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Journal of Autism and Developmental Disorders

Gepubliceerd in:

27-06-2022 | Original Paper

Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment

Auteurs: Kaan Okay, Pelin Ünal Varış, Süha Miral, Athanasia Pavlopoulou, Yavuz Oktay, Gökhan Karakülah

Gepubliceerd in: Journal of Autism and Developmental Disorders | Uitgave 3/2023

Abstract

Transposable elements (TEs) have been implicated in autism spectrum disorder (ASD). However, our understanding of their roles is far from complete. Herein, we explored de novo TE insertions (dnTEIs) and de novo variants (DNVs) across the genomes of dizygotic twins with ASD and their parents. The neuronal regulatory elements had a tendency to harbor dnTEIs that were shared between twins, but ASD-risk genes had dnTEIs that were unique to each twin. The dnTEIs were 4.6-fold enriched in enhancers that are active in embryonic stem cell (ESC)-neurons (p < 0.001), but DNVs were 1.5-fold enriched in active enhancers of astrocytes (p = 0.0051). Our findings suggest that dnTEIs and DNVs play a role in ASD etiology by disrupting enhancers of neurons and astrocytes.

Graphical Abstract

vorige artikel Active Viewing Facilitates Gaze to the Eye Region in Young Children with Autism Spectrum Disorder

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Aksoy, I., Utami, K. H., Winata, C. L., Hillmer, A. M., Rouam, S. L., Briault, S., Davila, S., Stanton, L. W., & Cacheux, V. (2017). Personalized genome sequencing coupled with iPSC technology identifies GTDC1 as a gene involved in neurodevelopmental disorders. Human Molecular Genetics, 26, 367–382. https://doi.org/10.1093/hmg/ddw393CrossRefPubMed

Anagnostou, E., Zwaigenbaum, L., Szatmari, P., Fombonne, E., Fernandez, B. A., Woodbury-Smith, M., Brian, J., Bryson, S., Smith, I. M., Drmic, I., Buchanan, J. A., Roberts, W., & Scherer, S. W. (2014). Autism spectrum disorder: Advances in evidence-based practice. CMAJ, 186, 509–519. https://doi.org/10.1503/cmaj.121756CrossRefPubMedPubMedCentral

Association, A. P. (2013). Diagnostic and statistical manual of mental disorders (DSM-5®). American Psychiatric Pub.CrossRef

Bennett, E. A., Keller, H., Mills, R. E., Schmidt, S., Moran, J. V., Weichenrieder, O., & Devine, S. E. (2008). Active Alu retrotransposons in the human genome. Genome Research, 18, 1875–1883. https://doi.org/10.1101/gr.081737.108CrossRefPubMedPubMedCentral

Borges-Monroy, R., Chu, C., Dias, C., Choi, J., Lee, S., Gao, Y., Shin, T., Park, P.J., Walsh, C.A., Lee, E.A., 2021. Whole-genome analysis of de novo and polymorphic retrotransposon insertions in Autism Spectrum Disorder. bioRxiv 2021.01.29.428895. https://doi.org/10.1101/2021.01.29.428895

Brandler, W. M., Antaki, D., Gujral, M., Kleiber, M. L., Whitney, J., Maile, M. S., Hong, O., Chapman, T. R., Tan, S., Tandon, P., Pang, T., Tang, S. C., Vaux, K. K., Yang, Y., Harrington, E., Juul, S., Turner, D. J., Thiruvahindrapuram, B., & Sebat, J. (2018). Paternally inherited cis-regulatory structural variants are associated with autism. Science, 360, 327–331. https://doi.org/10.1126/science.aan2261CrossRefPubMedPubMedCentral

Brouha, B., Schustak, J., Badge, R. M., Lutz-Prigge, S., Farley, A. H., Moran, J. V., & Kazazian, H. H. (2003). Hot L1s account for the bulk of retrotransposition in the human population. PNAS, 100, 5280–5285. https://doi.org/10.1073/pnas.0831042100CrossRefPubMedPubMedCentral

Cantrell, A. R., Tibbs, V. C., Westenbroek, R. E., Scheuer, T., & Catterall, W. A. (1999). Dopaminergic modulation of voltage-gated Na+ current in rat hippocampal neurons requires anchoring of cAMP-dependent protein kinase. J. Neurosci., 19, RC21–RC21.CrossRefPubMedPubMedCentral

Chaste, P., Klei, L., Sanders, S. J., Hus, V., Murtha, M. T., Lowe, J. K., Willsey, A. J., Moreno-De-Luca, D., Yu, T. W., Fombonne, E., Geschwind, D., Grice, D. E., Ledbetter, D. H., Mane, S. M., Martin, D. M., Morrow, E. M., Walsh, C. A., Sutcliffe, J. S., & Devlin, B. (2015). A Genome-wide association study of autism using the simons simplex collection: Does reducing phenotypic heterogeneity in autism increase genetic homogeneity? Biological Psychiatry, Autism Genotypes and Phenotypes, 77, 775–784. https://doi.org/10.1016/j.biopsych.2014.09.017CrossRef

Chen, S., Wang, J., Cicek, E., Roeder, K., Yu, H., & Devlin, B. (2020). De novo missense variants disrupting protein–protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types. Molecular Autism, 11, 76. https://doi.org/10.1186/s13229-020-00386-7CrossRefPubMedPubMedCentral

Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34, i884–i890. https://doi.org/10.1093/bioinformatics/bty560CrossRefPubMedPubMedCentral

Cordaux, R., & Batzer, M. A. (2009). The impact of retrotransposons on human genome evolution. Nature Reviews Genetics, 10, 691–703. https://doi.org/10.1038/nrg2640CrossRefPubMedPubMedCentral

Cupaioli, F. A., Fallerini, C., Mencarelli, M. A., Perticaroli, V., Filippini, V., Mari, F., Renieri, A., & Mezzelani, A. (2021). Autism spectrum disorders: Analysis of mobile elements at 7q11.23 Williams-Beuren region by comparative genomics. Genes, 12(10), 1605.CrossRefPubMedPubMedCentral

Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., & Durbin, R. (2011). The variant call format and VCFtools. Bioinformatics, 27, 2156–2158. https://doi.org/10.1093/bioinformatics/btr330CrossRefPubMedPubMedCentral

Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience. https://doi.org/10.1093/gigascience/giab008CrossRefPubMedPubMedCentral

Davis, L. K., Meyer, K. J., Rudd, D. S., Librant, A. L., Epping, E. A., Sheffield, V. C., & Wassink, T. H. (2008). Pax6 3′ deletion results in aniridia, autism and mental retardation. Human Genetics, 123, 371–378. https://doi.org/10.1007/s00439-008-0484-xCrossRefPubMedPubMedCentral

De Rubeis, S., He, X., Goldberg, A. P., Poultney, C. S., Samocha, K., Ercument Cicek, A., Kou, Y., Liu, L., Fromer, M., Walker, S., Singh, T., Klei, L., Kosmicki, J., Fu, S.-C., Aleksic, B., Biscaldi, M., Bolton, P. F., Brownfeld, J. M., & Buxbaum, J. D. (2014). Synaptic, transcriptional and chromatin genes disrupted in autism. Nature, 515, 209–215. https://doi.org/10.1038/nature13772CrossRefPubMedPubMedCentral

Donovan, A. P. A., & Basson, M. A. (2017). The neuroanatomy of autism—A developmental perspective. Journal of Anatomy, 230(1), 4–15. https://doi.org/10.1111/joa.12542CrossRefPubMed

Duttke, S. H., Chang, M. W., Heinz, S., & Benner, C. (2019). Identification and dynamic quantification of regulatory elements using total RNA. Genome Research. https://doi.org/10.1101/gr.253492.119CrossRefPubMedPubMedCentral

First, M. B., Spitzer, R. L., Gibbon, M., & Williams, J. B. (2002). Structured clinical interview for DSM-IV-TR axis I disorders, research version (patient). SCID-I/P New York.

Fishilevich, S., Nudel, R., Rappaport, N., Hadar, R., Plaschkes, I., Iny Stein, T., Rosen, N., Kohn, A., Twik, M., Safran, M., Lancet, D., & Cohen, D. (2017). GeneHancer: Genome-wide integration of enhancers and target genes in GeneCards. Database. https://doi.org/10.1093/database/bax028CrossRefPubMedPubMedCentral

Gao, T., & Qian, J. (2020). EnhancerAtlas 2.0: An updated resource with enhancer annotation in 586 tissue/cell types across nine species. Nucleic Acids Research, 48, D58–D64. https://doi.org/10.1093/nar/gkz980CrossRefPubMed

Gardner, E. J., Prigmore, E., Gallone, G., Danecek, P., Samocha, K. E., Handsaker, J., Gerety, S. S., Ironfield, H., Short, P. J., Sifrim, A., Singh, T., Chandler, K. E., Clement, E., Lachlan, K. L., Prescott, K., Rosser, E., FitzPatrick, D. R., Firth, H. V., & Hurles, M. E. (2019). Contribution of retrotransposition to developmental disorders. Nature Communications, 10, 4630. https://doi.org/10.1038/s41467-019-12520-yCrossRefPubMedPubMedCentral

Ghahramani Seno, M. M., Hu, P., Gwadry, F. G., Pinto, D., Marshall, C. R., Casallo, G., & Scherer, S. W. (2011). Gene and miRNA expression profiles in autism spectrum disorders. Brain Research, the Emerging Neuroscience of Autism Spectrum Disorders, 1380, 85–97. https://doi.org/10.1016/j.brainres.2010.09.046CrossRef

Gijón, M. A., Riekhof, W. R., Zarini, S., Murphy, R. C., & Voelker, D. R. (2008). Lysophospholipid acyltransferases and arachidonate recycling in Human neutrophils*. Journal of Biological Chemistry, 283, 30235–30245. https://doi.org/10.1074/jbc.M806194200CrossRefPubMedPubMedCentral

Hancks, D. C., & Kazazian, H. H. (2012). Active human retrotransposons: Variation and disease. Current Opinion in Genetics & Development, Molecular and Genetic Bases of Disease, 22, 191–203. https://doi.org/10.1016/j.gde.2012.02.006CrossRef

Hancks, D. C., & Kazazian, H. H. (2016). Roles for retrotransposon insertions in human disease. Mobile DNA, 7, 9. https://doi.org/10.1186/s13100-016-0065-9CrossRefPubMedPubMedCentral

Iossifov, I., O’Roak, B. J., Sanders, S. J., Ronemus, M., Krumm, N., Levy, D., Stessman, H. A., Witherspoon, K. T., Vives, L., Patterson, K. E., Smith, J. D., Paeper, B., Nickerson, D. A., Dea, J., Dong, S., Gonzalez, L. E., Mandell, J. D., Mane, S. M., & Wigler, M. (2014). The contribution of de novo coding mutations to autism spectrum disorder. Nature, 515, 216–221. https://doi.org/10.1038/nature13908CrossRefPubMedPubMedCentral

Kaufman, J., Birmaher, B., Brent, D., Rao, U., Flynn, C., Moreci, P., Williamson, D., & Ryan, N. (1997). Schedule for affective disorders and schizophrenia for school-age children-present and lifetime version (K-SADS-PL): Initial reliability and validity data. Journal of the American Academy of Child & Adolescent Psychiatry, 36, 980–988. https://doi.org/10.1097/00004583-199707000-00021CrossRef

Kazazian, H. H., & Moran, J. V. (2017). Mobile DNA in health and disease. New England Journal of Medicine, 377, 361–370. https://doi.org/10.1056/NEJMra1510092CrossRefPubMed

Kloosterman, W. P., Francioli, L. C., Hormozdiari, F., Marschall, T., Hehir-Kwa, J. Y., Abdellaoui, A., Lameijer, E.-W., Moed, M. H., Koval, V., Renkens, I., van Roosmalen, M. J., Arp, P., Karssen, L. C., Coe, B. P., Handsaker, R. E., Suchiman, E. D., Cuppen, E., & Thung, D. T. (2015). Characteristics of de novo structural changes in the human genome. Genome Research, 25, 792–801. https://doi.org/10.1101/gr.185041.114CrossRefPubMedPubMedCentral

Konopka, G., Wexler, E., Rosen, E., Mukamel, Z., Osborn, G. E., Chen, L., Lu, D., Gao, F., Gao, K., Lowe, J. K., & Geschwind, D. H. (2012). Modeling the functional genomics of autism using human neurons. Molecular Psychiatry, 17, 202–214. https://doi.org/10.1038/mp.2011.60CrossRefPubMed

Kousoulidou, L., Moutafi, M., Nicolaides, P., Hadjiloizou, S., Christofi, C., Paradesiotou, A., Anastasiadou, V., Sismani, C., & Patsalis, P. C. (2013). Screening of 50 cypriot patients with autism spectrum disorders or autistic features using 400K custom array-CGH. BioMed Research International, 2013, 1–5. https://doi.org/10.1155/2013/843027CrossRef

Krupp, D. R., Barnard, R. A., Duffourd, Y., Evans, S. A., Mulqueen, R. M., Bernier, R., Rivière, J.-B., Fombonne, E., & O’Roak, B. J. (2017). Exonic mosaic mutations contribute risk for autism spectrum disorder. The American Journal of Human Genetics, 101, 369–390. https://doi.org/10.1016/j.ajhg.2017.07.016CrossRefPubMed

Lesurf, R., Cotto, K. C., Wang, G., Griffith, M., Kasaian, K., Jones, S. J. M., Montgomery, S. B., Griffith, O. L., The Open Regulatory Annotation Consortium. (2016). ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Research, 44, D126–D132. https://doi.org/10.1093/nar/gkv1203CrossRefPubMed

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., 1000 Genome Project Data Processing Subgroup. (2009a). The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078–2079. https://doi.org/10.1093/bioinformatics/btp352CrossRefPubMedPubMedCentral

Li, H., & Durbin, R. (2009b). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760. https://doi.org/10.1093/bioinformatics/btp324CrossRefPubMedPubMedCentral

Li, H. (2011). Tabix: Fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics, 27, 718–719. https://doi.org/10.1093/bioinformatics/btq671CrossRefPubMedPubMedCentral

Lu, A.T.-H., Dai, X., Martinez-Agosto, J. A., & Cantor, R. M. (2012). Support for calcium channel gene defects in autism spectrum disorders. Molecular Autism, 3, 18. https://doi.org/10.1186/2040-2392-3-18CrossRefPubMedPubMedCentral

Malhotra, D., & Sebat, J. (2012). CNVs: Harbingers of a rare variant revolution in psychiatric genetics. Cell, 148, 1223–1241. https://doi.org/10.1016/j.cell.2012.02.039CrossRefPubMedPubMedCentral

McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016). The Ensembl variant effect predictor. Genome Biology, 17, 122. https://doi.org/10.1186/s13059-016-0974-4CrossRefPubMedPubMedCentral

McVey, M., Radut, D., & Sekelsky, J. J. (2004). End-joining repair of double-strand breaks in drosophila melanogaster is largely DNA ligase IV Independent. Genetics, 168(4), 2067–2076. https://doi.org/10.1534/genetics.104.033902CrossRefPubMedPubMedCentral

Mills, R. E., Bennett, E. A., Iskow, R. C., & Devine, S. E. (2007). Which transposable elements are active in the human genome? Trends in Genetics, 23, 183–191. https://doi.org/10.1016/j.tig.2007.02.006CrossRefPubMed

Mondal, B., Jin, H., Kallappagoudar, S., Sedkov, Y., Martinez, T., Sentmanat, M. F., Poet, G. J., Li, C., Fan, Y., Pruett-Miller, S. M., & Herz, H.-M. (2020). The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth. eLife, 9, e57519. https://doi.org/10.7554/eLife.57519CrossRefPubMedPubMedCentral

Nguyen, T. H., Nguyen, T. T. N., Le, B. V., Thanh, N. M., Nguyen, T. K. L., Nong, V. H., & Nguyen, H. H. (2017). Whole-exome sequencing identifies two novel missense mutations (p. L111P and p.R3048C) of RYR3 in a Vietnamese patient with autism spectrum disorders. Genes Genom, 39, 301–306. https://doi.org/10.1007/s13258-016-0495-2CrossRef

Nord, A. S., & West, A. E. (2020). Neurobiological functions of transcriptional enhancers. Nature Neuroscience, 23, 5–14. https://doi.org/10.1038/s41593-019-0538-5CrossRefPubMed

Okay, K., Varış, P. Ü., Miral, S., Ekinci, B., Yaraş, T., Karakülah, G., & Oktay, Y. (2021). Alternative splicing and gene co-expression network-based analysis of dizygotic twins with autism-spectrum disorder and their parents. Genomics, 113(4), 2561–2571. https://doi.org/10.1016/j.ygeno.2021.05.038CrossRefPubMed

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., … Eichler, E. E. (2012). Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature, 485, 246–250. https://doi.org/10.1038/nature10989CrossRefPubMedPubMedCentral

Ozonoff, S., Young, G. S., Carter, A., Messinger, D., Yirmiya, N., Zwaigenbaum, L., Bryson, S., Carver, L. J., Constantino, J. N., Dobkins, K., Hutman, T., Iverson, J. M., Landa, R., Rogers, S. J., Sigman, M., & Stone, W. L. (2011). Recurrence risk for autism spectrum disorders: A baby siblings research consortium study. Pediatrics, 128, e488–e495. https://doi.org/10.1542/peds.2010-2825CrossRefPubMedPubMedCentral

Petrelli, F., Pucci, L., & Bezzi, P. (2016). Astrocytes and microglia and their potential link with autism spectrum disorders. Frontiers in Cellular Neuroscience. https://doi.org/10.3389/fncel.2016.00021CrossRefPubMedPubMedCentral

Pinto, D., Pagnamenta, A. T., Klei, L., Anney, R., Merico, D., Regan, R., Conroy, J., Magalhaes, T. R., Correia, C., Abrahams, B. S., Almeida, J., Bacchelli, E., Bader, G. D., Bailey, A. J., Baird, G., Battaglia, A., Berney, T., Bolshakova, N., & Betancur, C. (2010). Functional impact of global rare copy number variation in autism spectrum disorders. Nature, 466, 368–372. https://doi.org/10.1038/nature09146CrossRefPubMedPubMedCentral

Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., Newburger, D., Dijamco, J., Nguyen, N., Afshar, P. T., Gross, S. S., Dorfman, L., McLean, C. Y., & DePristo, M. A. (2018). A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology, 36, 983–987. https://doi.org/10.1038/nbt.4235CrossRefPubMed

Qian, Y., Mancini-DiNardo, D., Judkins, T., Cox, H. C., Brown, K., Elias, M., Singh, N., Daniels, C., Holladay, J., Coffee, B., Bowles, K. R., & Roa, B. B. (2017). Identification of pathogenic retrotransposon insertions in cancer predisposition genes. Cancer Genetics, 216–217, 159–169. https://doi.org/10.1016/j.cancergen.2017.08.002CrossRefPubMed

Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841–842. https://doi.org/10.1093/bioinformatics/btq033CrossRefPubMedPubMedCentral

Rajaby, R., & Sung, W.-K. (2018). TranSurVeyor: An improved database-free algorithm for finding non-reference transpositions in high-throughput sequencing data. Nucleic Acids Research, 46, e122–e122. https://doi.org/10.1093/nar/gky685CrossRefPubMedPubMedCentral

Ronald, A., & Hoekstra, R. A. (2011). Autism spectrum disorders and autistic traits: A decade of new twin studies. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 156, 255–274. https://doi.org/10.1002/ajmg.b.31159CrossRef

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, 133–141. https://doi.org/10.1038/nrg3585CrossRefPubMed

Sanders, S. J., He, X., Willsey, A. J., Ercan-Sencicek, A. G., Samocha, K. E., Cicek, A. E., Murtha, M. T., Bal, V. H., Bishop, S. L., Dong, S., Goldberg, A. P., Jinlu, C., Keaney, J. F., Klei, L., Mandell, J. D., Moreno-De-Luca, D., Poultney, C. S., Robinson, E. B., & State, M. W. (2015). Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron, 87, 1215–1233. https://doi.org/10.1016/j.neuron.2015.09.016CrossRefPubMedPubMedCentral

Schmunk, G., Boubion, B. J., Smith, I. F., Parker, I., & Gargus, J. J. (2015). Shared functional defect in IP 3 R-mediated calcium signaling in diverse monogenic autism syndromes. Translational Psychiatry, 5, e643–e643. https://doi.org/10.1038/tp.2015.123CrossRefPubMedPubMedCentral

Schopler, E., Reichler, R. J., DeVellis, R. F., & Daly, K. (1980). Toward objective classification of childhood autism: Childhood autism rating scale (CARS). Journal of Autism and Developmental Disorders, 10, 91–103. https://doi.org/10.1007/BF02408436CrossRefPubMed

Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., Leotta, A., Pai, D., Zhang, R., Lee, Y.-H., Hicks, J., Spence, S. J., Lee, A. T., Puura, K., & Wigler, M. (2007). Strong association of de novo copy number mutations with autism. Science, 316, 445–449. https://doi.org/10.1126/science.1138659CrossRefPubMedPubMedCentral

Stewart, C., Kural, D., Strömberg, M. P., Walker, J. A., Konkel, M. K., Stütz, A. M., Urban, A. E., Grubert, F., Lam, H. Y. K., Lee, W.-P., Busby, M., Indap, A. R., Garrison, E., Huff, C., Xing, J., Snyder, M. P., Jorde, L. B., Batzer, M. A., Project 1000 Genomes. (2011). A comprehensive map of mobile element insertion polymorphisms in humans. PLOS Genetics, 7, e1002236. https://doi.org/10.1371/journal.pgen.1002236CrossRefPubMedPubMedCentral

Stricker, R., & Reiser, G. (2014). Functions of the neuron-specific protein ADAP1 (centaurin-α1) in neuronal differentiation and neurodegenerative diseases, with an overview of structural and biochemical properties of ADAP1. Biological Chemistry, 395, 1321–1340. https://doi.org/10.1515/hsz-2014-0107CrossRefPubMed

Thormann, A., Halachev, M., McLaren, W., Moore, D. J., Svinti, V., Campbell, A., Kerr, S. M., Tischkowitz, M., Hunt, S. E., Dunlop, M. G., Hurles, M. E., Wright, C. F., Firth, H. V., Cunningham, F., & FitzPatrick, D. R. (2019). Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP. Nature Communications, 10, 2373. https://doi.org/10.1038/s41467-019-10016-3CrossRefPubMedPubMedCentral

Thung, D. T., de Ligt, J., Vissers, L. E., Steehouwer, M., Kroon, M., de Vries, P., Slagboom, E. P., Ye, K., Veltman, J. A., & Hehir-Kwa, J. Y. (2014). Mobster: Accurate detection of mobile element insertions in next generation sequencing data. Genome Biology, 15, 488. https://doi.org/10.1186/s13059-014-0488-xCrossRefPubMedPubMedCentral

Tibbs, V. C., Gray, P. C., Catterall, W. A., & Murphy, B. J. (1998). AKAP15 Anchors cAMP-dependent protein kinase to brain sodium channels *. Journal of Biological Chemistry, 273, 25783–25788. https://doi.org/10.1074/jbc.273.40.25783CrossRefPubMed

Toral-Lopez, J., Huerta, L. M. G., Messina-Baas, O., & Cuevas-Covarrubias, S. A. (2020). Submicroscopic 11p13 deletion including the elongator acetyltransferase complex subunit 4 gene in a girl with language failure, intellectual disability and congenital malformations: A case report. World J Clin Cases, 8, 5296–5303.CrossRefPubMedPubMedCentral

Velmeshev, D., Schirmer, L., Jung, D., Haeussler, M., Perez, Y., Mayer, S., Bhaduri, A., Goyal, N., Rowitch, D. H., & Kriegstein, A. R. (2019). Single-cell genomics identifies cell type-specific molecular changes in autism. Science, 364(6441), 685–689.CrossRefPubMedPubMedCentral

Veltman, J. A., & Brunner, H. G. (2012). De novo mutations in human genetic disease. Nature Reviews Genetics, 13, 565–575. https://doi.org/10.1038/nrg3241CrossRefPubMed

Wang, H., Xing, J., Grover, D., Hedges, D. J., Han, K., Walker, J. A., & Batzer, M. A. (2005). SVA elements: A hominid-specific retroposon family. Journal of Molecular Biology, 354, 994–1007. https://doi.org/10.1016/j.jmb.2005.09.085CrossRefPubMed

Werling, D. M., Brand, H., An, J.-Y., Stone, M. R., Zhu, L., Glessner, J. T., Collins, R. L., Dong, S., Layer, R. M., Markenscoff-Papadimitriou, E., Farrell, A., Schwartz, G. B., Wang, H. Z., Currall, B. B., Zhao, X., Dea, J., Duhn, C., Erdman, C. A., & Sanders, S. J. (2018). An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nature Genetics, 50, 727–736. https://doi.org/10.1038/s41588-018-0107-yCrossRefPubMedPubMedCentral

Wheelwright, S., Auyeung, B., Allison, C., & Baron-Cohen, S. (2010). Defining the broader, medium and narrow autism phenotype among parents using the autism spectrum quotient (AQ). Molecular Autism, 1(1), 10. https://doi.org/10.1186/2040-2392-1-10CrossRefPubMedPubMedCentral

Williams, S. M., An, J. Y., Edson, J., Watts, M., Murigneux, V., Whitehouse, A. J. O., Jackson, C. J., Bellgrove, M. A., Cristino, A. S., & Claudianos, C. (2019). An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder. Molecular Psychiatry, 24, 1707–1719. https://doi.org/10.1038/s41380-018-0049-xCrossRefPubMed

Xu, B., Roos, J. L., Levy, S., van Rensburg, E. J., Gogos, J. A., & Karayiorgou, M. (2008). Strong association of de novo copy number mutations with sporadic schizophrenia. Nature Genetics, 40, 880–885. https://doi.org/10.1038/ng.162CrossRefPubMed

Yandım, C., & Karakülah, G. (2019). Expression dynamics of repetitive DNA in early human embryonic development. BMC Genomics, 20, 439. https://doi.org/10.1186/s12864-019-5803-1CrossRefPubMedPubMedCentral

Yant, S. R., & Kay, M. A. (2003). Nonhomologous-end-joining Factors regulate DNA repair fidelity during sleeping beauty element transposition in mammalian CELLS. Molecular and Cellular Biology, 23(23), 8505–8518. https://doi.org/10.1128/MCB.23.23.8505-8518.2003CrossRefPubMedPubMedCentral

Ye, T., Ip, J. P. K., Fu, A. K. Y., & Ip, N. Y. (2014). Cdk5-mediated phosphorylation of RapGEF2 controls neuronal migration in the developing cerebral cortex. Nature Communications, 5, 4826. https://doi.org/10.1038/ncomms5826CrossRefPubMed

Yui, K., Imataka, G., Nakamura, H., Ohara, N., & Naito, Y. (2015). Eicosanoids derived from arachidonic acid and their family prostaglandins and cyclooxygenase in psychiatric disorders. Current Neuropharmacology, 13, 776–785.CrossRefPubMedPubMedCentral

Zhang, J., Feuk, L., Duggan, G. E., Khaja, R., & Scherer, S. W. (2006). Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenetic and Genome Research, 115(3–4), 205–214. https://doi.org/10.1159/000095916CrossRefPubMed

Zhang, Y., Li, S., Abyzov, A., & Gerstein, M. B. (2017). Landscape and variation of novel retroduplications in 26 human populations. PLOS Computational Biology, 13, e1005567. https://doi.org/10.1371/journal.pcbi.1005567CrossRefPubMedPubMedCentral

Zhao, X., Leotta, A., Kustanovich, V., Lajonchere, C., Geschwind, D. H., Law, K., Law, P., Qiu, S., Lord, C., Sebat, J., Ye, K., & Wigler, M. (2007). A unified genetic theory for sporadic and inherited autism. PNAS, 104, 12831–12836. https://doi.org/10.1073/pnas.0705803104CrossRefPubMedPubMedCentral

Titel: Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment
Auteurs: Kaan Okay
Pelin Ünal Varış
Süha Miral
Athanasia Pavlopoulou
Yavuz Oktay
Gökhan Karakülah
Publicatiedatum: 27-06-2022
Uitgeverij: Springer US
Gepubliceerd in: Journal of Autism and Developmental Disorders / Uitgave 3/2023
Print ISSN: 0162-3257
Elektronisch ISSN: 1573-3432
DOI: https://doi.org/10.1007/s10803-022-05636-6

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