., Miyake, N., & Matsumoto, N. (2015) · Journal of Human Genetics · doi:10.1038/jhg.2015.13 · Cited by 48
Kim, Y. S., & State, M. W. (2014) · International Journal of Epidemiology · doi:10.1093/ije/dyu037 · Cited by 50
Wang, Q., Li, M., Yang, Z., Hu, X., Wu, H.-M., Ni, P., Ren, H., Deng, W., Li, M., Ma, X., et al. (2015) · Scientific Reports · doi:10.1038/srep18209 · Cited by 49
Epigenetic Basis of Neuronal and Synaptic Plasticity
Karpova, N. N., Sales, A. J., & Joca, S. R. L. (2016) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026616666160414124628 · Cited by 51
Developmental trajectories for young children with 16p11.2 copy number variation
Bernier, R., Hudac, C. M., Chen, Q., Zeng, C., Wallace, A. S., Gerdts, J., Earl, R. K., Peterson, J. L., Wolken, A., Peters, A., et al. (2017) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32525 · Cited by 50
“The explosion of recent findings fromsequencingstudies indicates thatcomplexdiseases, suchasautism spectrum disorder (ASD), are defined by a phenotype that does not have a unitary cause, but, rather, originates by contribution from multiple genetic and environmental factors [O’Roak et al., 2012; Sanders et al., 2015].”
BackgroundSelf-citationKuo, H., & Liu, F. (2018) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2018.00422 · Cited by 48
Huang, T., Yen, T., Qiu, L. R., Chuang, H., Lerch, J. P., & Hsueh, Y. (2019) · Molecular Autism · doi:10.1186/s13229-019-0257-5 · Cited by 47
Resolving the Synaptic versus Developmental Dichotomy of Autism Risk Genes
Heavner, W. E., & Smith, S. E. P. (2020) · Trends in Neurosciences · doi:10.1016/j.tins.2020.01.009 · Cited by 50
“Moreover, both NMDAR2A [52] and NMDAR2B [53] are ASD-linked genes.”
Riehmer, V., Erger, F., Herkenrath, P., Seland, S., Jackels, M., Wiater, A. H., Heller, R., Beck, B. B., & Netzer, C. (2017) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.38285 · Cited by 47
CNTNAP4 deficiency in dopaminergic neurons initiates parkinsonian phenotypes
Zhang, W., Zhou, M., Lu, W., Gong, J., Gao, F., Li, Y., Xu, X., Lin, Y., Zhang, X., Ding, L., et al. (2020) · Theranostics · doi:10.7150/thno.40798 · Cited by 49
“Increasing evidence supports the fact that CNTNAP4 may be related to autism, childhood-onset schizophrenia, and epilepsy, highlighting the possible important role that CNTNAP4 may have in neurological development [14-17].”
BackgroundMKS1 regulates ciliary INPP5E levels in Joubert syndrome
Slaats, G. G. G., Isabella, C. R., Kroes, H. Y., Dempsey, J. C., Gremmels, H., Monroe, G. R., Phelps, I. G., Duran, K. J., Adkins, J. R., Kumar, S. A., et al. (2015) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2015-103250 · Cited by 47
Developmental neurogenetics and multimodal neuroimaging of sex differences in autism
Chen, C., & Horn, J. D. V. (2016) · Brain Imaging and Behavior · doi:10.1007/s11682-015-9504-3 · Cited by 55
Oberman, L. M., Ifert‐Miller, F., Najib, U., Bashir, S., Gonzalez–Heydrich, J., Picker, J. D., Rotenberg, A., & Pascual‐Leone, Á. (2016) · Journal of Child and Adolescent Psychopharmacology · doi:10.1089/cap.2015.0166 · Cited by 50
“Several recent large-scale exome sequencing and association studies support this claim (Iossi-fov et al. 2012; Neale et al. 2012; O’Roak et al. 2012).”
Girard, S., Bourassa, C. V., Perreault, L. L., Legault, M., Barhdadi, A., Ambalavanan, A., Brendgen, M. R., Vitaro, F., Noreau, A., Dionne, G., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0164212 · Cited by 49
Li, N., Xu, Y., Li, G., Yu, T., Yao, R., Wang, X., & Wang, J. (2017) · Medicine · doi:10.1097/md.0000000000006914 · Cited by 47
Jin, Z., Li, Z., Liu, Z., Jiang, Y. W., Cai, X., & Wu, J. (2017) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12383 · Cited by 51
“Another study revealed that highly probable ASD genes tended to be more closely connected in a co-expression network, especially in specific regions of mid-fetal deep cortical projection neurons (Willsey et al., 2013).”
BackgroundResultInfluentialKalsner, L., Twachtman‐Bassett, J., Tokarski, K., Stanley, C. M., Dumont-Mathieu, T. M., Cotney, J. L., & Chamberlain, S. J. (2017) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.354 · Cited by 48
“Several genes which have been consistently found to contribute to ASD risk, such as CHD8 (Neale et al., 2012; O’Roak et al., 2012; Talkowski et al., 2012), were not fully assessed in our analysis as they were not included in the gene panel for the majority of our patients.”
BackgroundInfluentialRebuilding essential active zone functions within a synapse
Tan, C., Wang, S. S. H., de Nola, G., & Kaeser, P. S. (2022) · Neuron · doi:10.1016/j.neuron.2022.01.026 · Cited by 40
Ellis, S. E., Panitch, R., West, A. B., & Arking, D. E. (2016) · Translational Psychiatry · doi:10.1038/tp.2016.87 · Cited by 48
Sørensen, I. F., Edwards, S. M., Rohde, P. D., & Sørensen, P. (2017) · Scientific Reports · doi:10.1038/s41598-017-02281-3 · Cited by 47
Discovery of Rare Mutations in Autism: Elucidating Neurodevelopmental Mechanisms
Uzun, E. D. G., Sciarra, L. N., Maguire, A. M., Pescosolido, M. F., van Dyck, L. I., & Morrow, E. M. (2015) · Neurotherapeutics · doi:10.1007/s13311-015-0363-9 · Cited by 45
“Such single-hit genes provide important data, but it is difficult to interpret whether they are truly associated with ASD without recurrent hits [3–5, 176].”
BackgroundInfluentialThe Social Brain Network and Autism
Misra, V. (2014) · Annals of Neurosciences · doi:10.5214/ans.0972.7531.210208 · Cited by 48
“3 mutations, deletions Structural and functional organization of the dendritic spine and synaptic junction Schizophrenia, ASds, Id (34) HTR3A 11q23.”
BackgroundAn emerging role for Wnt and GSK3 signaling pathways in schizophrenia
Singh, K. K. (2013) · Clinical Genetics · doi:10.1111/cge.12111 · Cited by 46
“CHD7 and CHD8) have recently been discovered in autism, suggesting defects in Wnt signaling may generally underlie neuropsychiatric disorders (Table 1) (39, 40).”
BackgroundGenome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism
Papale, L. A., Zhang, Q., Li, S., Chen, K., Keleş, S., & Alisch, R. S. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv411 · Cited by 46
Autism Spectrum Disorder - A Complex Genetic Disorder
Ivanov, H. Y., Stoyanova, V. K., Popov, N. T., & Vachev, T. I. (2015) · Folia Medica · doi:10.1515/folmed-2015-0015 · Cited by 46
Merner, N. D., d’Arc, B. F., Bell, S. C., Maussion, G., Peng, H., Gauthier, J., Crapper, L., Hamdan, F. F., Michaud, J. L., Mottron, L., et al. (2016) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.37566 · Cited by 48
Neural stem cells in neuropsychiatric disorders
Sacco, R., Cacci, E., & Novarino, G. (2017) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2017.12.005 · Cited by 48
Sceniak, M. P., Fedder-Semmes, K. N., Wang, Q., Droubi, S., Babcock, K., Patwardhan, S., Wright-Zornes, J., Pham, L., & Sabo, S. L. (2019) · Journal of Cell Science · doi:10.1242/jcs.232892 · Cited by 50
VLDL-specific increases of fatty acids in autism spectrum disorder correlate with social interaction
Usui, N., Iwata, K., Miyachi, T., Takagai, S., Wakusawa, K., Nara, T., Tsuchiya, K. J., Matsumoto, K., Kurita, D., Kameno, Y., et al. (2020) · EBioMedicine · doi:10.1016/j.ebiom.2020.102917 · Cited by 45
“Among the lipoprotein-related genes, HDL binding protein (HDLBP) [85, 86], LDL receptor related protein 2 (LRP2) [87], and LPL [88], also were reported as ASD genes.”
BackgroundLi, W., & Mills, A. A. (2014) · Epigenomics · doi:10.2217/epi.14.31 · Cited by 46
Abnormal neocortex arealization and Sotos-like syndrome–associated behavior in Setd2 mutant mice
Xu, L., Zheng, Y., Li, X., Wang, A., Huo, D., Li, Q., Wang, S., Luo, Z., Liu, Y., Xu, F., et al. (2021) · Science Advances · doi:10.1126/sciadv.aba1180 · Cited by 45
Davunetide: Peptide Therapeutic in Neurological Disorders
Magen, I., & Gozes, I. (2014) · Current Medicinal Chemistry · doi:10.2174/0929867321666140217124945 · Cited by 45
“At the gene level, deletion of the ADNP locus was found to be associated with mental retardation [28] and recent findings discovered ADNP mutations in autism Recently, de novo mutations in the ADNP gene were found in individuals with autism [29, 30].”
BackgroundYu, J., Crouch, J. M., Jamal, S. M., Bamshad, M. J., & Tabor, H. K. (2014) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.36610 · Cited by 45
“2014 Wiley Periodicals, Inc. Key words: exome sequencing; whole genome sequencing; return of results Correspondence to: Joon-Ho Yu, M.P.H., Ph.D., Department of Pediatrics, School of Medicine, University of Washington, Box 356320, 1959 NE Pacific St. HSB RR349, Seattle, WA 98195.”
BackgroundCurrent Progress and Challenges in the Search for Autism Biomarkers
Voineagu, I., & Yoo, H. J. (2013) · Disease Markers · doi:10.1155/2013/476276 · Cited by 50
“[59] B.”
BackgroundNovel roles of amyloid-beta precursor protein metabolites in fragile X syndrome and autism
Westmark, C. J., Sokol, D. K., Maloney, B., & Lahiri, D. K. (2016) · Molecular Psychiatry · doi:10.1038/mp.2016.134 · Cited by 45
Hoang, N., Cytrynbaum, C. S., & Scherer, S. W. (2017) · Patient Education and Counseling · doi:10.1016/j.pec.2017.07.029 · Cited by 46
Regulatory genes and pathways disrupted in autism spectrum disorders
Ayhan, F., & Konopka, G. (2018) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2018.08.017 · Cited by 46
Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma
Hoffman, M., Gillmor, A. H., Kunz, D. J., Johnston, M. J. G., Nikolić, A., Narta, K., Zarrei, M., King, J., Ellestad, K. I., Dang, N. H., et al. (2019) · Cancer Research · doi:10.1158/0008-5472.can-18-3441 · Cited by 47
“The expected rates of emergence of de novo nsSNVs is very low, based on recent literature evidence on trios that included probands affected by disorders with high heritability (48,49).”
BackgroundYin, F., Futagawa, T., Li, D., Ma, Y., Lu, M., Lu, L., Li, S., Chen, Y., Cao, Y., Yang, Z. Z., et al. (2014) · Stem Cells and Development · doi:10.1089/scd.2014.0261 · Cited by 44
“Both Caspr2 and Caspr4 have recently been identified as risk genes of ASDs [10,18].”
BackgroundAstrocytic β-catenin signaling via TCF7L2 regulates synapse development and social behavior
Szewczyk, Ł. M., Lipiec, M. A., Liszewska, E., Meyza, K. Z., Urban‐Ciećko, J., Kondrakiewicz, L., Goncerzewicz, A., Rafalko, K., Krawczyk, T. G., Bogaj, K., et al. (2023) · Molecular Psychiatry · doi:10.1038/s41380-023-02281-y · Cited by 49
“The CTNNB1 gene, which encodes β -catenin, and TCF7L2 are high-con fi dence risk genes that are implicated in psychiatric disorders [1], particularly autism spectrum disorder (ASD) [2 – 4], characterized by de fi cits in social interaction and communication.”
BackgroundCopy number variation associated with meiotic arrest in idiopathic male infertility
Eggers, S., DeBoer, K., van den Bergen, J., Gordon, L., White, S. J., Jamsai, D., McLachlan, R. I., Sinclair, A. H., & O’Bryan, M. K. (2014) · Fertility and Sterility · doi:10.1016/j.fertnstert.2014.09.030 · Cited by 45
A rare WNT1 missense variant overrepresented in ASD leads to increased Wnt signal pathway activation
Martin, P.-M., Yang, X., Robin, N. C., Lam, E. T., Rabinowitz, J. S., Erdman, C. A., Quinn, J. F., Weiss, L. A., Hamilton, S. P., Kwok, P.-Y., et al. (2013) · Translational Psychiatry · doi:10.1038/tp.2013.75 · Cited by 44
Big data challenges and opportunities in high-throughput sequencing
Ward, R. M., Schmieder, R., Highnam, G., & Mittelman, D. (2013) · Systems Biomedicine · doi:10.4161/sysb.24470 · Cited by 44
Genetic diagnosis of autism spectrum disorders: The opportunity and challenge in the genomics era
Jiang, Y., Wang, Y., Xu, X., Choy, K. W., Pursley, A. N., & Cheung, S. W. (2014) · Critical Reviews in Clinical Laboratory Sciences · doi:10.3109/10408363.2014.910747 · Cited by 47
“P1894L (1 mis-sense in additional cases) (58) 3 AMT Aminomethyltransferase p.”
BackgroundInfluentialBowers, J. M., Perez‐Pouchoulen, M., Roby, C. R., Ryan, T. E., & McCarthy, M. M. (2014) · Endocrinology · doi:10.1210/en.2014-1486 · Cited by 44
Specific Roles of NMDA Receptor Subunits in Mental Disorders
Yamamoto, H., Hagino, Y., Kasai, S., & Ikeda, K. (2015) · Current Molecular Medicine · doi:10.2174/1566524015666150330142807 · Cited by 48
“Genetic variants of GluN2A and GluN2B in human have reportedly been associated with mental retardation, epilepsy, and autism [22, 57, 58].”
BackgroundA network of autism linked genes stabilizes two pools of synaptic GABAA receptors
Tong, X.-J., Hu, Z., Liu, Y., Anderson, D. C., & Kaplan, J. M. (2015) · eLife · doi:10.7554/elife.09648 · Cited by 43
Inborn error metabolic screening in individuals with nonsyndromic autism spectrum disorders
Campistol, J., Díez‐Juan, M., Póo, L. C., Miguel, A. F., Casado, M., Cazorla, À. G., Lozano, R., & Artuch, R. (2016) · Developmental Medicine & Child Neurology · doi:10.1111/dmcn.13114 · Cited by 44
Schmunk, G., Nguyen, R. L., Ferguson, D. L., Kumar, K., Parker, I., & Gargus, J. J. (2017) · Scientific Reports · doi:10.1038/srep40740 · Cited by 44
Vallée, A., Vallée, J.-N., & Lecarpentier, Y. (2018) · Molecular Psychiatry · doi:10.1038/s41380-018-0131-4 · Cited by 44
“Genomic analysis of ASD has revealed a major role for several core WNT/β-catenin pathway loci such as WNT1 [67], WNT2 [61], WNT3 [68], WNT7A [69], APC [70], βcatenin [9, 71], TCF4 [72, 73], and TCF7 [74].”
BackgroundDissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders
Chow, J. C., Jensen, M., Amini, H., Hormozdiari, F., Penn, O., Shifman, S., Girirajan, S., & Hormozdiari, F. (2019) · Genome Medicine · doi:10.1186/s13073-019-0678-y · Cited by 45
Self-citation
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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