Analysis of Copy Number Variation in Alzheimer's Disease in a Cohort of Clinically Characterized and Neuropathologically Verified Individuals

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Swaminathan, Shanker ^a   Huentelman, Matthew J ^b,c   Corneveaux, Jason J ^b,c   Myers, Amanda J ^d,e   Faber, Kelley M ^a   Foroud, Tatiana ^a   Mayeux, Richard ^f   Shen, Li ^a   Kim, Sungeun ^a   Turk, Mari ^b,c   Hardy, John ^g   Reiman, Eric M ^b,c,h   Saykin, Andrew J ^a  

^a INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^c ARIZONA ALZHEIMER S CONSORTIUM   (United States)

^d UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF SOUTH FLORIDA   (United States)

^f Department of Epidemiology   (United States)

^g UNIVERSITY COLLEGE LONDON   (United Kingdom)

^h BANNER ALZHEIMER S INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HLA DR ANTIGEN;

ADULT; ALZHEIMER DISEASE; ARTICLE; CASE CONTROL STUDY; CAUCASIAN; CHRFAM7A GENE; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA MICROARRAY; DOPEY2 GENE; FEMALE; GENE; GENE DELETION; GENE DUPLICATION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC RISK; HLA DRA GENE; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; MILD COGNITIVE IMPAIRMENT; NEUROPATHOLOGY; RELN GENE; RISK FACTOR;

ALZHEIMER DISEASE; CASE-CONTROL STUDIES; COHORT STUDIES; DNA COPY NUMBER VARIATIONS; GENOME-WIDE ASSOCIATION STUDY; HUMANS;

NIA;

EID: 84870806539     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0050640     Document Type: Article

References (63)

1. Alzheimer's Association, Thies W, Bleiler L, (2011) 2011 Alzheimer's disease facts and figures. Alzheimers Dement 7: 208-244.
2. Petersen RC, Roberts RO, Knopman DS, Boeve BF, Geda YE, et al. (2009) Mild cognitive impairment: ten years later. Arch Neurol 66: 1447-1455.
3. Gatz M, Reynolds CA, Fratiglioni L, Johansson B, Mortimer JA, et al. (2006) Role of genes and environments for explaining Alzheimer disease. Arch Gen Psychiatry 63: 168-174.
4. Bekris LM, Yu CE, Bird TD, Tsuang DW, (2010) Genetics of Alzheimer disease. J Geriatr Psychiatry Neurol 23: 213-227.
5. Harold D, Abraham R, Hollingworth P, Sims R, Gerrish A, et al. (2009) Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Nat Genet 41: 1088-1093.
6. Lambert JC, Heath S, Even G, Campion D, Sleegers K, et al. (2009) Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease. Nat Genet 41: 1094-1099.
7. Jun G, Naj AC, Beecham GW, Wang LS, Buros J, et al. (2010) Meta-analysis confirms CR1, CLU, and PICALM as alzheimer disease risk loci and reveals interactions with APOE genotypes. Arch Neurol 67: 1473-1484.
8. Seshadri S, Fitzpatrick AL, Ikram MA, DeStefano AL, Gudnason V, et al. (2010) Genome-wide analysis of genetic loci associated with Alzheimer disease. JAMA 303: 1832-1840.
9. Naj AC, Beecham GW, Martin ER, Gallins PJ, Powell EH, et al. (2010) Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease provides genetic evidence for folate-pathway abnormalities. PLoS Genet 6: e1001130.
10. Naj AC, Jun G, Beecham GW, Wang LS, Vardarajan BN, et al. (2011) Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet 43: 436-441.
11. Hollingworth P, Harold D, Sims R, Gerrish A, Lambert JC, et al. (2011) Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Nat Genet 43: 429-435.
12. Wijsman EM, Pankratz ND, Choi Y, Rothstein JH, Faber KM, et al. (2011) Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE. PLoS Genet 7: e1001308.
13. Slooter AJ, Cruts M, Kalmijn S, Hofman A, Breteler MM, et al. (1998) Risk estimates of dementia by apolipoprotein E genotypes from a population-based incidence study: the Rotterdam Study. Arch Neurol 55: 964-968.
14. Verhaaren BF, Vernooij MW, Koudstaal PJ, Uitterlinden AG, Duijn CM, et al. (2012) Alzheimer's Disease Genes and Cognition in the Nondemented General Population. Biol Psychiatry.
15. Cook EH Jr, Scherer SW, (2008) Copy-number variations associated with neuropsychiatric conditions. Nature 455: 919-923.
16. Heinzen EL, Need AC, Hayden KM, Chiba-Falek O, Roses AD, et al. (2010) Genome-wide scan of copy number variation in late-onset Alzheimer's disease. J Alzheimers Dis 19: 69-77.
17. Brouwers N, Cauwenberghe CV, Engelborghs S, Lambert JC, Bettens K, et al. (2012) Alzheimer risk associated with a copy number variation in the complement receptor 1 increasing C3b/C4b binding sites. Mol Psychiatry 17: 223-233.
18. Shaw CA, Li Y, Wiszniewska J, Chasse S, Zaidi SN, et al. (2011) Olfactory copy number association with age at onset of Alzheimer disease. Neurology 76: 1302-1309.
19. Ghani M, Pinto D, Lee JH, Grinberg Y, Sato C, et al. (2012) Genome-wide survey of large rare copy number variants in Alzheimer's disease among Caribbean hispanics. G3 (Bethesda) 2: 71-78.
20. Swaminathan S, Kim S, Shen L, Risacher SL, Foroud T, et al. (2011) Genomic Copy Number Analysis in Alzheimer's Disease and Mild Cognitive Impairment: An ADNI Study. Int J Alzheimers Dis 2011: 729478.
21. Swaminathan S, Shen L, Kim S, Inlow M, West JD, et al. (2012) Analysis of Copy Number Variation in Alzheimer's Disease: the NIA-LOAD/NCRAD Family Study. Curr Alzheimer Res 9: 801-814.
22. Corneveaux JJ, Myers AJ, Allen AN, Pruzin JJ, Ramirez M, et al. (2010) Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals. Hum Mol Genet 19: 3295-3301.
23. Webster JA, Gibbs JR, Clarke J, Ray M, Zhang W, et al. (2009) Genetic control of human brain transcript expression in Alzheimer disease. Am J Hum Genet 84: 445-458.
24. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, et al. (2007) A survey of genetic human cortical gene expression. Nat Genet 39: 1494-1499.
25. Crook R, Hardy J, Duff K, (1994) Single-day apolipoprotein E genotyping. J Neurosci Methods 53: 125-127.
26. Hawkins JR, Khripin Y, Valdes AM, Weaver TA, (2002) Miniaturized sealed-tube allele-specific PCR. Hum Mutat 19: 543-553.
27. Saykin AJ, Shen L, Foroud TM, Potkin SG, Swaminathan S, et al. (2010) Alzheimer's Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans. Alzheimers Dement 6: 265-273.
28. Wang K, Li M, Hadley D, Liu R, Glessner J, et al. (2007) PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 17: 1665-1674.
29. Diskin SJ, Li M, Hou C, Yang S, Glessner J, et al. (2008) Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res 36: e126.
30. Need AC, Ge D, Weale ME, Maia J, Feng S, et al. (2009) A genome-wide investigation of SNPs and CNVs in schizophrenia. PLoS Genet 5: e1000373.
31. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
32. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
33. Bertram L, McQueen MB, Mullin K, Blacker D, Tanzi RE, (2007) Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat Genet 39: 17-23.
34. Wallace BC, Schmid CH, Lau J, Trikalinos TA, (2009) Meta-Analyst: software for meta-analysis of binary, continuous and diagnostic data. BMC Med Res Methodol 9: 80.
35. Borenstein M, Hedges L, Higgins J, Rothstein H (2005) Comprehensive Meta-analysis Version 2, Biostat, Englewood NJ.
36. Hamza TH, Zabetian CP, Tenesa A, Laederach A, Montimurro J, et al. (2010) Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nat Genet 42: 781-785.
37. Guo Y, Deng X, Zheng W, Xu H, Song Z, et al. (2011) HLA rs3129882 variant in Chinese Han patients with late-onset sporadic Parkinson disease. Neurosci Lett 501: 185-187.
38. International Multiple Sclerosis Genetics Consortium, Hafler DA, Compston A, Sawcer S, Lander ES, et al. (2007) Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med 357: 851-862.
39. Hoppenbrouwers IA, Aulchenko YS, Janssens AC, Ramagopalan SV, Broer L, et al. (2009) Replication of CD58 and CLEC16A as genome-wide significant risk genes for multiple sclerosis. J Hum Genet 54: 676-680.
40. Ma SL, Tang NL, Tam CW, Lui VW, Suen EW, et al. (2008) Association between HLA-A alleles and Alzheimer's disease in a southern Chinese community. Dement Geriatr Cogn Disord 26: 391-397.
41. Lehmann DJ, Barnardo MC, Fuggle S, Quiroga I, Sutherland A, et al. (2006) Replication of the association of HLA-B7 with Alzheimer's disease: a role for homozygosity? J Neuroinflammation 3: 33.
42. Guerini FR, Tinelli C, Calabrese E, Agliardi C, Zanzottera M, et al. (2009) HLA-A*01 is associated with late onset of Alzheimer's disease in Italian patients. Int J Immunopathol Pharmacol 22: 991-999.
43. Listi F, Candore G, Balistreri CR, Grimaldi MP, Orlando V, et al. (2006) Association between the HLA-A2 allele and Alzheimer disease. Rejuvenation Res 9: 99-101.
44. Riley B, Williamson M, Collier D, Wilkie H, Makoff A, (2002) A 3-Mb map of a large Segmental duplication overlapping the alpha7-nicotinic acetylcholine receptor gene (CHRNA7) at human 15q13-q14. Genomics 79: 197-209.
45. Gault J, Robinson M, Berger R, Drebing C, Logel J, et al. (1998) Genomic organization and partial duplication of the human alpha7 neuronal nicotinic acetylcholine receptor gene (CHRNA7). Genomics 52: 173-185.
46. Feher A, Juhasz A, Rimanoczy A, Csibri E, Kalman J, et al. (2009) Association between a genetic variant of the alpha-7 nicotinic acetylcholine receptor subunit and four types of dementia. Dement Geriatr Cogn Disord 28: 56-62.
47. de Lucas-Cerrillo AM, Maldifassi MC, Arnalich F, Renart J, Atienza G, et al. (2011) Function of partially duplicated human alpha77 nicotinic receptor subunit CHRFAM7A gene: potential implications for the cholinergic anti-inflammatory response. J Biol Chem 286: 594-606.
48. Araud T, Graw S, Berger R, Lee M, Neveu E, et al. (2011) The chimeric gene CHRFAM7A, a partial duplication of the CHRNA7 gene, is a dominant negative regulator of alpha7*nAChR function. Biochem Pharmacol 82: 904-914.
49. Seripa D, Matera MG, Franceschi M, Daniele A, Bizzarro A, et al. (2008) The RELN locus in Alzheimer's disease. J Alzheimers Dis 14: 335-344.
50. Kramer PL, Xu H, Woltjer RL, Westaway SK, Clark D, et al. (2011) Alzheimer disease pathology in cognitively healthy elderly: a genome-wide study. Neurobiol Aging 32: 2113-2122.
51. Rachidi M, Delezoide AL, Delabar JM, Lopes C, (2009) A quantitative assessment of gene expression (QAGE) reveals differential overexpression of DOPEY2, a candidate gene for mental retardation, in Down syndrome brain regions. Int J Dev Neurosci 27: 393-398.
52. Rachidi M, Lopes C, Delezoide AL, Delabar JM, (2006) C21orf5, a human candidate gene for brain abnormalities and mental retardation in Down syndrome. Cytogenet Genome Res 112: 16-22.
53. Martins-de-Souza D, Guest PC, Mann DM, Roeber S, Rahmoune H, et al. (2012) Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration. J Proteome Res 11: 2533-2543.
54. Rovelet-Lecrux A, Hannequin D, Raux G, Le Meur N, Laquerriere A, et al. (2006) APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy. Nat Genet 38: 24-26.
55. Sleegers K, Brouwers N, Gijselinck I, Theuns J, Goossens D, et al. (2006) APP duplication is sufficient to cause early onset Alzheimer's dementia with cerebral amyloid angiopathy. Brain 129: 2977-2983.
56. McNaughton D, Knight W, Guerreiro R, Ryan N, Lowe J, et al. (2012) Duplication of amyloid precursor protein (APP), but not prion protein (PRNP) gene is a significant cause of early onset dementia in a large UK series. Neurobiol Aging 33: 426 e413-421.
57. Antonell A, Gelpi E, Sanchez-Valle R, Martinez R, Molinuevo JL, et al. (2012) Breakpoint sequence analysis of an AbetaPP locus duplication associated with autosomal dominant Alzheimer's disease and severe cerebral amyloid angiopathy. J Alzheimers Dis 28: 303-308.
58. Autism Genome Project Consortium, Szatmari P, Paterson AD, Zwaigenbaum L, Roberts W, et al (2007) Mapping autism risk loci using genetic linkage and chromosomal rearrangements. Nat Genet 39: 319-328.
59. Rujescu D, Ingason A, Cichon S, Pietilainen OP, Barnes MR, et al. (2009) Disruption of the neurexin 1 gene is associated with schizophrenia. Hum Mol Genet 18: 988-996.
60. Gomez Ravetti M, Rosso OA, Berretta R, Moscato P, (2010) Uncovering molecular biomarkers that correlate cognitive decline with the changes of hippocampus' gene expression profiles in Alzheimer's disease. PLoS One 5: e10153.
61. Chaudhury AR, Gerecke KM, Wyss JM, Morgan DG, Gordon MN, et al. (2003) Neuregulin-1 and erbB4 immunoreactivity is associated with neuritic plaques in Alzheimer disease brain and in a transgenic model of Alzheimer disease. J Neuropathol Exp Neurol 62: 42-54.
62. Woo RS, Lee JH, Yu HN, Song DY, Baik TK, (2010) Expression of ErbB4 in the apoptotic neurons of Alzheimer's disease brain. Anat Cell Biol 43: 332-339.
63. Woo RS, Lee JH, Yu HN, Song DY, Baik TK, (2011) Expression of ErbB4 in the neurons of Alzheimer's disease brain and APP/PS1 mice, a model of Alzheimer's disease. Anat Cell Biol 44: 116-127.