Genetic association analysis: Lessons from the study of Alzheimers Disease

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 573, Issue 1-2, 2005, Pages 152-159

  Brookes, Anthony J ^a,b   Prince, Jonathan A ^b  

^a UNIVERSITY OF LEICESTER   (United Kingdom)

^b KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Alzheimers Disease; Association study; Genotyping technology; Multi site variation (MSV); Single nucleotide polymorphism (SNP)

Indexed keywords

ALZHEIMER DISEASE; COMPLEX FORMATION; CORRELATION ANALYSIS; DATA ANALYSIS; GENE FREQUENCY; GENE IDENTIFICATION; GENE MAPPING; GENE TECHNOLOGY; GENETIC ANALYSIS; GENETIC RISK; GENETIC TRAIT; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HAPLOTYPE; HUMAN; PHENOTYPE; PLEIOTROPY; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVIEW; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; TECHNIQUE;

EID: 17044380861     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2004.08.017     Document Type: Review

References (39)

1. K.E. Lohmueller, C.L. Pearce, M. Pike, E.S. Lander, and J.N. Hirschhorn Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease Nat. Genet. 33 2003 177 182
2. L. Fratiglioni, D. De Ronchi, and H. Aguero-Torres Worldwide prevalence and incidence of dementia Drugs Aging 15 1999 365 375
3. M. Gatz, N.L. Pedersen, S. Berg, B. Johansson, K. Johansson, J.A. Mortimer, S.F. Posner, M. Viitanen, B. Winblad, and A. Ahlbom Heritability for Alzheimer's disease: the study of dementia in Swedish twins J. Gerontol. A Biol. Sci. Med. Sci. 52 1997 M117 M125
4. A. Goate, M.C. Chartier-Harlin, M. Mullan, J. Brown, F. Crawford, L. Fidani, L. Giuffra, A. Haynes, N. Irving, L. James, R. Mant, P. Newton, K. Rooke, P. Roques, C. Talbot, M. Pericak-Vance, A. Roses, R. Williamson, M. Rossor, M. Owen, and J. Hardy Segregation of a missense mutation in the amyloid precursor protein gene with familial Alzheimer's disease Nature 349 1991 704 706
5. R. Sherrington, E.I. Rogaev, Y. Liang, E.A. Rogaeva, G. Levesque, M. Ikeda, H. Chi, C. Lin, G. Li, K. Holman, T. Tsuda, L. Mar, J.-F. Foncin, A.C. Bruni, M.P. Montesi, S. Sorbi, I. Rainero, L. Pinessi, L. Nee, I. Chumakov, D. Pollen, A. Brookes, P. Sanseau, R.J. Polinsky, W. Wasco, H.A.R. Da Silva, J.L. Haines, M.A. Pericak-Vance, R.E. Tanzi, A.D. Roses, P.E. Fraser, J.M. Rommens, and P.H. St George-Hyslop Cloning of a gene bearing missense mutations in early-onset familial Alzheimer's disease Nature 375 1995 754 760
6. E.I. Rogaev, R. Sherrington, E.A. Rogaeva, G. Levesque, M. Ikeda, Y. Liang, H. Chi, C. Lin, K. Holman, T. Tsuda, L. Mar, S. Sorbi, B. Nacmias, S. Piacentini, L. Amaducci, I. Chumakov, D. Cohen, L. Lannfelt, P.E. Fraser, J.M. Rommens, and P.H. St George-Hyslop Familial Alzheimer's disease in kindreds with missense mutations in a gene on chromosome 1 related to the Alzheimer's disease type 3 gene Nature 376 1995 775 778
7. P. Kehoe, F. Wavrant-De Vrieze, R. Crook, W.S. Wu, P. Holmans, I. Fenton, G. Spurlock, N. Norton, H. Williams, N. Williams, S. Lovestone, J. Perez-Tur, M. Hutton, M.C. Chartier-Harlin, S. Shears, K. Roehl, J. Booth, W. Van Voorst, D. Ramic, J. Williams, A. Goate, J. Hardy, and M.J. Owen A full genome scan for late onset Alzheimer's disease Hum. Mol. Genet. 8 1999 237 245
8. A. Myers, P. Holmans, H. Marshall, J. Kwon, D. Meyer, D. Ramic, S. Shears, J. Booth, F.W. DeVrieze, R. Crook, M. Hamshere, R. Abraham, N. Tunstall, F. Rice, S. Carty, S. Lillystone, P. Kehoe, V. Rudrasingham, L. Jones, S. Lovestone, J. Perez-Tur, J. Williams, M.J. Owen, J. Hardy, and A.M. Goate Susceptibility locus for Alzheimer's disease on chromosome 10 Science 290 2000 2304 2305
9. D. Blacker, L. Bertram, A.J. Saunders, T.J. Moscarillo, M.S. Albert, H. Wiener, R.T. Perry, J.S. Collins, L.E. Harrell, R.C. Go, A. Mahoney, T. Beaty, M.D. Fallin, D. Avramopoulos, G.A. Chase, M.F. Folstein, M.G. McInnis, S.S. Bassett, K.J. Doheny, E.W. Pugh, and R.E. Tanzi Results of a high-resolution genome screen of 437 Alzheimer's disease families Hum. Mol. Genet. 12 2003 23 32
10. W.J. Strittmatter, A.M. Saunders, D. Schmechel, M.A. Pericak-Vance, J. Enghild, G.S. Salvesen, and A.D. Roses Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease Proc. Natl. Acad. Sci. 90 1993 1977 1981
11. E. Warwick Daw, H. Payami, E.J. Nemens, D. Nochlin, T.D. Bird, G.D. Schellenberg, and E.M. Wijsman The number of trait loci in late-onset Alzheimer disease Am. J. Hum. Genet. 66 2000 196 204
12. K.G. Becker, K.C. Barnes, T.J. Bright, and S.A. Wang The genetic association database Nature 36 2004 431 432
13. J.K. Pritchard Are rare variants responsible for susceptibility to complex diseases? Am J. Hum. Genet. 69 2002 124 137
14. M.L. Freedman, D. Reich, K.L. Penney, G.J. McDonald, A.A. Mignault, N. Patterson, S.B. Gabriel, E.J. Topol, J.W. Smoller, C.N. Pato, M.T. Pato, T.L. Petryshen, L.N. Kolonel, E.S. Lander, P. Sklar, B. Henderson, J.N. Hirschhorn, and D. Altshuler Assessing the impact of population stratification on genetic association studies Nat. Genet. 36 2004 388 393
15. J.A. Prince, L. Feuk, H.F. Gu, B. Johansson, M. Gatz, K. Blennow, and A.J. Brookes Genetic variation in a haplotype block spanning IDE influences Alzheimer disease Hum. Mutat. 22 2003 363 371
16. D. Fredman, S.J. White, S. Potter, E.E. Eichler, J.T. Dunnen, and A.J. Brookes Complex SNP-related sequence variation in segmental genome duplications Nat. Genet. 36 2004 861 866
17. J.A. Bailey, A.M. Yavor, L. Viggiano, D. Misceo, J.E. Horvath, N. Archidiacono, S. Schwartz, M. Rocchi, and E.E. Eichler Human-specific duplication and mosaic transcripts: the recent paralogous structure of chromosome 22 Am. J. Hum. Genet. 70 2002 83 100
18. W.M. Howell, M. Jobs, U. Gyllensten, and A.J. Brookes Dynamic allele-specific hybridization. A new method for scoring single nucleotide polymorphisms Nat. Biotechnol. 17 1999 87 88
19. J.A. Prince, L. Feuk, W.M. Howell, M. Jobs, T. Emahazion, K. Blennow, and A.J. Brookes Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation Genome Res. 11 2001 152 162
20. M. Jobs, W.M. Howell, L. Stromqvist, T. Mayr, and A.J. Brookes DASH-2: flexible, low-cost, and high-throughput SNP genotyping by dynamic allele-specific hybridization on membrane arrays Genome Res. 13 2003 916 924
21. T. Emahazion, L. Feuk, M. Jobs, S.L. Sawyer, D. Fredman, D. St Clair, J.A. Prince, and A.J. Brookes SNP association studies in Alzheimer's disease highlight problems for complex disease analysis Trends Genet. 17 2001 407 413
22. L. Feuk, J.A. Prince, K. Blennow, and A.J. Brookes Further evidence for role of a promoter variant in the TNFRSF6 gene in Alzheimer disease Hum. Mutat. 21 2003 53 60
23. P.G. Kehoe, C. Russ, S. McIlory, H. Williams, P. Holmans, C. Holmes, D. Liolitsa, D. Vahidassr, J. Powell, B. McGleenon, M. Liddell, R. Plomin, K. Dynan, N. Williams, J. Neal, N.J. Cairns, G. Wilcock, P. Passmore, S. Lovestone, J. Williams, and M.J. Owen Variation in DCP1, encoding ACE, is associated with susceptibility to Alzheimer disease Nat. Genet. 21 1999 71 72
24. P.G. Kehoe, H. Katzov, L. Feuk, A.M. Bennet, B. Johansson, B. Wiman, U. de Faire, N.J. Cairns, G.K. Wilcock, A.J. Brookes, K. Blennow, and J.A. Prince Haplotypes extending across ACE are associated with Alzheimer's disease Hum. Mol. Genet. 12 2003 859 867
25. Y. Narain, A. Yip, T. Murphy, C. Brayne, D. Easton, J.G. Evans, J. Xuereb, N. Cairns, M.M. Esiri, R.A. Furlong, and D.C. Rubinsztein The ACE gene and Alzheimer's disease susceptibility J. Med. Genet. 37 2000 695 697
26. J.S. Elkins, V.C. Douglas, and S.C. Johnston Alzheimer disease risk and genetic variation in ACE. A meta-analysis Neurology 62 2004 363 368
27. R. Cox, N. Bouzekri, S. Martin, L. Southam, A. Hugill, M. Golamaully, R. Cooper, A. Adeyemo, F. Soubrier, R. Ward, G.M. Lathrop, F. Matsuda, and M. Farrall Angiotensin-1-converting enzyme (ACE) plasma concentration is influenced by multiple ACE-linked quantitative trait nucleotides Hum. Mol. Genet. 11 2002 2969 2977
28. W.M. Howell, and A.J. Brookes Evaluation of multiple presenilin 2 SNPs for association with early-onset sporadic Alzheimer disease Am. J. Med. Genet. 111 2002 157 163
29. E. Leroy, R. Boyer, G. Auburger, B. Leube, G. Ulm, E. Mezey, G. Harta, M.J. Brownstein, S. Jonnalagada, T. Chernova, A. Dehejia, C. Lavedan, T. Gasser, P.J. Steinbach, K.D. Wilkinson, and M.H. Polymeropoulos The ubiquitin pathway in Parkinson's disease Nature 395 1998 451 452
30. D.M. Maraganore, T.G. Lesnick, A. Elbaz, M.C. Chartier-Harlin, T. Gasser, R. Kruger, N. Hattori, G.D. Mellick, A. Quattrone, J. Satoh, T. Toda, J. Wang, J.P. Ioannidis, M. de Andrade, and W.A. Rocca UCHL1 is a Parkinson's disease susceptibility gene Ann. Neurol. 55 2004 512 521
31. N. Ertekin-Taner, J. Ronald, H. Asahara, L. Younkin, M. Hella, S. Jain, E. Gnida, S. Younkin, D. Fadale, Y. Ohyagi, A. Singleton, L. Scanlin, M. de Andrade, R. Petersen, N. Graff-Radford, M. Hutton, and S. Younkin Fine mapping of the alpha-T catenin gene to a quantitative trait locus on chromosome 10 in late-onset Alzheimer's disease pedigrees Hum. Mol. Genet. 12 2003 3133 3143
32. U. Finckh, K. van Hadeln, T. Muller-Thomsen, A. Alberici, G. Binetti, C. Hock, R.M. Nitsch, G. Stoppe, J. Reiss, and A. Gal Association of late-onset Alzheimer disease with a genotype of PLAU, the gene encoding urokinase-type plasminogen activator on chromosome 10q22.2 Neurogenetics 4 2003 213 217
33. N. Ertekin-Taner, M. Allen, D. Fadale, L. Scanlin, L. Younkin, R.C. Petersen, N. Graff-Radford, and S.G. Younkin Genetic variants in a haplotype block spanning IDE are significantly associated with plasma Abeta42 levels and risk for Alzheimer disease Hum. Mutat. 23 2004 334 342
34. L.M. Steinmetz, H. Sinha, D.R. Richards, J.I. Spiegelman, P.J. Oefner, J.H. McCusker, and R.W. Davis Dissecting the architecture of a quantitative trait locus in yeast Nature 416 2002 326 330
35. The International HapMap Consortium The International HapMap Project Nature 426 2003 789 796
36. G.C. Johnson, L. Esposito, B.J. Barratt, A.N. Smith, J. Heward, G. Di Genova, H. Ueda, H.J. Cordell, I.A. Eaves, F. Dudbridge, R.C. Twells, F. Payne, W. Hughes, S. Nutland, H. Stevens, P. Carr, E. Tuomilehto-Wolf, J. Tuomilehto, S.C. Gough, D.G. Clayton, and J.A. Todd Haplotype tagging for the identification of common disease genes Nat. Genet. 29 2001 233 237
37. J.E. Eichner, S.T. Dunn, G. Perveen, D.M. Thompson, K.E. Stewart, and B.C. Stroehla Apolipoprotein E polymorphism and cardiovascular disease: a HuGE review Am. J. Epidemiol. 155 2002 487 495
38. H.F. Gu, S. Efendic, S. Nordman, C-G. Östenson, K. Brismar, A.J. Brookes, and J.A. Prince Quantitative trait loci near the insulin-degrading enzyme gene (IDE) contribute to variation in plasma insulin levels Diabetes 53 2004 2137 2142
39. S. Karamohamed, S. Demissie, J. Volcjak, C. Liu, N. Heard-Costa, J. Liu, C.M. Shoemaker, C.I. Panhuysen, J.B. Meigs, P. Wilson, L.D. Atwood, L.A. Cupples, and A. Herbert Polymorphisms in the insulin-degrading enzyme gene are associated with type 2 diabetes in men from the NHLBI Framingham Heart Study Diabetes 52 2003 1562 1567