• American Psychiatric Association. Diagnostic and statistical manual of mental disorders. 5th ed. 2013.

    Book 

    Google Scholar
     

  • Ramaswami G, Geschwind DH. Genetics of autism spectrum disorder. Handb Clin Neurol. 2018;147:321–9.

    PubMed 
    Article 

    Google Scholar
     

  • Chaste P, Roeder K, Devlin B. The Yin and Yang of autism genetics: how rare de novo and common variations affect liability. Annu Rev Genomics Hum Genet. 2017;18:167–87.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Hodges H, Fealko C, Soares N. Autism spectrum disorder: definition, epidemiology, causes, and clinical evaluation. Transl Pediatr. 2020;9(Suppl 1):S55-65.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Veatch OJ, Maxwell-Horn AC, Malow BA. Sleep in autism spectrum disorders. Curr Sleep Med Rep. 2015;1:131–40.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Veatch OJ, Sutcliffe JS, Warren ZE, Keenan BT, Potter MH, Malow BA. Shorter sleep duration is associated with social impairment and comorbidities in ASD. Autism Res. 2017;10:1221–38.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Cohen S, Fulcher BD, Rajaratnam SMW, Conduit R, Sullivan JP, St Hilaire MA, et al. Sleep patterns predictive of daytime challenging behavior in individuals with low-functioning autism. Autism Res. 2018;11:391–403.

    PubMed 
    Article 

    Google Scholar
     

  • Malow B, Adkins KW, McGrew SG, Wang L, Goldman SE, Fawkes D, et al. Melatonin for sleep in children with autism: a controlled trial examining dose, tolerability, and outcomes. J Autism Dev Disord. 2012;42:1729–37 author reply 1738.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Visscher PM, Yang J. A plethora of pleiotropy across complex traits. Nat Genet. 2016;48:707–8.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Halu A, De Domenico M, Arenas A, Sharma A. The multiplex network of human diseases. NPJ Syst Biol Appl. 2019;5:15.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ingiosi AM, Schoch H, Wintler T, Singletary KG, Righelli D, Roser LG, et al. Shank3 modulates sleep and expression of circadian transcription factors. Elife. 2019;8: e42819.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Angelakos CC, Watson AJ, O’Brien WT, Krainock KS, Nickl-Jockschat T, Abel T. Hyperactivity and male-specific sleep deficits in the 16p11.2 deletion mouse model of autism. Autism Res. 2017;10:572–84.

    PubMed 
    Article 

    Google Scholar
     

  • Gupta T, Morgan HR, Bailey JA, Certel SJ. Functional conservation of MBD proteins: MeCP2 and Drosophila MBD proteins alter sleep. Genes Brain Behav. 2016;15:757–74.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Mullegama SV, Pugliesi L, Burns B, Shah Z, Tahir R, Gu Y, et al. MBD5 haploinsufficiency is associated with sleep disturbance and disrupts circadian pathways common to Smith-Magenis and fragile X syndromes. Eur J Hum Genet. 2015;23:781–9.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Veatch OJ, Pendergast JS, Allen MJ, Leu RM, Johnson CH, Elsea SH, et al. Genetic variation in melatonin pathway enzymes in children with autism spectrum disorder and comorbid sleep onset delay. J Autism Dev Disord. 2015;45:100–10.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Doldur-Balli F, Imamura T, Veatch OJ, Gong NN, Lim DC, Hart MP, et al. Synaptic dysfunction connects autism spectrum disorder and sleep disturbances: a perspective from studies in model organisms. Sleep Med Rev. 2022;62: 101595.

    PubMed 
    Article 

    Google Scholar
     

  • Abel T, Havekes R, Saletin JM, Walker MP. Sleep, plasticity and memory from molecules to whole-brain networks. Curr Biol. 2013;23:R774-788.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Veatch OJ, Keenan BT, Gehrman PR, Malow BA, Pack AI. Pleiotropic genetic effects influencing sleep and neurological disorders. Lancet Neurol. 2017;16:158–70.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Veatch OJ, Reynolds A, Katz T, Weiss SK, Loh A, Wang L, et al. Sleep in children with autism spectrum disorders: how are measures of parent report and actigraphy related and affected by sleep education? Behav Sleep Med. 2016;14:665–76.

    PubMed 
    Article 

    Google Scholar
     

  • Marinelli M, Pappa I, Bustamante M, Bonilla C, Suarez A, Tiesler CM, et al. Heritability and genome-wide association analyses of sleep duration in children: the EAGLE consortium. Sleep. 2016;39:1859–69.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Fischbach GD, Lord C. The Simons Simplex Collection: a resource for identification of autism genetic risk factors. Neuron. 2010;68:192–5.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Abrahams BS, Arking DE, Campbell DB, Mefford HC, Morrow EM, Weiss LA, et al. SFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs). Mol Autism. 2013;4:36.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Banerjee-Basu S, Packer A. SFARI Gene: an evolving database for the autism research community. Dis Model Mech. 2010;3:133–5.

    PubMed 
    Article 

    Google Scholar
     

  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv. 2012. https://doi.org/10.48550/arXiv.1207.3907.

  • Iossifov I, O’Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 2014;515:216–21.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Sanders SJ, He X, Willsey AJ, Ercan-Sencicek AG, Samocha KE, Cicek AE, et al. Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron. 2015;87:1215–33.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Krumm N, Turner TN, Baker C, Vives L, Mohajeri K, Witherspoon K, et al. Excess of rare, inherited truncating mutations in autism. Nat Genet. 2015;47:582–8.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Quinlan AR. BEDTools: the Swiss-army tool for genome feature analysis. Curr Protoc Bioinformatics. 2014;47:11.12.1-34.

    Article 

    Google Scholar
     

  • McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, et al. The Ensembl variant effect predictor. Genome Biol. 2016;17:122.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc. 2015;10:1556–66.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Res. 2001;11:863–74.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013;Chapter 7:Unit7.20.

    PubMed 

    Google Scholar
     

  • Schwarz JM, Rödelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7:575–6.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Reva B, Antipin Y, Sander C. Determinants of protein function revealed by combinatorial entropy optimization. Genome Biol. 2007;8:R232.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Chun S, Fay JC. Identification of deleterious mutations within three human genomes. Genome Res. 2009;19:1553–61.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Shihab HA, Rogers MF, Gough J, Mort M, Cooper DN, Day INM, et al. An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics. 2015;31:1536–43.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the functional effect of amino acid substitutions and indels. PLoS ONE. 2012;7: e46688.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K, et al. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet. 2015;24:2125–37.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Jagadeesh KA, Wenger AM, Berger MJ, Guturu H, Stenson PD, Cooper DN, et al. M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nat Genet. 2016;48:1581–6.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47:D607–13.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium Nat Genet. 2000;25:25–9.

    CAS 
    PubMed 

    Google Scholar
     

  • The Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. 2019;47:D330–8.

    Article 
    CAS 

    Google Scholar
     

  • Alexa A, Rahnenführer J, Lengauer T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 2006;22:1600–7.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Grossmann S, Bauer S, Robinson PN, Vingron M. Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics. 2007;23:3024–31.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, et al. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009;25:288–9.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Serdarevic F, Tiemeier H, Jansen PR, Alemany S, Xerxa Y, Neumann A, et al. Polygenic risk scores for developmental disorders, neuromotor functioning during infancy, and autistic traits in childhood. Biol Psychiatry. 2020;87:132–8.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Torkamani A, Wineinger NE, Topol EJ. The personal and clinical utility of polygenic risk scores. Nat Rev Genet. 2018;19:581–90.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Rojas DC. The role of glutamate and its receptors in autism and the use of glutamate receptor antagonists in treatment. J Neural Transm (Vienna). 2014;121:891–905.

    CAS 
    Article 

    Google Scholar
     

  • Scammell TE, Arrigoni E, Lipton JO. Neural circuitry of wakefulness and sleep. Neuron. 2017;93:747–65.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Vyazovskiy VV, Olcese U, Lazimy YM, Faraguna U, Esser SK, Williams JC, et al. Cortical firing and sleep homeostasis. Neuron. 2009;63:865–78.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Porkka-Heiskanen T. Sleep homeostasis. Curr Opin Neurobiol. 2013;23:799–805.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Krone LB, Yamagata T, Blanco-Duque C, Guillaumin MCC, Kahn MC, van der Vinne V, et al. A role for the cortex in sleep-wake regulation. Nat Neurosci. 2021;24:1210–5.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Morairty SR, Dittrich L, Pasumarthi RK, Valladao D, Heiss JE, Gerashchenko D, et al. A role for cortical nNOS/NK1 neurons in coupling homeostatic sleep drive to EEG slow wave activity. Proc Natl Acad Sci U S A. 2013;110:20272–7.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Jenni OG, Achermann P, Carskadon MA. Homeostatic sleep regulation in adolescents. Sleep. 2005;28:1446–54.

    PubMed 
    Article 

    Google Scholar
     

  • Goldman SE, Alder ML, Burgess HJ, Corbett BA, Hundley R, Wofford D, et al. Characterizing sleep in adolescents and adults with autism spectrum disorders. J Autism Dev Disord. 2017;47:1682–95.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ballester P, Martínez MJ, Javaloyes A, Inda M-D-M, Fernández N, Gázquez P, et al. Sleep problems in adults with autism spectrum disorder and intellectual disability. Autism Res. 2019;12:66–79.

    PubMed 
    Article 

    Google Scholar
     

  • Smemo S, Tena JJ, Kim K-H, Gamazon ER, Sakabe NJ, Gómez-Marín C, et al. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. 2014;507:371–5.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Lane JM, Liang J, Vlasac I, Anderson SG, Bechtold DA, Bowden J, et al. Genome-wide association analyses of sleep disturbance traits identify new loci and highlight shared genetics with neuropsychiatric and metabolic traits. Nat Genet. 2017;49:274–81.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Krieger I, Grossman-Giron A, Comaneshter D, Weinstein O, Kridin K, Cohen AD, et al. The co-occurrence of autistic spectrum disorder and schizophrenia: a nationwide population-based study. J Psychiatr Res. 2021;138:280–3.

    PubMed 
    Article 

    Google Scholar
     

  • Zhai L, Zhang H, Zhang D. Sleep duration and depression among adults: a meta-analysis of prospective studies. Depress Anxiety. 2015;32:664–70.

    PubMed 
    Article 

    Google Scholar
     

  • Zhang J, Paksarian D, Lamers F, Hickie IB, He J, Merikangas KR. Sleep patterns and mental health correlates in US adolescents. J Pediatr. 2017;182:137–43.

    PubMed 
    Article 

    Google Scholar
     

  • Fang H, Wu Y, Narzisi G, O’Rawe JA, Barrón LTJ, Rosenbaum J, et al. Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med. 2014;6:89.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–24.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Pejaver V, Mooney SD, Radivojac P. Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges. Hum Mutat. 2017;38:1092–108.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Walters-Sen LC, Hashimoto S, Thrush DL, Reshmi S, Gastier-Foster JM, Astbury C, et al. Variability in pathogenicity prediction programs: impact on clinical diagnostics. Mol Genet Genomic Med. 2015;3:99–110.

    PubMed 
    Article 

    Google Scholar
     

  • Care MA, Needham CJ, Bulpitt AJ, Westhead DR. Deleterious SNP prediction: be mindful of your training data! Bioinformatics. 2007;23:664–72.

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Knecht C, Mort M, Junge O, Cooper DN, Krawczak M, Caliebe A. IMHOTEP-a composite score integrating popular tools for predicting the functional consequences of non-synonymous sequence variants. Nucleic Acids Res. 2017;45: e13.

    PubMed 

    Google Scholar
     

  • Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, et al. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med. 2017;9:113.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Skunca N, Altenhoff A, Dessimoz C. Quality of computationally inferred gene ontology annotations. PLoS Comput Biol. 2012;8: e1002533.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Rights and permissions

    Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

    Disclaimer:

    This article is autogenerated using RSS feeds and has not been created or edited by OA JF.

    Click here for Source link (https://www.biomedcentral.com/)