Identification of novel candidate genes for Alzheimer's disease by autozygosity mapping using genome wide SNP data

Journal of Alzheimer's Disease

Volumn 23, Issue 2, 2011, Pages 349-359

  Sherva, Richard ^a   Baldwin, Clinton T ^a   Inzelberg, Rivka ^b   Vardarajan, Badri ^a   Cupples, L Adrienne ^c   Lunetta, Kathryn ^c   Bowirrat, Abdalla ^d   Naj, Adam ^e   Pericak Vance, Margaret ^e   Friedland, Robert P ^f   Farrer, Lindsay A ^a,c  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

^c BOSTON UNIVERSITY   (United States)

^d Rebecca Sieff Government Hospital   (Israel)

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

^f University of Louisville School of Medicine   (United States)

Author keywords

Alzheimer's disease; genome wide association study; meta analysis; population groups

Indexed keywords

AGPAT PROTEIN; MEMBRANE PROTEIN; UNCLASSIFIED DRUG;

AGED; ALZHEIMER DISEASE; ARTICLE; AUTOZYGOSITY; CHROMOSOME 2; CHROMOSOME 6; CHROMOSOME 9; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DISEASE ASSOCIATION; FEMALE; GENE IDENTIFICATION; GENE MAPPING; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOTYPE; HOMOZYGOSITY; HUMAN; HYPOTHESIS; INBREEDING; MAJOR CLINICAL STUDY; MALE; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; ZYGOSITY;

EID: 79951572644     PISSN: 13872877     EISSN: None     Source Type: Journal    
DOI: 10.3233/JAD-2010-100714     Document Type: Article

References (48)

1. Abraham R, Moskvina V, Sims R, Hollingworth P, Morgan A, Georgieva L, Dowzell K, Cichon S, Hillmer AM, O'Donovan MC, Williams J, Owen MJ, Kirov G (2008) A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. BMC Med Genomics 1, 44.
2. Beecham GW, Martin ER, Li YJ, Slifer MA, Gilbert JR, Haines JL, Pericak-Vance MA (2009) Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease. Am J Hum Genet 84, 35-43.
3. Bertram L, Lange C, Mullin K, Parkinson M, Hsiao M, Hogan MF, Schjeide BM, Hooli B, Divito J, Ionita I, Jiang H, Laird N, Moscarillo T, Ohlsen KL, Elliott K, Wang X, Hu-Lince D, Ryder M, Murphy A, Wagner SL, Blacker D, Becker KD, Tanzi RE (2008) Genome-wide association analysis reveals putative Alzheimer's disease susceptibility loci in addition to APOE. Am J Hum Genet 83, 623-632.
4. Carrasquillo MM, Zou F, Pankratz VS, Wilcox SL, Ma L, Walker LP, Younkin SG, Younkin CS, Younkin LH, Bisceglio GD, Ertekin-Taner N, Crook JE, Dickson DW, Petersen RC, Graff-Radford NR, Younkin SG (2009) Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease. Nat Genet 41, 192-198.
5. Coon KD, Myers AJ, Craig DW, Webster JA, Pearson JV, Lince DH, Zismann VL, Beach TG, Leung D, Bryden L, Halperin RF, Marlowe L, Kaleem M, Walker DG, Ravid R, Heward CB, Rogers J, Papassotiropoulos A, Reiman EM, Hardy J, Stephan DA (2007) A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's disease. J Clin Psychiatry 68, 613-618. (Pubitemid 46663046)
6. Grupe A, Abraham R, Li Y, Rowland C, Hollingworth P, Morgan A, Jehu L, Segurado R, Stone D, Schadt E, Karnoub M, Nowotny P, Tacey K, Catanese J, Sninsky J, Brayne C, Rubinsztein D, Gill M, Lawlor B, Lovestone S, Holmans P, O'Donovan M, Morris JC, Thal L, Goate A, Owen MJ, Williams J (2007) Evidence for novel susceptibility genes for late-onset Alzheimer's disease from a genome-wide association study of putative functional variants. Hum Mol Genet 16, 865-873. (Pubitemid 47064316)
7. Li H,Wetten S, Li L, St Jean PL, Upmanyu R, Surh L, Hosford D, Barnes MR, Briley JD, Borrie M, Coletta N, Delisle R, Dhalla D, Ehm MG, Feldman HH, Fornazzari L, Gauthier S, Goodgame N, Guzman D, Hammond S, Hollingworth P, Hsiung GY, Johnson J, Kelly DD, Keren R, Kertesz A, King KS, Lovestone S, Loy-English I, Matthews PM, Owen MJ, Plumpton M, Pryse-Phillips W, Prinjha RK, Richardson JC, Saunders A, Slater AJ, St George-Hyslop PH, Stinnett SW, Swartz JE, Taylor RL, Wherrett J, Williams J, Yarnall DP, Gibson RA, Irizarry MC, Middleton LT, Roses AD (2008) Candidate single-nucleotide polymorphisms from a genomewide association study of Alzheimer disease. Arch Neurol 65, 45-53.
8. Harold D, Abraham R, Hollingworth P, Sims R, Gerrish A, Hamshere ML, Pahwa JS, Moskvina V, Dowzell K,Williams A, Jones N, Thomas C, Stretton A, Morgan AR, Lovestone S, Powell J, Proitsi P, Lupton MK, Brayne C, Rubinsztein DC, Gill M, Lawlor B, Lynch A, Morgan K, Brown KS, Passmore PA, Craig D, McGuinness B, Todd S, Holmes C, Mann D, Smith AD, Love S, Kehoe PG, Hardy J, Mead S, Fox N, Rossor M, Collinge J, Maier W, Jessen F, Schurmann B, van den Bussche H, Heuser I, Kornhuber J, Wiltfang J, Dichgans M, Frolich L, Hampel H, Hull M, Rujescu D, Goate AM, Kauwe JS, Cruchaga C, Nowotny P, Morris JC, Mayo K, Sleegers K, Bettens K, Engelborghs S, De Deyn PP, Van BroeckhovenC,Livingston G, Bass NJ, Gurling H, McQuillin A, Gwilliam R, Deloukas P, Al-Chalabi A, Shaw CE, Tsolaki M, Singleton AB, Guerreiro R, Muhleisen TW, Nothen MM, Moebus S, Jockel KH, Klopp N,Wichmann HE, Carrasquillo MM, Pankratz VS, Younkin SG, Holmans PA, O'Donovan M, Owen MJ, Williams J (2009) Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Nat Genet 41, 1088-1093.
9. Lambert JC, Heath S, Even G, Campion D, Sleegers K, Hiltunen M, Combarros O, Zelenika D, Bullido MJ, Tavernier B, Letenneur L, Bettens K, Berr C, Pasquier F, Fievet N, Barberger-Gateau P, Engelborghs S, De Deyn P, Mateo I, Franck A, Helisalmi S, Porcellini E, Hanon O, European Alzheimer's Disease Initiative Investigators, de Pancorbo MM,Lendon C, Dufouil C, Jaillard C, LeveillardT, AlvarezV, Bosco P, Mancuso M, Panza F, Nacmias B, Bossu P, Piccardi P, Annoni G, Seripa D, Galimberti D, Hannequin D, Licastro F, Soininen H, Ritchie K, Blanche H, Dartigues JF, Tzourio C, Gut I, Van Broeckhoven C, Alperovitch A, Lathrop M, Amouyel P (2009) Genome-wide association study identifies variants atCLUandCR1associated with Alzheimer's disease. Nat Genet 41, 1094-1099.
10. Avramopoulos D (2009) Genetics of Alzheimer's disease: recent advances. Genome Med 1, 34.
11. Rogaeva E, Meng Y, Lee JH, Gu Y, Kawarai T, Zou F, Katayama T, Baldwin CT, Cheng R, Hasegawa H, Chen F, Shibata N, Lunetta KL, Pardossi-Piquard R, Bohm C, Wakutani Y, Cupples LA, Cuenco KT, Green RC, Pinessi L, Rainero I, Sorbi S, Bruni A, Duara R, Friedland RP, Inzelberg R, HampeW, Bujo H, Song YQ, Andersen OM,Willnow TE, Graff-Radford N, Petersen RC, Dickson D, Der SD, Fraser PE, Schmitt-Ulms G, Younkin S, Mayeux R, Farrer LA, St George-Hyslop P (2007) The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease. Nat Genet 39, 168-177. (Pubitemid 46184347)
12. Bowirrat A, Treves TA, Friedland RP, Korczyn AD (2001) Prevalence of Alzheimer's type dementia in an elderly Arab population. Eur J Neurol 8, 119-123. (Pubitemid 32269630)
13. Bowirrat A, Friedland RP, Chapman J, Korczyn AD (2000) The very high prevalence of AD in an Arab population is not explained by APOE epsilon4 allele frequency. Neurology 55, 731.
14. Curtis D, Vine AE, Knight J (2008) Study of regions of extended homozygosity provides a powerful method to explore haplotype structure of human populations. Ann Hum Genet 72, 261-278. (Pubitemid 351228465)
15. Bacolod MD, Schemmann GS,Wang S, Shattock R, Giardina SF, Zeng Z, Shia J, Stengel RF, Gerry N, Hoh J, Kirchhoff T, Gold B, Christman MF, Offit K, Gerald WL, Notterman DA, Ott J, Paty PB, Barany F (2008) The signatures of autozygosity among patients with colorectal cancer. Cancer Res 68, 2610-2621. (Pubitemid 351559606)
16. Wang S, Haynes C, Barany F, Ott J (2009) Genome-wide autozygosity mapping in human populations. Genet Epidemiol 33, 172-180.
17. Farrer LA, Bowirrat A, Friedland RP, Waraska K, Korczyn AD, Baldwin CT (2003) Identification of multiple loci for Alzheimer disease in a consanguineous Israeli-Arab community. Hum Mol Genet 12, 415-422. (Pubitemid 36285133)
18. Zuchner S, Gilbert JR, Martin ER, Leon-Guerrero CR, Xu PT, Browning C, Bronson PG, Whitehead P, Schmechel DE, Haines JL, Pericak-Vance MA (2008) Linkage and association study of late-onset Alzheimer disease families linked to 9p21.3. Ann Hum Genet 72, 725-731.
19. PerryRT,Wiener H, Harrell LE, Blacker D,Tanzi RE, Bertram L, Bassett SS, Go RC (2007) Follow-up mapping supports the evidence for linkage in the candidate region at 9q22 in the NIMH Alzheimer's disease Genetics Initiative cohort. Am J Med Genet B Neuropsychiatr Genet 144B, 220-227. (Pubitemid 46606647)
20. Pericak-VanceMA,BassMP,Yamaoka LH, Gaskell PC, Scott WK, TerwedowHA, MenoldMM,Conneally PM, SmallGW, Vance JM, Saunders AM, Roses AD, Haines JL (1997) Complete genomic screen in late-onset familial Alzheimer disease. Evidence for a new locus on chromosome 12. JAMA 278, 1237-1241. (Pubitemid 27435610)
21. Myers A, Holmans P, Marshall H, Kwon J, Meyer D, Ramic D, Shears S, Booth J, DeVrieze FW, Crook R, Hamshere M, Abraham R, Tunstall N, Rice F, Carty S, Lillystone S, Kehoe P, Rudrasingham V, Jones L, Lovestone S, Perez-Tur J, Williams J, Owen MJ, Hardy J, Goate AM (2000) Susceptibility locus for Alzheimer's disease on chromosome 10. Science 290, 2304-2305. (Pubitemid 32041572)
22. Rogaeva E, Premkumar S, Song Y, Sorbi S, Brindle N, Paterson A, Duara R, Levesque G, Yu G, Nishimura M, Ikeda M, O'Toole C, Kawarai T, Jorge R, Vilarino D, Bruni AC, Farrer LA, St George-Hyslop PH (1998) Evidence for an Alzheimer disease susceptibility locus on chromosome 12 and for further locus heterogeneity. JAMA 280, 614-618. (Pubitemid 28502637)
23. Pericak-Vance MA, Grubber J, Bailey LR, Hedges D,West S, Santoro L, Kemmerer B, Hall JL, Saunders AM, Roses AD, Small GW, Scott WK, Conneally PM, Vance JM, Haines JL (2000) Identification of novel genes in late-onset Alzheimer's disease. Exp Gerontol 35, 1343-1352.
24. Meng Y, Baldwin CT, Bowirrat A, Waraska K, Inzelberg R, Friedland RP, Farrer LA (2006) Association of polymorphisms in the Angiotensin-converting enzyme gene with Alzheimer disease in an Israeli Arab community. Am J Hum Genet 78, 871-877.
25. 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. (Pubitemid 46026496)
26. Reitz C, Rogaeva E, Lee J, Tokuhiro S, Bettens K, Sleegers K, Tan E, Kimura R, Shibata N, Kamboh I, Prince J, Maier W, Riemenschneider M, Williams J, van Broeckhoven C, Farrer L, St George-Hyslop P, Mayeux R (2010) Association of SORL1 gene variants with Alzheimer's disease: a metaanalysis. Arch Neurol, in press.
27. Inzelberg R, Schechtman E, Abuful A, Masarwa M, Mazarib A, Strugatsky R, Farrer LA, Green RC, Friedland RP (2007) Education effects on cognitive function in a healthy aged Arab population. Int Psychogeriatr 19, 593-603. (Pubitemid 46707414)
28. Israeli-Korn SD, Masarwa M, Schechtman E, Abuful A, Strugatsky R, Avni S, Farrer LA, Friedland RP, Inzelberg R (2010) Hypertension increases the probability of Alzheimer's disease and of mild cognitive impairment in an Arab community in Northern Israel. Neuroepidemiology 34, 99-105.
29. Cavalli-Sforza LL, Bodmer WF (1971) The Genetics of Human Populations, WH Freeman & Co., New York.
30. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81, 559-575. (Pubitemid 47330214)
31. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959. (Pubitemid 30397141)
32. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38, 904-909. (Pubitemid 44141658)
33. Li Y, Abecasis G (2006) Mach 1.0: rapid haplotype reconstruction and missing genotype inference. Am J Hum Genet S79, 2290.
34. Roses AD, Lutz MW, Amrine-Madsen H, Saunders AM, CrenshawDG, Sundseth SS, Huentelman MJ,Welsh-Bohmer KA, Reiman EM (2010) A TOMM40 variable-length polymorphism predicts the age of late-onset Alzheimer's disease. Pharmacogenomics J 10(5), 375-384.
35. Takei N, Miyashita A, Tsukie T, Arai H, Asada T, Imagawa M, Shoji M, Higuchi S, Urakami K, Kimura H, Kakita A, Takahashi H, Tsuji S, Kanazawa I, Ihara Y, Odani S, Kuwano R, Japanese Genetic Study Consortium for Alzheimer Disease (2009) Genetic association study on in and around the APOE in late-onset Alzheimer disease in Japanese. Genomics 93, 441-448.
36. Yu CE, Seltman H, Peskind ER, Galloway N, Zhou PX, Rosenthal E, Wijsman EM, Tsuang DW, Devlin B, Schellenberg GD (2007) Comprehensive analysis of APOE and selected proximate markers for late-onset Alzheimer's disease: patterns of linkage disequilibrium and disease/marker association. Genomics 89, 655-665. (Pubitemid 46719797)
37. Corder EH, Saunders AM, Strittmatter WJ, Schmechel DE, Gaskell PC, SmallGW, Roses AD, Haines JL, Pericak-Vance MA (1993) Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families. Science 261, 921-923. (Pubitemid 23275809)
38. Miller CC, McLoughlin DM, Lau KF, Tennant ME, Rogelj B (2006) The X11 proteins, Abeta production and Alzheimer's disease. Trends Neurosci 29, 280-285.
39. Bertram L, Hiltunen M, Parkinson M, Ingelsson M, Lange C, Ramasamy K, Mullin K, Menon R, Sampson AJ, Hsiao MY, Elliott KJ,Velicelebi G, MoscarilloT, HymanBT,Wagner SL, Becker KD, Blacker D, Tanzi RE (2005) Family-based association between Alzheimer's disease and variants in UBQLN1. N Engl J Med 352, 884-894. (Pubitemid 40300297)
40. Yan SD, Chen X, Fu J, Chen M, Zhu H, Roher A, Slattery T, Zhao L, Nagashima M, Morser J, Migheli A, Nawroth P, Stern D, Schmidt AM (1996) RAGE and amyloid-beta peptide neurotoxicity in Alzheimer's disease. Nature 382, 685-691. (Pubitemid 26282167)
41. Deane R, Du Yan S, Submamaryan RK, LaRue B, Jovanovic S, Hogg E,Welch D, Manness L, Lin C, Yu J, Zhu H, Ghiso J, Frangione B, Stern A, Schmidt AM, Armstrong DL, Arnold B, Liliensiek B, Nawroth P, Hofman F, Kindy M, Stern D, Zlokovic B (2003) RAGE mediates amyloid-beta peptide transport across the blood-brain barrier and accumulation in brain. Nat Med 9, 907-913. (Pubitemid 36889934)
42. Aguado B, Campbell RD (1998) Characterization of a human lysophosphatidic acid acyltransferase that is encoded by a gene located in the class III region of the human major histocompatibility complex. J Biol Chem 273, 4096-4105. (Pubitemid 28103277)
43. Sayas CL, Moreno-Flores MT, Avila J, Wandosell F (1999) The neurite retraction induced by lysophosphatidic acid increases Alzheimer's disease-like Tau phosphorylation. J Biol Chem 274, 37046-37052.
44. Roses AD (2010) An inherited variable poly-T repeat genotype in TOMM40 in Alzheimer disease. Arch Neurol 67, 536-541.
45. Schellenberg GD, Boehnke M, Wijsman EM, Moore DK, Martin GM, Bird TD (1992) Genetic association and linkage analysis of the apolipoprotein CII locus and familial Alzheimer's disease. Ann Neurol 31, 223-227.
46. Yu CE, Payami H, Olson JM, Boehnke M, Wijsman EM, Orr HT, Kukull WA, Goddard KA, Nemens E, White JA (1994) The apolipoprotein E/CI/CII gene cluster and late-onset Alzheimer disease. Am J Hum Genet 54, 631-642. (Pubitemid 24089602)
47. Seshadri S, Fitzpatrick AL, Ikram MA, DeStefano AL, Gudnason V, Boada M, Bis JC, Smith AV, Carassquillo MM, Lambert JC, Harold D, Schrijvers EM, Ramirez-Lorca R, Debette S, Longstreth WT Jr, Janssens AC, Pankratz VS, Dartigues JF, Hollingworth P, Aspelund T, Hernandez I, Beiser A, Kuller LH, Koudstaal PJ, Dickson DW, Tzourio C, Abraham R, Antunez C, Du Y, Rotter JI, Aulchenko YS, Harris TB, Petersen RC, Berr C, Owen MJ, Lopez-Arrieta J, Varadarajan BN, Becker JT, Rivadeneira F, Nalls MA, Graff- Radford NR, Campion D, Auerbach S, Rice K, Hofman A, Jonsson PV, Schmidt H, Lathrop M, Mosley TH, Au R, Psaty BM, UitterlindenAG, Farrer LA, Lumley T, Ruiz A,Williams J, Amouyel P, Younkin SG, Wolf PA, Launer LJ, Lopez OL, van Duijn CM, Breteler MM, CHARGE Consortium, GERAD1 Consortium, EADI1 Consortium (2010) Genomewide analysis of genetic loci associated with Alzheimer disease. JAMA 303, 1832-1840.
48. Jun G, Naj AC, Beecham GW, Wang LS, Buros J, Gallins PJ, Buxbaum JD, Ertekin-Taner N, Fallin D, Friedland R, Inzelberg R, Kramer P, Rogaeva E, St George-Hyslop P, Cantwell L, Dombrosk BA, Saykin AJ, Reiman EM, Bennett DA, Morris JC, Lunetta KL, Martin ER, Montine TJ, Goate AM, Blacker D, Tsuang DW, Beekly D, Cupples AL, Hakonarson H, Kukull W, Foroud TM, Haines J, Mayeux R, Farrer LA, Pericak-Vance MA, Schellenberg GD (2010) Meta-analysis confirms CR1, CLU, and PICALM as Alzheimer's disease risk loci and reveals interactions with APOE genotypes. Arch Neurol, in press.