Copy number variation in Han Chinese individuals with autism spectrum disorder

详细信息    查看全文

• 作者：Matthew J Gazzellone (1) (2)
  Xue Zhou (1) (3) (4)
  Anath C Lionel (1) (2)
  Mohammed Uddin (1)
  Bhooma Thiruvahindrapuram (1)
  Shuang Liang (3)
  Caihong Sun (3)
  Jia Wang (3)
  Mingyang Zou (3)
  Kristiina Tammimies (1) (5)
  Susan Walker (1)
  Thanuja Selvanayagam (1)
  John Wei (1)
  Zhuozhi Wang (1)
  Lijie Wu (3)
  Stephen W Scherer (1) (2)
  
  1. The Centre for Applied Genomics and Program in Genetics and Genome Biology ; The Hospital for Sick Children ; Peter Gilgan Centre for Research and Learning ; 686 Bay Street ; Room 139800 ; Toronto ; Ontario ; M5G 0A4 ; Canada
  2. Department of Molecular Genetics and McLaughlin Centre ; University of Toronto ; Toronto ; Ontario ; M5S 1A1 ; Canada
  3. Department of Children鈥檚 and Adolescent Health ; Public Health College of Harbin Medical University ; Harbin ; Heilongjiang ; 150086 ; People鈥檚 Republic of China
  4. Heilongjiang Provincial Centre for Disease Control and Prevention ; Harbin ; Heilongjiang ; 150030 ; People鈥檚 Republic of China
  5. Center of Neurodevelopmental Disorders ; Department of Women鈥檚 and Children鈥檚 Health ; Karolinska Institutet ; Stockholm ; 113 30 ; Sweden
  
• 关键词：Autism spectrum disorder (ASD) ; Copy number variations (CNVs) ; Microarray diagnostic testing ; Han Chinese
• 刊名：Journal of Neurodevelopmental Disorders
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：6
• 期：1
• 全文大小：358 KB
• 参考文献：1. Devlin, B, Scherer, SW (2012) Genetic architecture in autism spectrum disorder. Curr Opin Genet Dev 22: pp. 229-237 CrossRef
  2. Pinto, D, Delaby, E, Merico, D, Barbosa, M, Merikangas, A, Klei, L, Thiruvahindrapuram, B, Xu, X, Ziman, R, Wang, Z, Vorstman, JA, Thompson, A, Regan, R, Pilorge, M, Pellecchia, G, Pagnamenta, AT, Oliveira, B, Marshall, CR, Magalhaes, TR, Lowe, JK, Howe, JL, Griswold, AJ, Gilbert, J, Duketis, E, Dombroski, BA, De Jonge, MV, Cuccaro, M, Crawford, EL, Correia, CT, Conroy, J (2014) Convergence of genes and cellular pathways dysregulated in autism spectrum disorders. Am J Hum Genet 94: pp. 677-694 CrossRef
  3. Marshall, CR, Noor, A, Vincent, JB, Lionel, AC, Feuk, L, Skaug, J, Shago, M, Moessner, R, Pinto, D, Ren, Y, Thiruvahindrapduram, B, Fiebig, A, Schreiber, S, Friedman, J, Ketelaars, CE, Vos, YJ, Ficicioglu, C, Kirkpatrick, S, Nicolson, R, Sloman, L, Summers, A, Gibbons, CA, Teebi, A, Chitayat, D, Weksberg, R, Thompson, A, Vardy, C, Crosbie, V, Luscombe, S, Baatjes, R (2008) Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet 82: pp. 477-488 CrossRef
  4. Pinto, D, Pagnamenta, AT, Klei, L, Anney, R, Merico, D, Regan, R, Conroy, J, Magalhaes, TR, Correia, C, Abrahams, BS, Almeida, J, Bacchelli, E, Bader, GD, Bailey, AJ, Baird, G, Battaglia, A, Berney, T, Bolshakova, N, Bolte, S, Bolton, PF, Bourgeron, T, Brennan, S, Brian, J, Bryson, SE, Carson, AR, Casallo, G, Casey, J, Chung, BH, Cochrane, L, Corsello, C (2010) Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466: pp. 368-372 CrossRef
  5. Miller, DT, Adam, MP, Aradhya, S, Biesecker, LG, Brothman, AR, Carter, NP, Church, DM, Crolla, JA, Eichler, EE, Epstein, CJ, Faucett, WA, Feuk, L, Friedman, JM, Hamosh, A, Jackson, L, Kaminsky, EB, Kok, K, Krantz, ID, Kuhn, RM, Lee, C, Ostell, JM, Rosenberg, C, Scherer, SW, Spinner, NB, Stavropoulos, DJ, Tepperberg, JH, Thorland, EC, Vermeesch, JR, Waggoner, DJ, Watson, MS (2010) Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 86: pp. 749-764 CrossRef
  6. Elsabbagh, M, Divan, G, Koh, YJ, Kim, YS, Kauchali, S, Marcin, C, Montiel-Nava, C, Patel, V, Paula, CS, Wang, C, Yasamy, MT, Fombonne, E (2012) Global prevalence of autism and other pervasive developmental disorders. Autism Res 5: pp. 160-179 CrossRef
  7. Sun, X, Allison, C, Matthews, FE, Sharp, SJ, Auyeung, B, Baron-Cohen, S, Brayne, C (2013) Prevalence of autism in mainland China. Hong Kong and Taiwan: a systematic review and meta-analysis. Mol Autism 4: pp. 7 CrossRef
  8. Zhou, X, Xu, Y, Wang, J, Zhou, H, Liu, X, Ayub, Q, Wang, X, Tyler-Smith, C, Wu, L, Xue, Y (2011) Replication of the association of a MET variant with autism in a Chinese Han population. PLoS One 6: pp. e27428 CrossRef
  9. Park, H, Kim, JI, Ju, YS, Gokcumen, O, Mills, RE, Kim, S, Lee, S, Suh, D, Hong, D, Kang, HP, Yoo, YJ, Shin, JY, Kim, HJ, Yavartanoo, M, Chang, YW, Ha, JS, Chong, W, Hwang, GR, Darvishi, K, Kim, H, Yang, SJ, Yang, KS, Hurles, ME, Scherer, SW, Carter, NP, Tyler-Smith, C, Lee, C, Seo, JS (2010) Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet 42: pp. 400-405 CrossRef
  10. Pinto, D, Darvishi, K, Shi, X, Rajan, D, Rigler, D, Fitzgerald, T, Lionel, AC, Thiruvahindrapuram, B, Macdonald, JR, Mills, R, Prasad, A, Noonan, K, Gribble, S, Prigmore, E, Donahoe, PK, Smith, RS, Park, JH, Hurles, ME, Carter, NP, Lee, C, Scherer, SW, Feuk, L (2011) Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 29: pp. 512-520 CrossRef
  11. MacDonald, JR, Ziman, R, Yuen, RK, Feuk, L, Scherer, SW (2014) The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res 42: pp. D986-D992 CrossRef
  12. Egger, G, Roetzer, KM, Noor, A, Lionel, AC, Mahmood, H, Schwarzbraun, T, Boright, O, Mikhailov, A, Marshall, CR, Windpassinger, C, Petek, E, Scherer, SW, Kaschnitz, W, Vincent, JB (2014) Identification of risk genes for autism spectrum disorder through copy number variation analysis in Austrian families. Neurogenetics 15: pp. 117-127 CrossRef
  13. Lautier, C, Goldwurm, S, Durr, A, Giovannone, B, Tsiaras, WG, Pezzoli, G, Brice, A, Smith, RJ (2008) Mutations in the GIGYF2 (TNRC15) gene at the PARK11 locus in familial Parkinson disease. Am J Hum Genet 82: pp. 822-833 CrossRef
  14. Yu, T, Yaguchi, Y, Echevarria, D, Martinez, S, Basson, MA (2011) Sprouty genes prevent excessive FGF signalling in multiple cell types throughout development of the cerebellum. Development 138: pp. 2957-2968 CrossRef
  15. Uddin, M, Tammimies, K, Pellecchia, G, Alipanahi, B, Hu, P, Wang, Z, Pinto, D, Lau, L, Nalpathamkalam, T, Marshall, CR, Blencowe, BJ, Frey, BJ, Merico, D, Yuen, RK, Scherer, SW (2014) Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder. Nat Genet 46: pp. 742-747 CrossRef
  16. Stafford, RL, Hinde, E, Knight, MJ, Pennella, MA, Ear, J, Digman, MA, Gratton, E, Bowie, JU (2011) Tandem SAM domain structure of human Caskin1: a presynaptic, self-assembling scaffold for CASK. Structure 19: pp. 1826-1836 CrossRef
  17. Bisbal, M, Conde, C, Donoso, M, Bollati, F, Sesma, J, Quiroga, S, Diaz Anel, A, Malhotra, V, Marzolo, MP, Caceres, A (2008) Protein kinase d regulates trafficking of dendritic membrane proteins in developing neurons. J Neurosci 28: pp. 9297-9308 CrossRef
  18. McGrath, LM, Yu, D, Marshall, C, Davis, LK, Thiruvahindrapuram, B, Li, B, Cappi, C, Gerber, G, Wolf, A, Schroeder, FA, Osiecki, L, O'Dushlaine, C, Kirby, A, Illmann, C, Haddad, S, Gallagher, P, Fagerness, JA, Barr, CL, Bellodi, L, Benarroch, F, Bienvenu, OJ, Black, DW, Bloch, MH, Bruun, RD, Budman, CL, Camarena, B, Cath, DC, Cavallini, MC, Chouinard, S, Coric, V (2014) Copy number variation in obsessive-compulsive disorder and tourette syndrome: a cross-disorder study. J Am Acad Child Adolesc Psychiatry 53: pp. 910-919 CrossRef
  19. Bochukova, EG, Huang, N, Keogh, J, Henning, E, Purmann, C, Blaszczyk, K, Saeed, S, Hamilton-Shield, J, Clayton-Smith, J, O'Rahilly, S, Hurles, ME, Farooqi, IS (2010) Large, rare chromosomal deletions associated with severe early-onset obesity. Nature 463: pp. 666-670 CrossRef
  20. Bi, W, Sapir, T, Shchelochkov, OA, Zhang, F, Withers, MA, Hunter, JV, Levy, T, Shinder, V, Peiffer, DA, Gunderson, KL, Nezarati, MM, Shotts, VA, Amato, SS, Savage, SK, Harris, DJ, Day-Salvatore, DL, Horner, M, Lu, XY, Sahoo, T, Yanagawa, Y, Beaudet, AL, Cheung, SW, Martinez, S, Lupski, JR, Reiner, O (2009) Increased LIS1 expression affects human and mouse brain development. Nat Genet 41: pp. 168-177 CrossRef
  21. Wu, JY, Kuban, KC, Allred, E, Shapiro, F, Darras, BT (2005) Association of Duchenne muscular dystrophy with autism spectrum disorder. J Child Neurol 20: pp. 790-795 CrossRef
  22. Chowanadisai, W, Graham, DM, Keen, CL, Rucker, RB, Messerli, MA (2013) Neurulation and neurite extension require the zinc transporter ZIP12 (slc39a12). Proc Natl Acad Sci U S A 110: pp. 9903-9908 CrossRef
  23. Matsunami, N, Hadley, D, Hensel, CH, Christensen, GB, Kim, C, Frackelton, E, Thomas, K, da Silva, RP, Stevens, J, Baird, L, Otterud, B, Ho, K, Varvil, T, Leppert, T, Lambert, CG, Leppert, M, Hakonarson, H (2013) Identification of rare recurrent copy number variants in high-risk autism families and their prevalence in a large ASD population. PLoS One 8: pp. e52239 CrossRef
  24. Carter, MT, Scherer, SW (2013) Autism spectrum disorder in the genetics clinic: a review. Clin Genet 83: pp. 399-407 CrossRef
  25. Kamien, B, Lionel, AC, Bain, N, Scherer, SW, Hunter, M (2014) Outfoxed by RBFOX1-A caution about ascertainment bias. Am J Med Genet A 164: pp. 1411-1418 CrossRef
  26. Poultney, CS, Goldberg, AP, Drapeau, E, Kou, Y, Harony-Nicolas, H, Kajiwara, Y, De Rubeis, S, Durand, S, Stevens, C, Rehnstrom, K, Palotie, A, Daly, MJ, Ma'ayan, A, Fromer, M, Buxbaum, JD (2013) Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. Am J Hum Genet 93: pp. 607-619 CrossRef
  27. Toyo-oka, K, Shionoya, A, Gambello, MJ, Cardoso, C, Leventer, R, Ward, HL, Ayala, R, Tsai, LH, Dobyns, W, Ledbetter, D, Hirotsune, S, Wynshaw-Boris, A (2003) 14-3-3epsilon is important for neuronal migration by binding to NUDEL: a molecular explanation for Miller-Dieker syndrome. Nat Genet 34: pp. 274-285 CrossRef
  28. Bruno, DL, Anderlid, BM, Lindstrand, A, van Ravenswaaij-Arts, C, Ganesamoorthy, D, Lundin, J, Martin, CL, Douglas, J, Nowak, C, Adam, MP, Kooy, RF, Van der Aa, N, Reyniers, E, Vandeweyer, G, Stolte-Dijkstra, I, Dijkhuizen, T, Yeung, A, Delatycki, M, Borgstrom, B, Thelin, L, Cardoso, C, van Bon, B, Pfundt, R, de Vries, BB, Wallin, A, Amor, DJ, James, PA, Slater, HR, Schoumans, J (2010) Further molecular and clinical delineation of co-locating 17p13.3 microdeletions and microduplications that show distinctive phenotypes. J Med Genet 47: pp. 299-311 CrossRef
  29. Curry, CJ, Rosenfeld, JA, Grant, E, Gripp, KW, Anderson, C, Aylsworth, AS, Saad, TB, Chizhikov, VV, Dybose, G, Fagerberg, C, Falco, M, Fels, C, Fichera, M, Graakjaer, J, Greco, D, Hair, J, Hopkins, E, Huggins, M, Ladda, R, Li, C, Moeschler, J, Nowaczyk, MJ, Ozmore, JR, Reitano, S, Romano, C, Roos, L, Schnur, RE, Sell, S, Suwannarat, P, Svaneby, D (2013) The duplication 17p13.3 phenotype: analysis of 21 families delineates developmental, behavioral and brain abnormalities, and rare variant phenotypes. Am J Med Genet A 161A: pp. 1833-1852 CrossRef
  30. Nagamani, SC, Zhang, F, Shchelochkov, OA, Bi, W, Ou, Z, Scaglia, F, Probst, FJ, Shinawi, M, Eng, C, Hunter, JV, Sparagana, S, Lagoe, E, Fong, CT, Pearson, M, Doco-Fenzy, M, Landais, E, Mozelle, M, Chinault, AC, Patel, A, Bacino, CA, Sahoo, T, Kang, SH, Cheung, SW, Lupski, JR, Stankiewicz, P (2009) Microdeletions including YWHAE in the Miller-Dieker syndrome region on chromosome 17p13.3 result in facial dysmorphisms, growth restriction, and cognitive impairment. J Med Genet 46: pp. 825-833 CrossRef
  31. Prasad, A, Merico, D, Thiruvahindrapuram, B, Wei, J, Lionel, AC, Sato, D, Rickaby, J, Lu, C, Szatmari, P, Roberts, W, Fernandez, BA, Marshall, CR, Hatchwell, E, Eis, PS, Scherer, SW (2012) A discovery resource of rare copy number variations in individuals with autism spectrum disorder. G3 (Bethesda) 2: pp. 1665-1685 CrossRef
  32. Jiang, YH, Yuen, RK, Jin, X, Wang, M, Chen, N, Wu, X, Ju, J, Mei, J, Shi, Y, He, M, Wang, G, Liang, J, Wang, Z, Cao, D, Carter, MT, Chrysler, C, Drmic, IE, Howe, JL, Lau, L, Marshall, CR, Merico, D, Nalpathamkalam, T, Thiruvahindrapuram, B, Thompson, A, Uddin, M, Walker, S, Luo, J, Anagnostou, E, Zwaigenbaum, L, Ring, RH (2013) Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. Am J Hum Genet 93: pp. 249-263 CrossRef
  
• 刊物主题：Neurosciences; Neurobiology; Neuropsychology; Psychiatry; Human Genetics; Pediatrics;
• 出版者：BioMed Central
• ISSN：1866-1955

文摘

Background Autism spectrum disorders (ASDs) are a group of neurodevelopmental conditions with a demonstrated genetic etiology. Rare (CNVs) account for a proportion of the genetic events involved, but the contribution of these events in non-European ASD populations has not been well studied. Here, we report on rare CNVs detected in a cohort of individuals with ASD of Han Chinese background. Methods DNA samples were obtained from 104 ASD probands and their parents who were recruited from Harbin, China. Samples were genotyped on the Affymetrix CytoScan HD platform. Rare CNVs were identified by comparing data with 873 technology-matched controls from Ontario and 1,235 additional population controls of Han Chinese ethnicity. Results Of the probands, 8.6% had at least 1 de novo CNV (overlapping the GIGYF2, SPRY1, 16p13.3, 16p11.2, 17p13.3-17p13.2, DMD, and NAP1L6 genes/loci). Rare inherited CNVs affected other plausible neurodevelopmental candidate genes including GRID2, LINGO2, and SLC39A12. A 24-kb duplication was also identified at YWHAE, a gene previously implicated in ASD and other developmental disorders. This duplication is observed at a similar frequency in cases and in population controls and is likely a benign Asian-specific copy number polymorphism. Conclusions Our findings help define genomic features relevant to ASD in the Han Chinese and emphasize the importance of using ancestry-matched controls in medical genetic interpretations.