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New Horizons for Molecular Genetics Diagnostic and Research in Autism Spectrum Disorder

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Personalized Food Intervention and Therapy for Autism Spectrum Disorder Management

Part of the book series: Advances in Neurobiology ((NEUROBIOL,volume 24))

Abstract

Autism spectrum disorder (ASD) is a highly heritable, heterogeneous, and complex pervasive neurodevelopmental disorder (PND) characterized by distinctive abnormalities of human cognitive functions, social interaction, and speech development.

Nowadays, several genetic changes including chromosome abnormalities, genetic variations, transcriptional epigenetics, and noncoding RNA have been identified in ASD. However, the association between these genetic modifications and ASDs has not been confirmed yet.

The aim of this review is to summarize the key findings in ASD from genetic viewpoint that have been identified from the last few decades of genetic and molecular research.

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References

  1. NHGRI. (2017). Learning about autism [Online]. Bethesda, MD: National Human Genome Research Institute. Retrieved from https://www.genome.gov/25522099/learning-aboutautism/

  2. De Rubeis, S., & Buxbaum, J. D. (2015). Genetics and genomics of autism spectrum disorder: Embracing complexity. Human Molecular Genetics, 24(R1), R24–R31.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. Geschwind, D. H., & State, M. W. (2015). Gene hunting in autism spectrum disorder: On the path to precision medicine. Lancet Neurology, 14(11), 1109–1120.

    Article  PubMed  Google Scholar 

  4. Ronemus, M., Iossifov, I., Levy, D., & Wigler, M. (2014). The role of de novo mutations in the genetics of autism spectrum disorders. Nature Reviews Genetics, 15(2), 133–141.

    Article  CAS  PubMed  Google Scholar 

  5. De Rubeis, S., He, X., Goldberg, A. P., Poultney, C. S., Samocha, K., Cicek, A. E., et al. (2014). Synaptic, transcriptional and chromatin genes disrupted in autism. Nature, 515(7526), 209–215.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. SFARI. The Simons Simplex Collection. 2011 2011/09/16/; Available from: https://www.sfari.org/funded-project/the-simons-simplex-collection.

  7. Consortium, A.S. Advancing autism research. 2019; Available from: https://genome.emory.edu/ASC.

  8. Treffert, D. A. (1970). Epidemiology of infantile autism. Archives of General Psychiatry, 22(5), 431–438.

    Article  CAS  PubMed  Google Scholar 

  9. Bailey, A., Le Couteur, A., Gottesman, I., Bolton, P., Simonoff, E., Yuzda, E., et al. (1995). Autism as a strongly genetic disorder: Evidence from a British twin study. Psychological Medicine, 25(1), 63–77.

    Article  CAS  PubMed  Google Scholar 

  10. Colvert, E., Tick, B., McEwen, F., Stewart, C., Curran, S. R., Woodhouse, E., et al. (2015). Heritability of autism spectrum disorder in a UK population-based twin sample. JAMA Psychiatry, 72(5), 415–423.

    PubMed  PubMed Central  Google Scholar 

  11. Hallmayer, J., Cleveland, S., Torres, A., Phillips, J., Cohen, B., Torigoe, T., et al. (2011). Genetic heritability and shared environmental factors among twin pairs with autism. Archives of General Psychiatry, 68(11), 1095–1102.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Rosenberg, R. E., Law, J. K., Yenokyan, G., McGready, J., Kaufmann, W. E., & Law, P. A. (2009). Characteristics and concordance of autism spectrum disorders among 277 twin pairs. Archives of Pediatrics & Adolescent Medicine, 163(10), 907–914.

    Article  Google Scholar 

  13. Gaugler, T., Klei, L., Sanders, S. J., Bodea, C. A., Goldberg, A. P., Lee, A. B., et al. (2014). Most genetic risk for autism resides with common variation. Nature Genetics, 46(8), 881–885.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Bonnet-Brilhault, F. (2011). Genotype/phenotype correlation in autism: Genetic models and phenotypic characterization. Encephale, 37(1), 68–74.

    Article  CAS  PubMed  Google Scholar 

  15. Devlin, B., & Scherer, S. W. (2012). Genetic architecture in autism spectrum disorder. Current Opinion in Genetics & Development, 22(3), 229–237.

    Article  CAS  Google Scholar 

  16. Lintas, C., & Persico, A. M. (2009). Autistic phenotypes and genetic testing: State-of-the-art for the clinical geneticist. Journal of Medical Genetics, 46(1), 1–8.

    Article  CAS  PubMed  Google Scholar 

  17. Toriello, H. V. (2012). Approach to the genetic evaluation of the child with autism. Pediatric Clinics of North America, 59(1), 113–128. xi.

    Article  PubMed  Google Scholar 

  18. Persico, A. M., & Napolioni, V. (2013). Autism genetics. Behavioural Brain Research, 251, 95–112.

    Article  PubMed  Google Scholar 

  19. Pieretti, M., Zhang, F. P., Fu, Y. H., Warren, S. T., Oostra, B. A., Caskey, C. T., et al. (1991). Absence of expression of the FMR-1 gene in fragile X syndrome. Cell, 66(4), 817–822.

    Article  CAS  PubMed  Google Scholar 

  20. Amir, R. E., Van den Veyver, I. B., Wan, M., Tran, C. Q., Francke, U., & Zoghbi, H. Y. (1999). Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpGbinding protein 2. Nature Genetics, 23(2), 185–188.

    Article  CAS  PubMed  Google Scholar 

  21. Ramocki, M. B., Tavyev, Y. J., & Peters, S. U. (2010). The MECP2 duplication syndrome. American Journal of Medical Genetics Part A, 152A(5), 1079–1088.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Ramocki, M. B., Peters, S. U., Tavyev, Y. J., Zhang, F., Carvalho, C. M., Schaaf, C. P., et al. (2009). Autism and other neuropsychiatric symptoms are prevalent in individuals with MeCP2 duplication syndrome. Annals of Neurology, 66(6), 771–782.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Chahrour, M., & Zoghbi, H. Y. (2007). The story of Rett syndrome: from clinic to neurobiology. Neuron, 56(3), 422–437.

    Article  CAS  PubMed  Google Scholar 

  24. Lugtenberg, D., Kleefstra, T., Oudakker, A. R., Nillesen, W. M., Yntema, H. G., Tzschach, A., et al. (2009). Structural variation in Xq28: MECP2 duplications in 1% of patients with unexplained XLMR and in 2% of male patients with severe encephalopathy. European Journal of Human Genetics, 17(4), 444–453.

    Article  CAS  PubMed  Google Scholar 

  25. Wiznitzer, M. (2004). Autism and tuberous sclerosis. Journal of Child Neurology, 19(9), 675–679.

    Article  PubMed  Google Scholar 

  26. Jeste, S. S., Sahin, M., Bolton, P., Ploubidis, G. B., & Humphrey, A. (2008). Characterization of autism in young children with tuberous sclerosis complex. Journal of Child Neurology, 23(5), 520–525.

    Article  PubMed  Google Scholar 

  27. Depienne, C., Moreno-De-Luca, D., Heron, D., Bouteiller, D., Gennetier, A., Delorme, R., et al. (2009). Screening for genomic rearrangements and methylation abnormalities of the 15q11-q13 region in autism spectrum disorders. Biological Psychiatry, 66(4), 349–359.

    Article  CAS  PubMed  Google Scholar 

  28. Cook Jr., E. H., Lindgren, V., Leventhal, B. L., Courchesne, R., Lincoln, A., Shulman, C., et al. (1997). Autism or atypical autism in maternally but not paternally derived proximal 15q duplication. American Journal of Human Genetics, 60(4), 928.

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Kielinen, M., Rantala, H., Timonen, E., Linna, S.-L., & Moilanen, I. (2004). Associated medical disorders and disabilities in children with autistic disorder: A population-based study. Autism, 8(1), 49–60.

    Article  PubMed  Google Scholar 

  30. Tucker, T., Giroux, S., Clément, V., Langlois, S., Friedman, J. M., & Rousseau, F. (2013). Prevalence of selected genomic deletions and duplications in a French–Canadian population-based sample of newborns. Molecular Genetics & Genomic Medicine, 1(2), 87.

    Article  CAS  Google Scholar 

  31. Wassink, T. H., Piven, J., & Patil, S. R. (2001). Chromosomal abnormalities in a clinic sample of individuals with autistic disorder. Psychiatric Genetics, 11(2), 57–63.

    Article  CAS  PubMed  Google Scholar 

  32. Al Ageeli, E., Drunat, S., Delanoë, C., Perrin, L., Baumann, C., Capri, Y., et al. (2014). Duplication of the 15q11-q13 region: Clinical and genetic study of 30 new cases. European Journal of Medical Genetics, 57(1), 5–14.

    Article  PubMed  Google Scholar 

  33. Bucan, M., Abrahams, B. S., Wang, K., Glessner, J. T., Herman, E. I., Sonnenblick, L. I., et al. (2009). Genome-wide analyses of exonic copy number variants in a family-based study point to novel autism susceptibility genes. PLoS Genetics, 5(6), e1000536.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Hogart, A., Wu, D., LaSalle, J. M., & Schanen, N. C. (2010). The comorbidity of autism with the genomic disorders of chromosome 15q11.2-q13. Neurobiology of Disease, 38(2), 181–191.

    Article  CAS  PubMed  Google Scholar 

  35. Menold, M. M., Shao, Y., Wolpert, C. M., Donnelly, S. L., Raiford, K. L., Martin, E. R., et al. (2001). Association analysis of chromosome 15 Gabaa receptor subunit genes in autistic disorder. Journal of Neurogenetics, 15(3–4), 245–259.

    Article  CAS  PubMed  Google Scholar 

  36. Nishimura, Y., Martin, C. L., Vazquez-Lopez, A., Spence, S. J., Alvarez-Retuerto, A. I., Sigman, M., et al. (2007). Genome-wide expression profiling of lymphoblastoid cell lines distinguishes different forms of autism and reveals shared pathways. Human Molecular Genetics, 16(14), 1682–1698.

    Article  CAS  PubMed  Google Scholar 

  37. Puffenberger, E. G., Jinks, R. N., Wang, H., Xin, B., Fiorentini, C., Sherman, E. A., et al. (2012). A homozygous missense mutation in HERC2 associated with global developmental delay and autism spectrum disorder. Human Mutation, 33(12), 1639–1646.

    Article  CAS  PubMed  Google Scholar 

  38. Tan, E.-S., Yong, M.-H., Lim, E. C., Li, Z.-H., Brett, M. S., & Tan, E.-C. (2014). Chromosome 15q11-q13 copy number gain detected by array-CGH in two cases with a maternal methylation pattern. Molecular Cytogenetics, 7, 32.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Filges, I., Sparagana, S., Sargent, M., Selby, K., Schlade-Bartusiak, K., Lueder, G. T., et al. (2014). Brain MRI abnormalities and spectrum of neurological and clinical findings in three patients with proximal 16p11.2 microduplication. American Journal of Medical Genetics. Part A, 164A(8), 2003–2012.

    Article  PubMed  CAS  Google Scholar 

  40. Hanson, E., Nasir, R. H., Fong, A., Lian, A., Hundley, R., Shen, Y., et al. (2010). Cognitive and behavioral characterization of 16p11.2 deletion syndrome. Journal of Developmental and Behavioral Pediatrics, 31(8), 649–657.

    Article  PubMed  Google Scholar 

  41. Kumar, R. A., Marshall, C. R., Badner, J. A., Babatz, T. D., Mukamel, Z., Aldinger, K. A., et al. (2009). Association and mutation analyses of 16p11.2 Autism candidate genes. PLoS One, 4(2), e4582.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  42. Weiss, L. A., Shen, Y., Korn, J. M., Arking, D. E., Miller, D. T., Fossdal, R., et al. (2008). Association between microdeletion and microduplication at 16p11.2 and autism. The New England Journal of Medicine, 358(7), 667–675.

    Article  CAS  PubMed  Google Scholar 

  43. Golzio, C., Willer, J., Talkowski, M. E., Oh, E. C., Taniguchi, Y., Jacquemont, S., et al. (2012). KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant. Nature, 485(7398), 363–367.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Angkustsiri, K., Goodlin-Jones, B., Deprey, L., Brahmbhatt, K., Harris, S., & Simon, T. J. (2014). Social impairments in chromosome 22q11.2 deletion syndrome (22q11.2DS): Autism spectrum disorder or a different endophenotype? Journal of Autism and Developmental Disorders, 44(4), 739–746.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Hiramoto, T., Kang, G., Suzuki, G., Satoh, Y., Kucherlapati, R., Watanabe, Y., et al. (2011). Tbx1: Identification of a 22q11.2 gene as a risk factor for autism spectrum disorder in a mouse model. Human Molecular Genetics, 20(24), 4775–4785.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Mukaddes, N. M., & Herguner, S. (2007). Autistic disorder and 22q11.2 duplication. The World Journal of Biological Psychiatry, 8(2), 127–130.

    Article  PubMed  Google Scholar 

  47. Ou, Z., Berg, J. S., Yonath, H., Enciso, V. B., Miller, D. T., Picker, J., et al. (2008). Microduplications of 22q11.2 are frequently inherited and are associated with variable phenotypes. Genetics in Medicine, 10(4), 267–277.

    Article  PubMed  Google Scholar 

  48. Radoeva, P. D., Coman, I. L., Salazar, C. A., Gentile, K. L., Higgins, A. M., Middleton, F. A., et al. (2014). Association between autism Spectrum disorder (ASD) in individuals with Velo-cardio-facial (22q11.2 deletion) syndrome and PRODH and COMT genotypes. Psychiatric Genetics, 24(6), 269.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Squarcione, C., Torti, M. C., Di Fabio, F., & Biondi, M. (2013). 22q11 deletion syndrome: A review of the neuropsychiatric features and their neurobiological basis. Neuropsychiatric Disease and Treatment, 9, 1873–1884.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  50. Vorstman, J. A. S., Breetvelt, E. J., Thode, K. I., Chow, E. W. C., & Bassett, A. S. (2013). Expression of autism spectrum and schizophrenia in patients with a 22q11.2 deletion. Schizophrenia Research, 143(1), 55–59.

    Article  PubMed  Google Scholar 

  51. Vorstman, J. A. S., Morcus, M. E. J., Duijff, S. N., Klaassen, P. W. J., Heineman-de Boer, J. A., Beemer, F. A., et al. (2006). The 22q11.2 deletion in children: High rate of autistic disorders and early onset of psychotic symptoms. Journal of the American Academy of Child and Adolescent Psychiatry, 45(9), 1104–1113.

    Article  PubMed  Google Scholar 

  52. Han, K., Holder, J. L., Schaaf, C. P., Lu, H., Chen, H., Kang, H., et al. (2013). SHANK3 overexpression causes manic-like behaviour with unique pharmacogenetic properties. Nature, 503(7474), 72–77.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Kolevzon, A., Angarita, B., Bush, L., Wang, A. T., Frank, Y., Yang, A., et al. (2014). Phelan-McDermid syndrome: A review of the literature and practice parameters for medical assessment and monitoring. Journal of Neurodevelopmental Disorders, 6(1), 39.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Phelan, K., & McDermid, H. E. (2012). The 22q13.3 deletion syndrome (Phelan-McDermid syndrome). Molecular Syndromology, 2(3–5), 186.

    CAS  PubMed  Google Scholar 

  55. Phelan, M. C., Rogers, R. C., Saul, R. A., Stapleton, G. A., Sweet, K., McDermid, H., et al. (2001). 22q13 deletion syndrome. American Journal of Medical Genetics, 101(2), 91–99.

    Article  CAS  PubMed  Google Scholar 

  56. Prasad, C., Prasad, A. N., Chodirker, B. N., Lee, C., Dawson, A. K., Jocelyn, L. J., et al. (2000). Genetic evaluation of pervasive developmental disorders: The terminal 22q13 deletion syndrome may represent a recognizable phenotype. Clinical Genetics, 57(2), 103–109.

    Article  CAS  PubMed  Google Scholar 

  57. Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., et al. (2007). Strong association of de novo copy number mutations with autism. Science, 316(5823), 445–449.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Dong, S., Walker, M. F., Carriero, N. J., DiCola, M., Willsey, A. J., Ye, A. Y., et al. (2014). De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder. Cell Reports, 9(1), 16–23.

    Article  CAS  PubMed  Google Scholar 

  59. Levy, D., Ronemus, M., Yamrom, B., Lee, Y.-H., Leotta, A., Kendall, J., et al. (2011). Rare de novo and transmitted copy-number variation in autistic spectrum disorders. Neuron, 70(5), 886–897.

    Article  CAS  PubMed  Google Scholar 

  60. Marshall, C. R., Noor, A., Vincent, J. B., Lionel, A. C., Feuk, L., Skaug, J., et al. (2008). Structural variation of chromosomes in autism spectrum disorder. American Journal of Human Genetics, 82(2), 477–488.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Morrow, E. M., Yoo, S.-Y., Flavell, S. W., Kim, T.-K., Lin, Y., Hill, R. S., et al. (2008). Identifying autism loci and genes by tracing recent shared ancestry. Science, 321(5886), 218–223.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Pinto, D., Pagnamenta, A. T., Klei, L., Anney, R., Merico, D., Regan, R., et al. (2010). Functional impact of global rare copy number variation in autism spectrum disorders. Nature, 466(7304), 368–372.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Sanders, S. J., Ercan-Sencicek, A. G., Hus, V., Luo, R., Murtha, M. T., Moreno-De-Luca, D., et al. (2011). Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism. Neuron, 70(5), 863–885.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Sanders, S. J., He, X., Willsey, A. J., Ercan-Sencicek, A. G., Samocha, K. E., Cicek, A. E., et al. (2015). Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron, 87(6), 1215.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., et al. (2004). Large-scale copy number polymorphism in the human genome. Science, 305(5683), 525–528.

    Article  CAS  PubMed  Google Scholar 

  66. Fan, Y., Du, X., Liu, X., Wang, L., Li, F., & Yu, Y. (2018). Rare copy number variations in a Chinese cohort of autism spectrum disorder. Frontiers in Genetics, 9, 665.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Wiśniowiecka-Kowalnik, B., & Nowakowska, B. A. (2019). Genetics and epigenetics of autism spectrum disorder—Current evidence in the field. Journal of Applied Genetics, 60, 37–47.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  68. Iossifov, I., Ronemus, M., Levy, D., Wang, Z., Hakker, I., Rosenbaum, J., et al. (2012). De novo gene disruptions in children on the autistic spectrum. Neuron, 74(2), 285–299.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Neale, B. M., Kou, Y., Liu, L., Ma’ayan, A., Samocha, K. E., Sabo, A., et al. (2012). Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature, 485(7397), 242.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. O’Roak, B. J., Deriziotis, P., Lee, C., Vives, L., Schwartz, J. J., Girirajan, S., et al. (2011). Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nature Genetics, 43(6), 585.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  71. Sanders, S. J., Murtha, M. T., Gupta, A. R., Murdoch, J. D., Raubeson, M. J., Willsey, A. J., et al. (2012). De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature, 485(7397), 237.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Kong, A., Frigge, M. L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G., et al. (2012). Rate of de novo mutations and the importance of father’s age to disease risk. Nature, 488(7412), 471–475.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Durand, C. M., Betancur, C., Boeckers, T. M., Bockmann, J., Chaste, P., Fauchereau, F., et al. (2007). Mutations in the gene encoding the synaptic scaffolding protein SHANK3 are associated with autism spectrum disorders. Nature Genetics, 39(1), 25.

    Article  CAS  PubMed  Google Scholar 

  74. Jamain, S., Quach, H., Betancur, C., Rastam, M., Colineaux, C., Gillberg, I. C., et al. (2003). Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. Nature Genetics, 34(1), 27–29.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Bundey, S., Hardy, C., Vickers, S., Kilpatrick, M. W., & Corbett, J. A. (1994). Duplication of the 15q11-13 region in a patient with autism, epilepsy and ataxia. Developmental Medicine and Child Neurology, 36(8), 736–742.

    Article  CAS  PubMed  Google Scholar 

  76. Thomas, N. S., Sharp, A. J., Browne, C. E., Skuse, D., Hardie, C., & Dennis, N. R. (1999). Xp deletions associated with autism in three females. Human Genetics, 104(1), 43–48.

    Article  CAS  PubMed  Google Scholar 

  77. Fine, S. E., Weissman, A., Gerdes, M., Pinto-Martin, J., Zackai, E. H., McDonald-McGinn, D. M., et al. (2005). Autism spectrum disorders and symptoms in children with molecularly confirmed 22q11.2 deletion syndrome. Journal of Autism and Developmental Disorders, 35(4), 461–470.

    Article  PubMed  PubMed Central  Google Scholar 

  78. Kumar, R. A., KaraMohamed, S., Sudi, J., Conrad, D. F., Brune, C., Badner, J. A., et al. (2008). Recurrent 16p11.2 microdeletions in autism. Human Molecular Genetics, 17(4), 628–638.

    Article  CAS  PubMed  Google Scholar 

  79. Anney, R., Klei, L., Pinto, D., Regan, R., Conroy, J., Magalhaes, T. R., et al. (2010). A genome-wide scan for common alleles affecting risk for autism. Human Molecular Genetics, 19(20), 4072–4082.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Cooper, G. M., Coe, B. P., Girirajan, S., Rosenfeld, J. A., Vu, T. H., Baker, C., et al. (2011). A copy number variation morbidity map of developmental delay. Nature Genetics, 43(9), 838–846.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Simons Vip, C. (2012). Simons Variation in Individuals Project (Simons VIP): A genetics-first approach to studying autism spectrum and related neurodevelopmental disorders. Neuron, 73(6), 1063–1067.

    Article  CAS  Google Scholar 

  82. Alarcon, M., Abrahams, B. S., Stone, J. L., Duvall, J. A., Perederiy, J. V., Bomar, J. M., et al. (2008). Linkage, association, and gene-expression analyses identify CNTNAP2 as an autism-susceptibility gene. American Journal of Human Genetics, 82(1), 150–159.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Weiss, L. A., Arking, D. E., Gene Discovery Project of Johns Hopkins & the Autism Consortium, Daly, M. J., & Chakravarti, A. (2009). A genome-wide linkage and association scan reveals novel loci for autism. Nature, 461(7265), 802–808.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Geschwind, D. H. (2008). Autism: Many genes, common pathways? Cell, 135(3), 391–395.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Lowe, J. K., Werling, D. M., Constantino, J. N., Cantor, R. M., & Geschwind, D. H. (2015). Social responsiveness, an autism endophenotype: Genomewide significant linkage to two regions on chromosome 8. The American Journal of Psychiatry, 172(3), 266–275.

    Article  PubMed  Google Scholar 

  86. Klei, L., Sanders, S. J., Murtha, M. T., Hus, V., Lowe, J. K., Willsey, A. J., et al. (2012). Common genetic variants, acting additively, are a major source of risk for autism. Molecular Autism, 3(1), 9.

    Article  PubMed  PubMed Central  Google Scholar 

  87. Ma, D., Salyakina, D., Jaworski, J. M., Konidari, I., Whitehead, P. L., Andersen, A. N., et al. (2009). A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Annals of Human Genetics, 73(Pt 3), 263–273.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Wang, K., Zhang, H., Ma, D., Bucan, M., Glessner, J. T., Abrahams, B. S., et al. (2009). Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature, 459(7246), 528–533.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Xia, K., Guo, H., Hu, Z., Xun, G., Zuo, L., Peng, Y., et al. (2014). Common genetic variants on 1p13.2 associate with risk of autism. Molecular Psychiatry, 19(11), 1212–1219.

    Article  CAS  PubMed  Google Scholar 

  90. Liang, S., Wang, X. L., Zou, M. Y., Wang, H., Zhou, X., Sun, C. H., et al. (2014). Family-based association study of ZNF533, DOCK4 and IMMP2L gene polymorphisms linked to autism in a northeastern Chinese Han population. Journal of Zhejiang University Science B, 15(3), 264–271.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Strauss, K. A., Puffenberger, E. G., Huentelman, M. J., Gottlieb, S., Dobrin, S. E., Parod, J. M., et al. (2006). Recessive symptomatic focal epilepsy and mutant contactin-associated protein-like 2. The New England Journal of Medicine, 354(13), 1370–1377.

    Article  CAS  PubMed  Google Scholar 

  92. Bakkaloglu, B., O’Roak, B. J., Louvi, A., Gupta, A. R., Abelson, J. F., Morgan, T. M., et al. (2008). Molecular cytogenetic analysis and resequencing of contactin associated protein-like 2 in autism spectrum disorders. American Journal of Human Genetics, 82(1), 165.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Peñagarikano, O., & Geschwind, D. H. (2012). What does CNTNAP2 reveal about autism spectrum disorder? Trends in Molecular Medicine, 18(3), 156.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  94. Berkel, S., Marshall, C. R., Weiss, B., Howe, J., Roeth, R., Moog, U., et al. (2010). Mutations in the SHANK2 synaptic scaffolding gene in autism spectrum disorder and mental retardation. Nature Genetics, 42(6), 489–491.

    Article  CAS  PubMed  Google Scholar 

  95. Berkel, S., Tang, W., Trevino, M., Vogt, M., Obenhaus, H. A., Gass, P., et al. (2012). Inherited and de novo SHANK2 variants associated with autism spectrum disorder impair neuronal morphogenesis and physiology. Human Molecular Genetics, 21(2), 344–357.

    Article  CAS  PubMed  Google Scholar 

  96. Kim, H. G., Kishikawa, S., Higgins, A. W., Seong, I. S., Donovan, D. J., Shen, Y., et al. (2008). Disruption of neurexin 1 associated with autism spectrum disorder. American Journal of Human Genetics, 82(1), 199–207.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Moessner, R., Marshall, C. R., Sutcliffe, J. S., Skaug, J., Pinto, D., Vincent, J., et al. (2007). Contribution of SHANK3 mutations to autism spectrum disorder. American Journal of Human Genetics, 81(6), 1289–1297.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Sato, D., Lionel, A. C., Leblond, C. S., Prasad, A., Pinto, D., Walker, S., et al. (2012). SHANK1 deletions in males with autism spectrum disorder. American Journal of Human Genetics, 90(5), 879–887.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Vaags, A. K., Lionel, A. C., Sato, D., Goodenberger, M., Stein, Q. P., Curran, S., et al. (2012). Rare deletions at the neurexin 3 locus in autism spectrum disorder. American Journal of Human Genetics, 90(1), 133–141.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Al‐Dewik, N., Mohd, H., Al‐Mureikhi, M., Ali, R., Al‐Mesaifri, F., Mahmoud, L., et al. (2019). Clinical exome sequencing in 509 Middle Eastern families with suspected Mendelian diseases: The Qatari experience. American Journal of Medical Genetics Part A, 179(6), 927–935.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  101. Helsmoortel, C., Vulto-van Silfhout, A. T., Coe, B. P., Vandeweyer, G., Rooms, L., van den Ende, J., et al. (2014). A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP. Nature Genetics, 46(4), 380–384.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Novarino, G., El-Fishawy, P., Kayserili, H., Meguid, N. A., Scott, E. M., Schroth, J., et al. (2012). Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Science, 338(6105), 394–397.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Yu, T. W., Chahrour, M. H., Coulter, M. E., Jiralerspong, S., Okamura-Ikeda, K., Ataman, B., et al. (2013). Using whole exome sequencing to identify inherited causes of autism. Neuron, 77(2), 259–273.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Hu, V. W., Sarachana, T., Kim, K. S., Nguyen, A., Kulkarni, S., Steinberg, M. E., et al. (2009). Gene expression profiling differentiates autism case-controls and phenotypic variants of autism spectrum disorders: Evidence for circadian rhythm dysfunction in severe autism. Autism Research, 2(2), 78–97.

    Article  PubMed  PubMed Central  Google Scholar 

  105. Luo, R., Sanders, S. J., Tian, Y., Voineagu, I., Huang, N., Chu, S. H., et al. (2012). Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders. American Journal of Human Genetics, 91(1), 38–55.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Voineagu, I., Wang, X., Johnston, P., Lowe, J. K., Tian, Y., Horvath, S., et al. (2011). Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature, 474(7351), 380–384.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Gupta, S., Ellis, S. E., Ashar, F. N., Moes, A., Bader, J. S., Zhan, J., et al. (2014). Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism. Nature Communications, 5, 5748.

    Article  CAS  PubMed  Google Scholar 

  108. Hormozdiari, F., Penn, O., Borenstein, E., & Eichler, E. E. (2015). The discovery of integrated gene networks for autism and related disorders. Genome Research, 25(1), 142–154.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Ch’ng, C., Kwok, W., Rogic, S., & Pavlidis, P. (2015). Meta-analysis of gene expression in autism spectrum disorder. Autism Research, 8(5), 593–608.

    Article  PubMed  PubMed Central  Google Scholar 

  110. Gregg, J. P., Lit, L., Baron, C. A., Hertz-Picciotto, I., Walker, W., Davis, R. A., et al. (2008). Gene expression changes in children with autism. Genomics, 91(1), 22–29.

    Article  CAS  PubMed  Google Scholar 

  111. Ning, L. F., Yu, Y. Q., GuoJi, E. T., Kou, C. G., Wu, Y. H., Shi, J. P., et al. (2015). Meta-analysis of differentially expressed genes in autism based on gene expression data. Genetics and Molecular Research, 14(1), 2146–2155.

    Article  CAS  PubMed  Google Scholar 

  112. Chien, W. H., Gau, S. S., Chen, C. H., Tsai, W. C., Wu, Y. Y., Chen, P. H., et al. (2013). Increased gene expression of FOXP1 in patients with autism spectrum disorders. Molecular Autism, 4(1), 23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Abbasy, S., Shahraki, F., Haghighatfard, A., Qazvini, M. G., Rafiei, S. T., Noshadirad, E., et al. (2018). Neuregulin1 types mRNA level changes in autism spectrum disorder, and is associated with deficit in executive functions. eBioMedicine, 37, 483–488.

    Article  PubMed  PubMed Central  Google Scholar 

  114. Pramparo, T., Lombardo, M. V., Campbell, K., Barnes, C. C., Marinero, S., Solso, S., et al. (2015). Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers. Molecular Systems Biology, 11(12), 841.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  115. Alter, M. D., Kharkar, R., Ramsey, K. E., Craig, D. W., Melmed, R. D., Grebe, T. A., et al. (2011). Autism and increased paternal age related changes in global levels of gene expression regulation. PLoS One, 6(2), e16715.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Anitha, A., Nakamura, N., Thanseem, I., Yamada, K., Iwayama, Y., Toyota, T., et al. (2012). Brain region-specific altered expression and association of mitochondria-related genes in autism. Molecular Autism, 3(1), 12.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  117. Chow, M. L., Pramparo, T., Winn, M. E., Barnes, C. C., Li, H.-R., Weiss, L., et al. (2012). Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages. PLoS Genetics, 8(3), e1002592.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Féron, F., Gepner, B., Lacassagne, E., Stephan, D., Mesnage, B., Blanchard, M.-P., et al. (2016). Olfactory stem cells reveal MOCOS as a new player in autism spectrum disorders. Molecular Psychiatry, 21(9), 1215–1224.

    Article  PubMed  CAS  Google Scholar 

  119. Ginsberg, M. R., Rubin, R. A., Falcone, T., Ting, A. H., & Natowicz, M. R. (2012). Brain transcriptional and epigenetic associations with autism. PLoS One, 7(9), e44736.

    Article  PubMed  PubMed Central  Google Scholar 

  120. Glatt, S. J., Tsuang, M. T., Winn, M., Chandler, S. D., Collins, M., Lopez, L., et al. (2012). Blood-based gene expression signatures of infants and toddlers with autism. Journal of the American Academy of Child and Adolescent Psychiatry, 51(9), 934–442.

    Article  PubMed  PubMed Central  Google Scholar 

  121. Chana, G., Laskaris, L., Pantelis, C., Gillett, P., Testa, R., Zantomio, D., et al. (2015). Decreased expression of mGluR5 within the dorsolateral prefrontal cortex in autism and increased microglial number in mGluR5 knockout mice: Pathophysiological and neurobehavioral implications. Brain, Behavior, and Immunity, 49, 197–205.

    Article  CAS  PubMed  Google Scholar 

  122. Ivanov, H. Y., Stoyanova, V. K., Popov, N. T., Bosheva, M., & Vachev, T. I. (2015). Blood-based gene expression in children with autism spectrum disorder. BioDiscovery, 17, e8966.

    Google Scholar 

  123. James, S. J., Shpyleva, S., Melnyk, S., Pavliv, O., & Pogribny, I. P. (2014). Elevated 5-hydroxymethylcytosine in the Engrailed-2 (EN-2) promoter is associated with increased gene expression and decreased MeCP2 binding in autism cerebellum. Translational Psychiatry, 4, e460.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Khan, A., Harney, J. W., Zavacki, A. M., & Sajdel-Sulkowska, E. M. (2014). Disrupted brain thyroid hormone homeostasis and altered thyroid hormone-dependent brain gene expression in autism spectrum disorders. Journal of Physiology and Pharmacology, 65(2), 257–272.

    CAS  PubMed  Google Scholar 

  125. Kong, S., Shimizu-Motohashi, Y., Campbell, M., Lee, I., Collins, C., Brewster, S., et al. (2013). Peripheral blood gene expression signature differentiates children with autism from unaffected siblings. Neurogenetics, 14(2), 143.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Kuwano, Y., Kamio, Y., Kawai, T., Katsuura, S., Inada, N., Takaki, A., et al. (2011). Autism-associated gene expression in peripheral leucocytes commonly observed between subjects with autism and healthy women having autistic children. PLoS One, 6(9), e24723.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Maekawa, M., Yamada, K., Toyoshima, M., Ohnishi, T., Iwayama, Y., Shimamoto, C., et al. (2015). Utility of scalp hair follicles as a novel source of biomarker genes for psychiatric illnesses. Biological Psychiatry, 78(2), 116–125.

    Article  CAS  PubMed  Google Scholar 

  128. Prandini, P., Zusi, C., Malerba, G., Itan, P., Pignatti, F., & Trabetti, E. (2014). Analysis of RBFOX1 gene expression in lymphoblastoid cell lines of Italian discordant autism spectrum disorders sib-pairs. Molecular and Cellular Probes, 28(5–6), 242–245.

    Article  CAS  PubMed  Google Scholar 

  129. Segura, M., Pedreño, C., Obiols, J., Taurines, R., Pàmias, M., Grünblatt, E., et al. (2015). Neurotrophin blood-based gene expression and social cognition analysis in patients with autism spectrum disorder. Neurogenetics, 16(2), 123–131.

    Article  CAS  PubMed  Google Scholar 

  130. Stamova, B., Green, P. G., Tian, Y., Hertz-Picciotto, I., Pessah, I. N., Hansen, R., et al. (2011). Correlations between gene expression and mercury levels in blood of boys with and without autism. Neurotoxicity Research, 19(1), 31–48.

    Article  CAS  PubMed  Google Scholar 

  131. Talebizadeh, Z., Aldenderfer, R., & Wen Chen, X. (2014). A proof-of-concept study: Exon-level expression profiling and alternative splicing in autism using lymphoblastoid cell lines. Psychiatric Genetics, 24(1), 1–9.

    Article  CAS  PubMed  Google Scholar 

  132. Taurines, R., Grünblatt, E., Schecklmann, M., Schwenck, C., Albantakis, L., Reefschläger, L., et al. (2011). Altered mRNA expression of monoaminergic candidate genes in the blood of children with attention deficit hyperactivity disorder and autism spectrum disorder. The World Journal of Biological Psychiatry, 12(Suppl), 1.

    Google Scholar 

  133. Tian, Y., Green, P. G., Stamova, B., Hertz-Picciotto, I., Pessah, I. N., Hansen, R., et al. (2011). Correlations of gene expression with blood lead levels in children with autism compared to typically developing controls. Neurotoxicity Research, 19(1), 1.

    Article  CAS  PubMed  Google Scholar 

  134. Voineagu, I., & Eapen, V. (2013). Converging pathways in autism spectrum disorders: Interplay between synaptic dysfunction and immune responses. Frontiers in Human Neuroscience, 7, 738.

    Article  PubMed  PubMed Central  Google Scholar 

  135. Walker, S. J., Fortunato, J., Gonzalez, L. G., & Krigsman, A. (2013). Identification of unique gene expression profile in children with regressive autism spectrum disorder (ASD) and ileocolitis. PLoS One, 8(3), e58058.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Williams, B. L., Hornig, M., Buie, T., Bauman, M. L., Cho Paik, M., Wick, I., et al. (2011). Impaired carbohydrate digestion and transport and mucosal dysbiosis in the intestines of children with autism and gastrointestinal disturbances. PLoS One, 6(9), e24585.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Yasuda, Y., Hashimoto, R., Yamamori, H., Ohi, K., Fukumoto, M., Umeda-Yano, S., et al. (2011). Gene expression analysis in lymphoblasts derived from patients with autism spectrum disorder. Molecular Autism, 2(1), 9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Zhubi, A., Chen, Y., Dong, E., Cook, E. H., Guidotti, A., & Grayson, D. R. (2014). Increased binding of MeCP2 to the GAD1 and RELN promoters may be mediated by an enrichment of 5-hmC in autism spectrum disorder (ASD) cerebellum. Translational Psychiatry, 4, e349.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Kang, H. J., Kawasawa, Y. I., Cheng, F., Zhu, Y., Xu, X., Li, M., et al. (2011). Spatiotemporal transcriptome of the human brain. Nature, 478(7370), 483.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Ziats, M. N., & Rennert, O. M. (2013). Sex-biased gene expression in the developing brain: Implications for autism spectrum disorders. Molecular Autism, 4, 10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Garbett, K., Ebert, P. J., Mitchell, A., Lintas, C., Manzi, B., Mirnics, K., et al. (2008). Immune transcriptome alterations in the temporal cortex of subjects with autism. Neurobiology of Disease, 30(3), 303–311.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Ziats, M. N., & Rennert, O. M. (2013). Aberrant expression of long noncoding RNAs in autistic brain. Journal of Molecular Neuroscience, 49(3), 589–593.

    Article  CAS  PubMed  Google Scholar 

  143. Enstrom, A. M., Lit, L., Onore, C. E., Gregg, J. P., Hansen, R. L., Pessah, I. N., et al. (2009). Altered gene expression and function of peripheral blood natural killer cells in children with autism. Brain, Behavior, and Immunity, 23(1), 124–133.

    Article  CAS  PubMed  Google Scholar 

  144. Hu, V. W., Frank, B. C., Heine, S., Lee, N. H., & Quackenbush, J. (2006). Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes. BMC Genomics, 7, 118.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  145. Emanuele, E., Boso, M., Cassola, F., Broglia, D., Bonoldi, I., Mancini, L., et al. (2010). Increased dopamine DRD4 receptor mRNA expression in lymphocytes of musicians and autistic individuals: Bridging the music-autism connection. Neuro Endocrinology Letters, 31(1), 122–125.

    PubMed  Google Scholar 

  146. Purcell, A. E., Jeon, O. H., Zimmerman, A. W., Blue, M. E., & Pevsner, J. (2001). Postmortem brain abnormalities of the glutamate neurotransmitter system in autism. Neurology, 57(9), 1618–1628.

    Article  CAS  PubMed  Google Scholar 

  147. Wong, C. C. Y., Meaburn, E. L., Ronald, A., Price, T. S., Jeffries, A. R., Schalkwyk, L. C., et al. (2013). Methylomic analysis of monozygotic twins discordant for autism spectrum disorder and related behavioural traits. Molecular Psychiatry, 19(4), 495.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  148. James, S. J., Melnyk, S., Jernigan, S., Hubanks, A., Rose, S., & Gaylor, D. W. (2008). Abnormal transmethylation/transsulfuration metabolism and DNA hypomethylation among parents of children with autism. Journal of Autism and Developmental Disorders, 38(10), 1966–1975.

    Article  PubMed  PubMed Central  Google Scholar 

  149. Nardone, S., Sams, D. S., Reuveni, E., Getselter, D., Oron, O., Karpuj, M., et al. (2014). DNA methylation analysis of the autistic brain reveals multiple dysregulated biological pathways. Translational Psychiatry, 4, e433.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Ladd-Acosta, C., Hansen, K. D., Briem, E., Fallin, M. D., Kaufmann, W. E., & Feinberg, A. P. (2013). Common DNA methylation alterations in multiple brain regions in autism. Molecular Psychiatry, 19(8), 862.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  151. Ladd-Acosta, C., Hansen, K. D., Briem, E., Fallin, M. D., Kaufmann, W. E., & Feinberg, A. P. (2014). Common DNA methylation alterations in multiple brain regions in autism. Molecular Psychiatry, 19(8), 862–871.

    Article  CAS  PubMed  Google Scholar 

  152. Daniele Fallin, M., Feinberg, J. I., Bakulski, K. M., Brown, S. C., Tryggvadottir, R., Feinberg, A. P., et al. (2015). Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort. International Journal of Epidemiology, 44(4), 1199–1210.

    Article  PubMed  PubMed Central  Google Scholar 

  153. Milekic, M. H., Xin, Y., O’Donnell, A., Kumar, K. K., Bradley-Moore, M., Malaspina, D., et al. (2014). Age-related sperm DNA methylation changes are transmitted to offspring and associated with abnormal behavior and dysregulated gene expression. Molecular Psychiatry, 20(8), 995.

    Article  PubMed  CAS  Google Scholar 

  154. Behnia, F., Parets, S. E., Kechichian, T., Yin, H., Dutta, E. H., Saade, G. R., et al. (2015). Fetal DNA methylation of autism spectrum disorders candidate genes: Association with spontaneous preterm birth. American Journal of Obstetrics and Gynecology, 212(4), 533.e531–533.e539.

    Article  CAS  Google Scholar 

  155. James, S. J., Shpyleva, S., Melnyk, S., Pavliv, O., & Pogribny, I. P. (2013). Complex epigenetic regulation of engrailed-2 (EN-2) homeobox gene in the autism cerebellum. Translational Psychiatry, 3, e232.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Nguyen, A., Rauch, T. A., Pfeifer, G. P., & Hu, V. W. (2010). Global methylation profiling of lymphoblastoid cell lines reveals epigenetic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain. The FASEB Journal, 24(8), 3036.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Bremer, A., Giacobini, M., Nordenskjöld, M., Brøndum-Nielsen, K., Mansouri, M., Dahl, N., et al. (2010). Screening for copy number alterations in loci associated with autism spectrum disorders by two-color multiplex ligation-dependent probe amplification. American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics, 153B(1), 280–285.

    Google Scholar 

  158. Chahrour, M., Jung, S. Y., Shaw, C., Zhou, X., Wong, S. T. C., Qin, J., et al. (2008). MeCP2, a key contributor to neurological disease, activates and represses transcription. Science (New York, N.Y.), 320(5880), 1224.

    Article  CAS  Google Scholar 

  159. Vorstman, J. A. S., Staal, W. G., van Daalen, E., van Engeland, H., Hochstenbach, P. F. R., & Franke, L. (2006). Identification of novel autism candidate regions through analysis of reported cytogenetic abnormalities associated with autism. Molecular Psychiatry, 11(1), 1.

    Article  CAS  PubMed  Google Scholar 

  160. Liu, X., Solehdin, F., Cohen, I. L., Gonzalez, M. G., Jenkins, E. C., Lewis, M. E. S., et al. (2011). Population- and family-based studies associate the MTHFR gene with idiopathic autism in simplex families. Journal of Autism and Developmental Disorders, 41(7), 938–944.

    Article  PubMed  Google Scholar 

  161. Mohammad, N. S., Jain, J. M. N., Chintakindi, K. P., Singh, R. P., Naik, U., & Akella, R. R. D. (2009). Aberrations in folate metabolic pathway and altered susceptibility to autism. Psychiatric Genetics, 19(4), 171–176.

    Article  PubMed  Google Scholar 

  162. Schanen, N. C. (2006). Epigenetics of autism spectrum disorders. Human Molecular Genetics, 15(suppl_2), R138–R150.

    Article  CAS  PubMed  Google Scholar 

  163. Lasalle, J. M. (2013). Autism genes keep turning up chromatin. OA Autism, 1(2), 14.

    Article  PubMed  PubMed Central  Google Scholar 

  164. Berko, E. R., Suzuki, M., Beren, F., Lemetre, C., Alaimo, C. M., Calder, R. B., et al. (2014). Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. PLoS Genetics, 10(5), e1004402.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  165. Irimia, M., Weatheritt, R. J., Ellis, J. D., Parikshak, N. N., Gonatopoulos-Pournatzis, T., Babor, M., et al. (2014). A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell, 159(7), 1511–1523.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Vogel-Ciernia, A., & Wood, M. A. (2014). Neuron-specific chromatin remodeling: A missing link in epigenetic mechanisms underlying synaptic plasticity, memory, and intellectual disability disorders. Neuropharmacology, 80, 18–27.

    Article  CAS  PubMed  Google Scholar 

  167. LoParo, D., & Waldman, I. D. (2015). The oxytocin receptor gene (OXTR) is associated with autism spectrum disorder: A meta-analysis. Molecular Psychiatry, 20(5), 640–646.

    Article  CAS  PubMed  Google Scholar 

  168. Lopez, A. J., & Wood, M. A. (2015). Role of nucleosome remodeling in neurodevelopmental and intellectual disability disorders. Frontiers in Behavioral Neuroscience, 9, 100.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  169. Kubota, T., & Mochizuki, K. (2016). Epigenetic effect of environmental factors on autism spectrum disorders. International Journal of Environmental Research and Public Health, 13(5), pii: E504.

    Article  CAS  Google Scholar 

  170. Quesnel-Vallieres, M., Dargaei, Z., Irimia, M., Gonatopoulos-Pournatzis, T., Ip, J. Y., Wu, M., et al. (2016). Misregulation of an activity-dependent splicing network as a common mechanism underlying autism spectrum disorders. Molecular Cell, 64(6), 1023–1034.

    Article  CAS  PubMed  Google Scholar 

  171. Wang, Y., Fang, Y., Zhang, F., Xu, M., Zhang, J., Yan, J., et al. (2014). Hypermethylation of the enolase gene (ENO2) in autism. European Journal of Pediatrics, 173(9), 1233–1244.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Frye, R. E., & Rossignol, D. A. (2011). Mitochondrial dysfunction can connect the diverse medical symptoms associated with autism spectrum disorders. Pediatric Research, 69(5 Pt 2), 41R–47R.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Rossignol, D. A., & Frye, R. E. (2012). Mitochondrial dysfunction in autism spectrum disorders: A systematic review and meta-analysis. Molecular Psychiatry, 17(3), 290–314.

    Article  CAS  PubMed  Google Scholar 

  174. Lombard, J. (1998). Autism: A mitochondrial disorder? Medical Hypotheses, 50(6), 497–500.

    Article  CAS  PubMed  Google Scholar 

  175. Valenti, D., de Bari, L., De Filippis, B., Henrion-Caude, A., & Vacca, R. A. (2014). Mitochondrial dysfunction as a central actor in intellectual disability-related diseases: An overview of down syndrome, autism, fragile X and Rett syndrome. Neuroscience and Biobehavioral Reviews, 46(Pt), 2.

    Google Scholar 

  176. Giulivi, C., Zhang, Y.-F., Omanska-Klusek, A., Ross-Inta, C., Wong, S., Hertz-Picciotto, I., et al. (2010). Mitochondrial dysfunction in autism. JAMA, 304(21), 2389–2396.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Oliveira, G., Diogo, L., Grazina, M., Garcia, P., Ataíde, A., Marques, C., et al. (2005). Mitochondrial dysfunction in autism spectrum disorders: A population-based study. Developmental Medicine and Child Neurology, 47(3), 185–189.

    Article  CAS  PubMed  Google Scholar 

  178. Goldenthal, M. J., Damle, S., Sheth, S., Shah, N., Melvin, J., Jethva, R., et al. (2015). Mitochondrial enzyme dysfunction in autism spectrum disorders; a novel biomarker revealed from buccal swab analysis. Biomarkers in Medicine, 9(10), 957–965.

    Article  CAS  PubMed  Google Scholar 

  179. Parikshak, N. N., Gandal, M. J., & Geschwind, D. H. (2015). Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders. Nature Reviews Genetics, 16(8), 441–458.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Napoli, E., Wong, S., Hertz-Picciotto, I., & Giulivi, C. (2014). Deficits in bioenergetics and impaired immune response in granulocytes from children with autism. Pediatrics, 133(5), 1405–1410.

    Article  Google Scholar 

  181. Weissman, J. R., Kelley, R. I., Bauman, M. L., Cohen, B. H., Murray, K. F., Mitchell, R. L., et al. (2008). Mitochondrial disease in autism spectrum disorder patients: A cohort analysis. PLoS One, 3(11), e3815.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  182. Palmieri, L., & Persico, A. M. (2010). Mitochondrial dysfunction in autism spectrum disorders: Cause or effect? Biochimica et Biophysica Acta, 1797(6–7), 1130–1137.

    Article  CAS  PubMed  Google Scholar 

  183. Fillano, J. J., Goldenthal, M. J., Rhodes, C. H., & Marín-García, J. (2002). Mitochondrial dysfunction in patients with hypotonia, epilepsy, autism, and developmental delay: HEADD syndrome. Journal of Child Neurology, 17(6), 435–439.

    Article  PubMed  Google Scholar 

  184. Gu, F., Chauhan, V., Kaur, K., Brown, W. T., LaFauci, G., Wegiel, J., et al. (2013). Alterations in mitochondrial DNA copy number and the activities of electron transport chain complexes and pyruvate dehydrogenase in the frontal cortex from subjects with autism. Translational Psychiatry, 3, e299.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Smith, M., Spence, M. A., & Flodman, P. (2009). Nuclear and mitochondrial genome defects in autisms. Annals of the New York Academy of Sciences, 1151, 102–132.

    Article  CAS  PubMed  Google Scholar 

  186. Pitceathly, R. D. S., Rahman, S., & Hanna, M. G. (2012). Single deletions in mitochondrial DNA--molecular mechanisms and disease phenotypes in clinical practice. Neuromuscular Disorders, 22(7), 577–586.

    Article  CAS  PubMed  Google Scholar 

  187. Haas, R. H., Parikh, S., Falk, M. J., Saneto, R. P., Wolf, N. I., Darin, N., et al. (2007). Mitochondrial disease: A practical approach for primary care physicians. Pediatrics, 120(6), 1326–1333.

    Article  PubMed  Google Scholar 

  188. Niyazov, D. M., Kahler, S. G., & Frye, R. E. (2016). Primary mitochondrial disease and secondary mitochondrial dysfunction: Importance of distinction for diagnosis and treatment. Molecular Syndromology, 7(3), 122–137.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Varga, N. Á., Pentelényi, K., Balicza, P., Gézsi, A., Reményi, V., Hársfalvi, V., et al. (2018). Mitochondrial dysfunction and autism: Comprehensive genetic analyses of children with autism and mtDNA deletion. Behavioral and Brain Functions, 14. https://doi.org/10.1186/s12993-018-0135-x

  190. Coolen, M., & Bally-Cuif, L. (2009). MicroRNAs in brain development and physiology. Current Opinion in Neurobiology, 19(5), 461–470.

    Article  CAS  PubMed  Google Scholar 

  191. Hu, Y., Ehli, E. A., & Boomsma, D. I. (2017). MicroRNAs as biomarkers for psychiatric disorders with a focus on autism spectrum disorder: Current progress in genetic association studies, expression profiling, and translational research. Autism Research, 10(7), 1184–1203.

    Article  PubMed  Google Scholar 

  192. Stamova, B., Ander, B. P., Barger, N., Sharp, F. R., & Schumann, C. M. (2015). Specific regional and age-related small noncoding RNA expression patterns within superior temporal gyrus of typical human brains are less distinct in autism brains. Journal of Child Neurology, 30(14), 1930–1946.

    Article  PubMed  PubMed Central  Google Scholar 

  193. Schumann, C. M., Sharp, F. R., Ander, B. P., & Stamova, B. (2017). Possible sexually dimorphic role of miRNA and other sncRNA in ASD brain. Molecular Autism, 8, 4.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  194. Abu-Elneel, K., Liu, T., Gazzaniga, F. S., Nishimura, Y., Wall, D. P., Geschwind, D. H., et al. (2008). Heterogeneous dysregulation of microRNAs across the autism spectrum. Neurogenetics, 9(3), 153–161.

    Article  CAS  PubMed  Google Scholar 

  195. Buyske, S. (2009). Comment on the article “Heterogeneous dysregulation of microRNAs across the autism spectrum” by Abu-Elneel et al. Neurogenetics, 10(2), 167.

    Article  PubMed  Google Scholar 

  196. Constantin, L. (2017). The role of microRNAs in cerebellar development and autism spectrum disorder during embryogenesis. Molecular Neurobiology, 54(9), 6944–6959.

    Article  CAS  PubMed  Google Scholar 

  197. Sarachana, T., Zhou, R., Chen, G., Manji, H. K., & Hu, V. W. (2010). Investigation of post-transcriptional gene regulatory networks associated with autism spectrum disorders by microRNA expression profiling of lymphoblastoid cell lines. Genome Medicine, 2(4), 23.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  198. Talebizadeh, Z., Butler, M. G., & Theodoro, M. F. (2008). Feasibility and relevance of examining lymphoblastoid cell lines to study role of microRNAs in autism. Autism Research, 1(4), 240–250.

    Article  PubMed  PubMed Central  Google Scholar 

  199. Wu, Y. E., Parikshak, N. N., Belgard, T. G., & Geschwind, D. H. (2016). Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder. Nature Neuroscience, 19(11), 1463–1476.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Mundalil Vasu, M., Anitha, A., Thanseem, I., Suzuki, K., Yamada, K., Takahashi, T., et al. (2014). Serum microRNA profiles in children with autism. Molecular Autism, 5, 40.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  201. Kichukova, T. M., Popov, N. T., Ivanov, I. S., & Vachev, T. I. (2017). Profiling of circulating serum microRNAs in children with autism spectrum disorder using stem-loop qRT-PCR assay. Folia Medica (Plovdiv)., 59(1), 43–52.

    Article  CAS  PubMed  Google Scholar 

  202. Weber, J. A., Baxter, D. H., Zhang, S., Huang, D. Y., Huang, K. H., Lee, M. J., et al. (2010). The microRNA spectrum in 12 body fluids. Clinical Chemistry, 56(11), 1733–1741.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Hicks, S. D., Ignacio, C., Gentile, K., & Middleton, F. A. (2016). Salivary miRNA profiles identify children with autism spectrum disorder, correlate with adaptive behavior, and implicate ASD candidate genes involved in neurodevelopment. BMC Pediatrics, 16, 52.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  204. Nguyen, L. S., Lepleux, M., Makhlouf, M., Martin, C., Fregeac, J., Siquier-Pernet, K., et al. (2016). Profiling olfactory stem cells from living patients identifies miRNAs relevant for autism pathophysiology. Molecular Autism, 7, 1.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  205. Mellios, N., & Sur, M. (2012). The emerging role of microRNAs in schizophrenia and autism spectrum disorders. Frontiers in Psychiatry, 3, 39.

    Article  PubMed  PubMed Central  Google Scholar 

  206. Rogelj, B. (2006). Brain-specific small nucleolar RNAs. Journal of Molecular Neuroscience, 28(2), 103–109.

    Article  CAS  PubMed  Google Scholar 

  207. Cavaillé, J., Buiting, K., Kiefmann, M., Lalande, M., Brannan, C. I., Horsthemke, B., et al. (2000). Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. PNAS, 97(26), 14311–14316.

    Article  PubMed  PubMed Central  Google Scholar 

  208. Dykens, E. M., Lee, E., & Roof, E. (2011). Prader-Willi syndrome and autism spectrum disorders: An evolving story. Journal of Neurodevelopmental Disorders, 3(3), 225–237.

    Article  PubMed  PubMed Central  Google Scholar 

  209. Gabriele, S., Sacco, R., & Persico, A. M. (2014). Blood serotonin levels in autism spectrum disorder: A systematic review and meta-analysis. European Neuropsychopharmacology, 24(6), 919–929.

    Article  CAS  PubMed  Google Scholar 

  210. Nakatani, J., Tamada, K., Hatanaka, F., Ise, S., Ohta, H., Inoue, K., et al. (2009). Abnormal behavior in a chromosome-engineered mouse model for human 15q11-13 duplication seen in autism. Cell, 137(7), 1235–1246.

    Article  PubMed  PubMed Central  Google Scholar 

  211. Rajasethupathy, P., Antonov, I., Sheridan, R., Frey, S., Sander, C., Tuschl, T., et al. (2012). A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell, 149(3), 693–707.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Wilkinson, B., & Campbell, D. B. (2013). Contribution of long noncoding RNAs to autism spectrum disorder risk. International Review of Neurobiology, 113, 35–59.

    Article  CAS  PubMed  Google Scholar 

  213. Minshew, N. J., & Keller, T. A. (2010). The nature of brain dysfunction in autism: Functional brain imaging studies. Current Opinion in Neurology, 23(2), 124–130.

    Article  PubMed  PubMed Central  Google Scholar 

  214. Kerin, T., Ramanathan, A., Rivas, K., Grepo, N., Coetzee, G. A., & Campbell, D. B. (2012). A noncoding RNA antisense to moesin at 5p14.1 in autism. Science Translational Medicine, 4(128), 128ra140.

    Article  Google Scholar 

  215. DeWitt, J. J., Grepo, N., Wilkinson, B., Evgrafov, O. V., Knowles, J. A., & Campbell, D. B. (2016). Impact of the autism-associated long noncoding RNA MSNP1AS on neuronal architecture and gene expression in human neural progenitor cells. Genes (Basel), 7(10), pii: E76.

    Article  CAS  Google Scholar 

  216. Vincent, J. B., Petek, E., Thevarkunnel, S., Kolozsvari, D., Cheung, J., Patel, M., et al. (2002). The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a complex multi-transcript system. Genomics, 80(3), 283–294.

    Article  CAS  PubMed  Google Scholar 

  217. Williams, J. M., Beck, T. F., Pearson, D. M., Proud, M. B., Cheung, S. W., & Scott, D. A. (2009). A 1q42 deletion involving DISC1, DISC2, and TSNAX in an autism spectrum disorder. American Journal of Medical Genetics Part A, 149A(8), 1758–1762.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  218. Wang, Y., Zhao, X., Ju, W., Flory, M., Zhong, J., Jiang, S., et al. (2015). Genome-wide differential expression of synaptic long noncoding RNAs in autism spectrum disorder. Translational Psychiatry, 5, e660.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  219. Parikshak, N. N., Swarup, V., Belgard, T. G., Irimia, M., Ramaswami, G., Gandal, M. J., et al. (2016). Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature, 540(7633), 423–427.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  220. Gudenas, B. L., Srivastava, A. K., & Wang, L. (2017). Integrative genomic analyses for identification and prioritization of long non-coding RNAs associated with autism. PLoS One, 12(5), e0178532.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  221. Noor, A., Whibley, A., Marshall, C. R., Gianakopoulos, P. J., Piton, A., Carson, A. R., et al. (2010). Disruption at the PTCHD1 locus on Xp22.11 in autism spectrum disorder and intellectual disability. Science Translational Medicine, 2(49), 49ra68.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  222. Velmeshev, D., Magistri, M., & Faghihi, M. A. (2013). Expression of non-protein-coding antisense RNAs in genomic regions related to autism spectrum disorders. Molecular Autism, 4(1), 32.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  223. Fallah, H., Ganji, M., Arsang-Jang, S., Sayad, A., & Taheri, M. (2019). Consideration of the role of MALAT1 long noncoding RNA and catalytic component of RNA-induced silencing complex (Argonaute 2, AGO2) in autism spectrum disorders: Yes, or no? Meta Gene, 19, 193–198.

    Article  Google Scholar 

  224. Bond, A. M., Vangompel, M. J., Sametsky, E. A., Clark, M. F., Savage, J. C., Disterhoft, J. F., et al. (2009). Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nature Neuroscience, 12(8), 1020–1027.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  225. Lipovich, L., Dachet, F., Cai, J., Bagla, S., Balan, K., Jia, H., et al. (2012). Activity-dependent human brain coding/noncoding gene regulatory networks. Genetics, 192(3), 1133–1148.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  226. Hammond, S. M. (2015). An overview of microRNAs. Advanced Drug Delivery Reviews, 87, 3–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Mohr, A. M., & Mott, J. L. (2015). Overview of microRNA biology. Seminars in Liver Disease, 35(1), 3–11.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  228. Toma, C., Torrico, B., Hervas, A., Salgado, M., Rueda, I., Valdes-Mas, R., et al. (2015). Common and rare variants of microRNA genes in autism spectrum disorders. The World Journal of Biological Psychiatry, 16, 376–386.

    Article  PubMed  Google Scholar 

  229. DeWitt, J. J., Hecht, P. M., Grepo, N., Wilkinson, B., Evgrafov, O. V., Morris, K. V., et al. (2016). Transcriptional gene silencing of the autism-associated long noncoding RNA MSNP1AS in human neural progenitor cells. Developmental Neuroscience, 38(5), 375–383.

    Article  CAS  PubMed  Google Scholar 

  230. Tang, J., Yu, Y., & Yang, W. (2017). Long noncoding RNA and its contribution to autism spectrum disorders. CNS Neuroscience & Therapeutics, 23(8), 645–656.

    Article  CAS  Google Scholar 

  231. Wang, P., Mokhtari, R., Pedrosa, E., Kirschenbaum, M., Bayrak, C., Zheng, D., et al. (2017). CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells. Molecular Autism, 8, 11.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Al-Dewik, N., Alsharshani, M. (2020). New Horizons for Molecular Genetics Diagnostic and Research in Autism Spectrum Disorder. In: Essa, M., Qoronfleh, M. (eds) Personalized Food Intervention and Therapy for Autism Spectrum Disorder Management. Advances in Neurobiology, vol 24. Springer, Cham. https://doi.org/10.1007/978-3-030-30402-7_2

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