A Discovery resource of rare copy number variations in individuals with autism spectrum disorder

G3: Genes, Genomes, Genetics

Volumn 2, Issue 12, 2012, Pages 1665-1685

  Prasad, Aparna ^a   Merico, Daniele ^a   Thiruvahindrapuram, Bhooma ^a   Wei, John ^a   Lionel, Anath C ^a,b   Sato, Daisuke ^a   Rickaby, Jessica ^a   Lu, Chao ^a   Szatmari, Peter ^c   Roberts, Wendy ^d   Fernandez, Bridget A ^e   Marshall, Christian R ^a,b   Hatchwell, Eli ^f   Eis, Peggy S ^f   Scherer, Stephen W ^a,b  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c MCMASTER UNIVERSITY   (Canada)

^d HOSPITAL FOR SICK CHILDREN   (Canada)

^e MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

^f Population Diagnostics Inc   (United States)

Author keywords

Abnormalities; Chromosomal; Cytogenetics; Gene copy; Molecular; Number; Pathways; Rare variants

Indexed keywords

ARTICLE; AUTISM; CHILD; CHROMOSOMAL ABNORMALITIES; COHORT ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; CYTOGENETICS; FEMALE; GENE DOSAGE; GENE LOCUS; GENETICS; GENOTYPE; HUMAN; HUMAN GENOME; MALE; MOLECULAR PATHWAYS; PHENOTYPE; RARE VARIANTS; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOMAL ABNORMALITIES; CYTOGENETICS; GENE COPY NUMBER; MOLECULAR PATHWAYS; RARE VARIANTS;

CHILD; CHILD DEVELOPMENT DISORDERS, PERVASIVE; COHORT STUDIES; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; FEMALE; GENETIC LOCI; GENOME, HUMAN; GENOTYPE; HUMANS; MALE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84883171661     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.112.004689     Document Type: Article

References (84)

1. Ardlie, K. G., K. L. Lunetta, and M. Seielstad, 2002 Testing for population subdivision and association in four case-control studies. Am. J. Hum. Genet. 71: 304-311.
2. Autism Genome Project ConsortiumSzatmari, P., A. D. Paterson, L. Zwaigenbaum, W. Roberts et al., 2007 Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat. Genet. 39: 319-328.
3. Banting, G. S., O. Barak, T. M. Ames, A. C. Burnham, M. D. Kardel et al., 2005 CECR2, a protein involved in neurulation, forms a novel chromatin remodeling complex with SNF2L. Hum. Mol. Genet. 14: 513-524.
4. Betancur, C., 2011 Etiological heterogeneity in autism spectrum disorders: More than 100 genetic and genomic disorders and still counting. Brain Res. 1380: 42-77.
5. Bierut, L. J., A. Agrawal, K. K. Bucholz, K. F. Doheny, C. Laurie et al., 2010 A genome-wide association study of alcohol dependence. Proc. Natl. Acad. Sci. USA 107: 5082-5087.
6. Binda, A. V., N. Kabbani, R. Lin, and R. Levenson, 2002 D2 and D3 dopamine receptor cell surface localization mediated by interaction with protein 4.1N. Mol. Pharmacol. 62: 507-513.
7. Blazejczyk, M., A. Sobczak, K. Debowska, M. B. Wisniewska, A. Kirilenko et al., 2009 Biochemical characterization and expression analysis of a novel EF-hand Ca2+ binding protein calmyrin2 (Cib2) in brain indicates its function in NMDA receptor mediated Ca2+ signaling. Arch. Biochem. Biophys. 487: 66-78.
8. Bruno, D. L., B. M. Anderlid, A. Lindstrand, C. van Ravenswaaij-Arts, D. Ganesamoorthy et al., 2010 Further molecular and clinical delineation of co-locating 17p13.3 microdeletions and microduplications that show distinctive phenotypes. J. Med. Genet. 47: 299-311.
9. Carter, M. T., S. M. Nikkel, B. A. Fernandez, C. R. Marshall, A. Noor et al., 2011 Hemizygous deletions on chromosome 1p21.3 involving the DPYD gene in individuals with autism spectrum disorder. Clin. Genet. 80: 435-443.
10. Christian, S. L., C. W. Brune, J. Sudi, R. A. Kumar, S. Liu et al., 2008 Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder. Biol. Psychiatry 63: 1111-1117.
11. Colella, S., C. Yau, J. M. Taylor, G. Mirza, H. Butler et al., 2007 QuantiSNP: an objective bayes hidden-markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res. 35: 2013-2025.
12. Conrad, D. F., D. Pinto, R. Redon, L. Feuk, O. Gokcumen et al., 2010 Origins and functional impact of copy number variation in the human genome. Nature 464: 704-712.
13. Cook, E. H. Jr, and S. W. Scherer, 2008 Copy-number variations associated with neuropsychiatric conditions. Nature 455: 919-923.
14. Curtis, C., A. G. Lynch, M. J. Dunning, I. Spiteri, J. C. Marioni et al., 2009 The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10: 588.
15. Devlin, B., and S. W. Scherer, 2012 Genetic architecture in autism spectrum disorder. Curr. Opin. Genet. Dev. 22: 229-237.
16. Erturk, O., K. Bilguvar, B. Korkmaz, Y. Bayri, F. Bayrakli et al., 2010 A patient with duchenne muscular dystrophy and autism demonstrates a hemizygous deletion affecting dystrophin. Am. J. Med. Genet. A. 152A: 1039-1042.
17. Ewing, R. M., P. Chu, F. Elisma, H. Li, P. Taylor et al., 2007 Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3: 89.
18. Ferro, E., and L. Trabalzini, 2010 RalGDS family members couple ras to ral signalling and that's not all. Cell. Signal. 22: 1804-1810.
19. Gao, Y., D. V. Vasilyev, M. B. Goncalves, F. V. Howell, C. Hobbs et al., 2010 loss of retrograde endocannabinoid signaling and reduced adult neurogenesis in diacylglycerol lipase knock-out mice. J. Neurosci. 30: 2017-2024.
20. Gareau, J. R., and C. D. Lima, 2010 The SUMO pathway: Emerging mechanisms that shape specificity, conjugation and recognition. Nat. Rev. Mol. Cell Biol. 11: 861-871.
21. Glessner, J. T., K. Wang, G. Cai, O. Korvatska, C. E. Kim et al., 2009 Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 459: 569-573.
22. Graubert, T. A., P. Cahan, D. Edwin, R. R. Selzer, T. A. Richmond et al., 2007 A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet. 3: e3.
23. Griswold, A. J., D. Ma, S. J. Sacharow, J. L. Robinson, J. M. Jaworski et al., 2011 A de novo 1.5 mb microdeletion on chromosome 14q23.2-23.3 in a patient with autism and spherocytosis. Autism Res. 4: 221-227.
24. Haraguchi, M., H. Tsujimoto, M. Fukushima, I. Higuchi, H. Kuribayashi et al., 2002 Targeted deletion of both thymidine phosphorylase and uridine phosphorylase and consequent disorders in mice. Mol. Cell. Biol. 22: 5212-5221.
25. Hester, S. D., L. Reid, N. Nowak, W. D. Jones, J. S. Parker et al., 2009 Comparison of comparative genomic hybridization technologies across microarray platforms. J. Biomol. Tech. 20: 135-151.
26. Hinton, V. J., S. E. Cyrulnik, R. J. Fee, A. Batchelder, J. M. Kiefel et al., 2009 Association of autistic spectrum disorders with dystrophinopathies. Pediatr. Neurol. 41: 339-346.
27. International HapMap 3 ConsortiumAltshuler, D. M., R. A. Gibbs, L. Peltonen, D. M. Altshuler et al., 2010 Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58.
28. Ivanovic, A., I. Horresh, N. Golan, I. Spiegel, H. Sabanay et al., 2012 The cytoskeletal adapter protein 4.1G organizes the internodes in peripheral myelinated nerves. J. Cell Biol. 196: 337-344.
29. Jacquemont, M. L., D. Sanlaville, R. Redon, O. Raoul, V. Cormier-Daire et al., 2006 Array-based comparative genomic hybridisation identifies high frequency of cryptic chromosomal rearrangements in patients with syndromic autism spectrum disorders. J. Med. Genet. 43: 843-849.
30. Keilhoff, G., S. Wiegand, and H. Fansa, 2012 Vav deficiency impedes peripheral nerve regeneration in mice. Restor. Neurol. Neurosci. 30: 463-479
31. Korn, J. M., F. G. Kuruvilla, S. A. McCarroll, A. Wysoker, J. Nemesh et al., 2008 Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat. Genet. 40: 1253-1260.
32. Krawczak, M., S. Nikolaus, H. von Eberstein, P. J. Croucher, N. E. El Mokhtari et al., 2006 PopGen: Population-based recruitment of patients and controls for the analysis of complex genotype-phenotype relationships. Community Genet. 9: 55-61.
33. Kudryashova, E., J. Wu, L. A. Havton, and M. J. Spencer, 2009 Deficiency of the E3 ubiquitin ligase TRIM32 in mice leads to a myopathy with a neurogenic component. Hum. Mol. Genet. 18: 1353-1367.
34. Lai, W. R., M. D. Johnson, R. Kucherlapati, and P. J. Park, 2005 Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 21: 3763-3770.
35. Lee, C., and S. W. Scherer, 2010 The clinical context of copy number variation in the human genome. Expert Rev. Mol. Med. 12: e8.
36. Lesch, K. P., N. Timmesfeld, T. J. Renner, R. Halperin, C. Roser et al., 2008 Molecular genetics of adult ADHD: Converging evidence from genome-wide association and extended pedigree linkage studies. J. Neural Transm. 115: 1573-1585.
37. Li, X. F., L. Kiedrowski, F. Tremblay, F. R. Fernandez, M. Perizzolo et al., 2006 Importance of K+-dependent Na+/Ca2+-exchanger 2, NCKX2, in motor learning and memory. J. Biol. Chem. 281: 6273-6282.
38. Lionel, A. C., J. Crosbie, N. Barbosa, T. Goodale, B. Thiruvahindrapuram et al., 2011 Rare copy number variation discovery and cross-disorder comparisons identify risk genes for ADHD. Sci. Transl. Med. 3: 95ra75.
39. López, L. C., H. O. Akman, A. Garcia-Cazorla, B. Dorado, R. Marti et al., 2009 Unbalanced deoxynucleotide pools cause mitochondrial DNA instability in thymidine phosphorylase-deficient mice. Hum. Mol. Genet. 18: 714-722.
40. Marshall, C. R., A. Noor, J. B. Vincent, A. C. Lionel, L. Feuk et al., 2008 Structural variation of chromosomes in autism spectrum disorder. Am. J. Hum. Genet. 82: 477-488.
41. Marui, T., O. Hashimoto, E. Nanba, C. Kato, M. Tochigi et al., 2004 Association between the neurofibromatosis-1 (NF1) locus and autism in the japanese population. Am. J. Med. Genet. B. Neuropsychiatr. Genet. 131B: 43-47.
42. McCarroll, S. A., F. G. Kuruvilla, J. M. Korn, S. Cawley, J. Nemesh et al., 2008 Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40: 1166-1174.
43. Meechan, D. W., E. S. Tucker, T. M. Maynard, and A. S. LaMantia, 2009 Diminished dosage of 22q11 genes disrupts neurogenesis and cortical development in a mouse model of 22q11 deletion/DiGeorge syndrome. Proc. Natl. Acad. Sci. USA 106: 16434-16445.
44. Merico, D., R. Isserlin, O. Stueker, A. Emili, and G. D. Bader, 2010 Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS ONE 5: e13984.
45. Miller, D. T., M. P. Adam, S. Aradhya, L. G. Biesecker, A. R. Brothman et al., 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: 749-764.
46. Miyashita, T., S. Y. Yeo, Y. Hirate, H. Segawa, H. Wada et al., 2004 PlexinA4 is necessary as a downstream target of Islet2 to mediate slit signaling for promotion of sensory axon branching. Development 131: 3705-3715.
47. Neale, B. M., Y. Kou, L. Liu, A. Ma'ayan, K. E. Samocha et al., 2012 Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 485: 242-245.
48. Noor, A., A. Whibley, C. R. Marshall, P. J. Gianakopoulos, A. Piton et al., 2010 Disruption at the PTCHD1 locus on Xp22.11 in autism spectrum disorder and intellectual disability. Sci. Transl. Med. 2: 49ra68.
49. O'Roak, B. J., P. Deriziotis, C. Lee, L. Vives, J. J. Schwartz et al., 2011 Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat. Genet. 43: 585-589.
50. O'Roak, B. J., L. Vives, S. Girirajan, E. Karakoc, N. Krumm et al., 2012 Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485: 246-250.
51. Pagnamenta, A. T., E. Bacchelli, M. V. de Jonge, G. Mirza, T. S. Scerri et al., 2010 Characterization of a family with rare deletions in CNTNAP5 and DOCK4 suggests novel risk loci for autism and dyslexia. Biol. Psychiatry 68: 320-328.
52. Pinto,D., A. T. Pagnamenta, L.Klei, R. Anney,D.Merico et al., 2010 Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466: 368-372.
53. Pinto, D., K. Darvishi, X. Shi, D. Rajan, D. Rigler et al., 2011 Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat. Biotechnol. 29: 512-520.
54. Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. Ferreira et al., 2007 PLINK: a tool set for whole-genome association and populationbased linkage analyses. Am. J. Hum. Genet. 81: 559-575.
55. Redies, C., N. Hertel, and C. A. Hubner, 2012 Cadherins and neuropsychiatric disorders. Brain Res. 1470: 130-144.
56. Redon, R., S. Ishikawa, K. R. Fitch, L. Feuk, G. H. Perry et al., 2006 Global variation in copy number in the human genome. Nature 444: 444-454.
57. Rivero, O., S. Sich, S. Popp, A. Schmitt, B. Franke et al., 2012 Impact of the ADHD-susceptibility gene CDH13 on development and function of brain networks. Eur. Neuropsychopharmacol. (in press).
58. Rual, J. F., K. Venkatesan, T. Hao, T. Hirozane-Kishikawa, A. Dricot et al., 2005 Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
59. Sabbir, M. G., N. Wigle, S. Loewen, Y. Gu, C. Buse et al., 2010 Identification and characterization of Dlc1 isoforms in the mouse and study of the biological function of a single gene trapped isoform. BMC Biol. 8: 17.
60. Salyakina, D., H. N. Cukier, J. M. Lee, S. Sacharow, L. D. Nations et al., 2011 Copy number variants in extended autism spectrum disorder families reveal candidates potentially involved in autism risk. PLoS ONE 6: e26049.
61. Sanders, S. J., A. G. Ercan-Sencicek, V. Hus, R. Luo, M. T. Murtha et al., 2011 Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism. Neuron 70: 863-885.
62. Sanders, S. J., M. T. Murtha, A. R. Gupta, J. D. Murdoch, M. J. Raubeson et al., 2012 De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485: 237-241.
63. Sato, D., A. C. Lionel, C. S. Leblond, A. Prasad, D. Pinto et al., 2012 SHANK1 deletions in males with autism spectrum disorder. Am. J. Hum. Genet. 90: 879-887.
64. Schaaf, C. P., A. Sabo, Y. Sakai, J. Crosby, D. Muzny et al., 2011 Oligogenic heterozygosity in individuals with high-functioning autism spectrum disorders. Hum. Mol. Genet. 20: 3366-3375.
65. Scherer, S. W., and G. Dawson, 2011 Risk factors for autism: translating genomic discoveries into diagnostics. Hum. Genet. 130: 123-148.
66. Sebat, J., B. Lakshmi, D. Malhotra, J. Troge, C. Lese-Martin et al., 2007 Strong association of de novo copy number mutations with autism. Science 316: 445-449.
67. Serajee, F. J., H. Zhong, R. Nabi, and A. H. Huq, 2003 The metabotropic glutamate receptor 8 gene at 7q31: partial duplication and possible association with autism. J. Med. Genet. 40: e42.
68. Shen, L., F. Liang, L. D. Walensky, and R. L. Huganir, 2000 Regulation of AMPA receptor GluR1 subunit surface expression by a 4.1N-linked actin cytoskeletal association. J. Neurosci. 20: 7932-7940.
69. Shen, Y., K. A. Dies, I. A. Holm, C. Bridgemohan, M. M. Sobeih et al., 2010 Clinical genetic testing for patients with autism spectrum disorders. Pediatrics 125: e727-e735.
70. Sherr, E. H., 2003 The ARX story (epilepsy, mental retardation, autism, and cerebral malformations): One gene leads to many phenotypes. Curr. Opin. Pediatr. 15: 567-571.
71. Shinawi, M., and S. W. Cheung, 2008 The array CGH and its clinical applications. Drug Discov. Today 13: 760-770.
72. Stewart, A. F., S. Dandona, L. Chen, O. Assogba, M. Belanger et al., 2009 Kinesin family member 6 variant Trp719Arg does not associate with angiographically defined coronary artery disease in the ottawa heart genomics study. J. Am. Coll. Cardiol. 53: 1471-1472.
73. Suto, F., Y. Murakami, F. Nakamura, Y. Goshima, and H. Fujisawa, 2003 Identification and characterization of a novel mouse plexin, plexin-A4. Mech. Dev. 120: 385-396.
74. Szklarczyk, D., A. Franceschini, M. Kuhn, M. Simonovic, A. Roth et al., 2011 The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 39: D561- D568.
75. Vaags, A. K., A. C. Lionel, D. Sato, M. Goodenberger, Q. P. Stein et al., 2012 Rare deletions at the neurexin 3 locus in autism spectrum disorder. Am. J. Hum. Genet. 90: 133-141.
76. van Kuilenburg, A. B., R. Meinsma, E. Beke, B. Assmann, A. Ribes et al., 2004 Beta-ureidopropionase deficiency: an inborn error of pyrimidine degradation associated with neurological abnormalities. Hum. Mol. Genet. 13: 2793-2801.
77. van Kuilenburg, A. B., J. Meijer, A. N. Mul, R. C. Hennekam, J. M. Hoovers et al., 2009 Analysis of severely affected patients with dihydropyrimidine dehydrogenase deficiency reveals large intragenic rearrangements of DPYD and a de novo interstitial deletion del(1)(p13.3p21.3). Hum. Genet. 125: 581-590.
78. Venkatraman, E. S., and A. B. Olshen, 2007 A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663.
79. Wakayama, Y., M. Inoue, H. Kojima, M. Murahashi, S. Shibuya et al., 2000 Aciculin and its relation to dystrophin: Immunocytochemical studies in human normal and duchenne dystrophy quadriceps muscles. Acta Neuropathol. 99: 654-662.
80. Waldvogel, H. J., K. Baer, R. G. Snell, M. J. During, R. L. Faull et al., 2003 Distribution of gephyrin in the human brain: an immunohistochemical analysis. Neuroscience 116: 145-156.
81. Wilkinson, K. A., Y. Nakamura, and J.M. Henley, 2010 Targets and consequences of protein SUMOylation in neurons. Brain Res. Brain Res. Rev. 64: 195-212.
82. Williams, P. G., and J. H. Hersh, 1998 Brief report: the association of neurofibromatosis type 1 and autism. J. Autism Dev. Disord. 28: 567-571.
83. Winchester, L., C. Yau, and J. Ragoussis, 2009 Comparing CNV detection methods for SNP arrays. Brief. Funct. Genomics Proteomics 8: 353-366.
84. Wu, J. Y., K. C. Kuban, E. Allred, F. Shapiro, and B. T. Darras, 2005 Association of duchenne muscular dystrophy with autism spectrum disorder. J. Child Neurol. 20: 790-795.