Prioritization of Copy Number Variation Loci Associated with Autism from AutDB-An Integrative Multi-Study Genetic Database

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Menashe, Idan ^a,b   Larsen, Eric C ^a   Banerjee Basu, Sharmila ^a  

^a MindSpec McLean   (United States)

^b BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ASPERGER SYNDROME; COPY NUMBER VARIATION; FEMALE; GENE DELETION; GENE DUPLICATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC SUSCEPTIBILITY; HUMAN; INFORMATION PROCESSING; INHERITANCE; MAJOR CLINICAL STUDY; MALE; POPULATION GENETICS; RANK SUM TEST; AUTISM; CHROMOSOMAL MAPPING; GENETIC PREDISPOSITION; GENETICS;

AUTISTIC DISORDER; CHROMOSOME MAPPING; DATABASES, GENETIC; DNA COPY NUMBER VARIATIONS; FEMALE; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MALE;

EID: 84879154137     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0066707     Document Type: Article

References (51)

1. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
2. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
3. Lee JA, Lupski JR, (2006) Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders. Neuron 52: 103-121.
4. Stankiewicz P, Lupski JR, (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61: 437-455.
5. Lord C, Cook EH, Leventhal BL, Amaral DG, (2000) Autism spectrum disorders. Neuron 28: 355-363.
6. Nazeer A, Ghaziuddin M (2012) Autism spectrum disorders: clinical features and diagnosis. Pediatr Clin North Am 59: 19-25, ix.
7. Muhle R, Trentacoste SV, Rapin I, (2004) The genetics of autism. Pediatrics 113: e472-486.
8. Hallmayer J, Cleveland S, Torres A, Phillips J, Cohen B, et al. (2011) Genetic Heritability and Shared Environmental Factors Among Twin Pairs With Autism. Arch Gen Psychiatry.
9. Anney R, Klei L, Pinto D, Regan R, Conroy J, et al. (2010) A genome-wide scan for common alleles affecting risk for autism. Hum Mol Genet 19: 4072-4082.
10. Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, et al. (2009) Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 459: 569-573.
11. Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, et al. (2010) Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466: 368-372.
12. Weiss LA, (2009) Autism genetics: emerging data from genome-wide copy-number and single nucleotide polymorphism scans. Expert Rev Mol Diagn 9: 795-803.
13. Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, et al. (2011) Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron 70: 898-907.
14. Sanders SJ, Ercan-Sencicek AG, Hus V, Luo R, Murtha MT, 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.
15. Swanwick CC, Larsen EC, Banerjee-Basu S (2011) Genetic Heterogeneity of Autism Spectrum Disorders. In: Deutsch SI, Urbano MR, editors. Autism Spectrum Disorders: The Role of Genetics in Diagnosis and Treatment: InTech. pp. 65.
16. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, 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.
17. Shen Y, Dies KA, Holm IA, Bridgemohan C, Sobeih MM, et al. (2010) Clinical genetic testing for patients with autism spectrum disorders. Pediatrics 125: e727-735.
18. Basu SN, Kollu R, Banerjee-Basu S, (2009) AutDB: a gene reference resource for autism research. Nucleic Acids Res 37: D832-836.
19. Zogopoulos G, Ha KC, Naqib F, Moore S, Kim H, et al. (2007) Germ-line DNA copy number variation frequencies in a large North American population. Hum Genet 122: 345-353.
20. Shaikh TH, Gai X, Perin JC, Glessner JT, Xie H, et al. (2009) High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications. Genome Res 19: 1682-1690.
21. International HapMap C, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58.
22. Zhang J, Feuk L, Duggan GE, Khaja R, Scherer SW, (2006) Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet Genome Res 115: 205-214.
23. Newschaffer CJ, Croen LA, Daniels J, Giarelli E, Grether JK, et al. (2007) The epidemiology of autism spectrum disorders. Annu Rev Public Health 28: 235-258.
24. Pruitt KD, Tatusova T, Brown GR, Maglott DR, (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40: D130-135.
25. Kumar RA, Marshall CR, Badner JA, Babatz TD, Mukamel Z, et al. (2009) Association and mutation analyses of 16p11.2 autism candidate genes. PLoS One 4: e4582.
26. Schaaf CP, Sabo A, Sakai Y, Crosby J, Muzny D, et al. (2011) Oligogenic heterozygosity in individuals with high-functioning autism spectrum disorders. Hum Mol Genet 20: 3366-3375.
27. Golzio C, Willer J, Talkowski ME, Oh EC, Taniguchi Y, et al. (2012) KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant. Nature 485: 363-367.
28. Itsara A, Cooper GM, Baker C, Girirajan S, Li J, et al. (2009) Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet 84: 148-161.
29. Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, et al. (2011) An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities. Genet Med 13: 777-784.
30. Marshall CR, Scherer SW, (2012) Detection and characterization of copy number variation in autism spectrum disorder. Methods Mol Biol 838: 115-135.
31. Walsh KM, Bracken MB, (2011) Copy number variation in the dosage-sensitive 16p11.2 interval accounts for only a small proportion of autism incidence: a systematic review and meta-analysis. Genet Med 13: 377-384.
32. McCarthy SE, Makarov V, Kirov G, Addington AM, McClellan J, et al. (2009) Microduplications of 16p11.2 are associated with schizophrenia. Nat Genet 41: 1223-1227.
33. Shinawi M, Liu P, Kang SH, Shen J, Belmont JW, et al. (2010) Recurrent reciprocal 16p11.2 rearrangements associated with global developmental delay, behavioural problems, dysmorphism, epilepsy, and abnormal head size. J Med Genet 47: 332-341.
34. Degenhardt F, Priebe L, Herms S, Mattheisen M, Muhleisen TW, et al. (2012) Association between copy number variants in 16p11.2 and major depressive disorder in a German case-control sample. Am J Med Genet B Neuropsychiatr Genet 159B: 263-273.
35. Jacquemont S, Reymond A, Zufferey F, Harewood L, Walters RG, et al. (2011) Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus. Nature 478: 97-102.
36. de Anda FC, Rosario AL, Durak O, Tran T, Graff J, et al. (2012) Autism spectrum disorder susceptibility gene TAOK2 affects basal dendrite formation in the neocortex. Nat Neurosci 15: 1022-1031.
37. Hogart A, Wu D, LaSalle JM, Schanen NC, (2010) The comorbidity of autism with the genomic disorders of chromosome 15q11.2-q13. Neurobiol Dis 38: 181-191.
38. Buiting K, (2010) Prader-Willi syndrome and Angelman syndrome. Am J Med Genet C Semin Med Genet 154C: 365-376.
39. Burnside RD, Pasion R, Mikhail FM, Carroll AJ, Robin NH, et al. (2011) Microdeletion/microduplication of proximal 15q11.2 between BP1 and BP2: a susceptibility region for neurological dysfunction including developmental and language delay. Hum Genet 130: 517-528.
40. de Kovel CG, Trucks H, Helbig I, Mefford HC, Baker C, et al. (2010) Recurrent microdeletions at 15q11.2 and 16p13.11 predispose to idiopathic generalized epilepsies. Brain 133: 23-32.
41. van Bon BWM, Mefford HC, de Vries BBA (1993) 15q13.3 Microdeletion.
42. Gau SS, Liao HM, Hong CC, Chien WH, Chen CH, (2012) Identification of two inherited copy number variants in a male with autism supports two-hit and compound heterozygosity models of autism. Am J Med Genet B Neuropsychiatr Genet 159B: 710-717.
43. Allen-Brady K, Miller J, Matsunami N, Stevens J, Block H, et al. (2009) A high-density SNP genome-wide linkage scan in a large autism extended pedigree. Mol Psychiatry 14: 590-600.
44. Coon H, Villalobos ME, Robison RJ, Camp NJ, Cannon DS, et al. (2010) Genome-wide linkage using the Social Responsiveness Scale in Utah autism pedigrees. Mol Autism 1: 8.
45. Griggs BL, Ladd S, Saul RA, DuPont BR, Srivastava AK, (2008) Dedicator of cytokinesis 8 is disrupted in two patients with mental retardation and developmental disabilities. Genomics 91: 195-202.
46. Brunetti-Pierri N, Berg JS, Scaglia F, Belmont J, Bacino CA, et al. (2008) Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities. Nat Genet 40: 1466-1471.
47. Li J, Zhou G, Ji W, Feng G, Zhao Q, et al. (2011) Common variants in the BCL9 gene conferring risk of schizophrenia. Arch Gen Psychiatry 68: 232-240.
48. Kalkman HO, (2012) A review of the evidence for the canonical Wnt pathway in autism spectrum disorders. Mol Autism 3: 10.
49. Leblond CS, Heinrich J, Delorme R, Proepper C, Betancur C, et al. (2012) Genetic and functional analyses of SHANK2 mutations suggest a multiple hit model of autism spectrum disorders. PLoS Genet 8: e1002521.
50. Gjorlund MD, Nielsen J, Pankratova S, Li S, Korshunova I, et al. (2012) Neuroligin-1 induces neurite outgrowth through interaction with neurexin-1beta and activation of fibroblast growth factor receptor-1. FASEB J 26: 4174-4186.
51. Morris CP, Baune BT, Domschke K, Arolt V, Swagell CD, et al. (2012) KPNA3 variation is associated with schizophrenia, major depression, opiate dependence and alcohol dependence. Dis Markers 33: 163-170.