Association studies in candidate genes: Strategies to select SNPs to be tested

Human Heredity

Volumn 56, Issue 4, 2003, Pages 151-159

  Cousin, E ^a   Genin, E ^b   Mace, S ^a   Ricard, S ^a   Chansac, C ^a   Del Zompo, M ^c   Deleuze, J F ^a  

^a SANOFI   (France)

^b INSERM   (France)

^c UNIVERSITY OF CAGLIARI   (Italy)

Author keywords

Association; Candidate gene; Power; Selection; SNP

Indexed keywords

ALLELE; ARTICLE; CALCULATION; DISEASE PREDISPOSITION; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC MODEL; GENETIC PREDISPOSITION; HAPLOTYPE; HUMAN; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; APOLIPOPROTEINS E; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; GENE FREQUENCY; GENETIC MARKERS; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MUCINS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 1642588404     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000073200     Document Type: Article

References (20)

1. Risch N, Merikangas K: The future of genetic studies of complex human diseases. Science 1996;273:1516-1517.
2. Collins FS, Geyer MS, Chakravarti A: Variations on a theme: cataloguing human DNA sequence variation. Science 1997;278:1580-1581.
3. Chakravarti A: It's raining SNPs, hallelujah? Nat Genet 1998;19:216-217.
4. Pritchard JK, Przeworski M: Linkage disequilibrium in humans: models and data. Am J Hum Genet 2001;69:1-14.
5. Abecasis GR, Noguchi E, Heinzmann A, Traherne JA, Bhattacharyya S, Leaves NI, Anderson GG, Zhang Y, Lench NJ, Carey A, Cardon LR, Moffatt MF, Cookson WOC: Extent and distribution of linkage disequilibrium in three genomic regions. Am J Hum Genet 2001;68:191-197.
6. Cambien F, Poirier O, Nicaud V, Herrmann SM, Mallet C, Ricard S, Behague I, Hallet V, Blanc H, Loukaci V, Thillet J, Evans A, Ruidavets JB, Arveiler D, Luc G, Tiret L: Sequence diversity in 36 candidate genes for cardiovascular disorders. Am J Hum Genet 1999;65:183-191.
7. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N, Lane CR, Lim EP, Kalyanaraman N, Nemesh J, Ziaugra L, Friedland L, Rolfe A, Warrington J, Lipshutz R, Daley GQ, Lander ES: Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 1999;22:231-238.
8. Dunning AM, Durocher F, Healey CS, Teare MD, McBride SE, Carlomagno F, Xu CF, Dawson E, Rhodes S, Ueda S, Lai E, Luben RN, Van Rensburg EJ, Mannermaa A, Kataja V, Rennart G, Dunham I, Purvis I, Easton D, Ponder BAJ: The extent of linkage disequilibrium in four populations with distinct demographic histories. Am J Hum Genet 2000;67:1544-1554.
9. Johnson GCJ, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RC, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SC, Clayton DG, Todd JA: Haplotype tagging for the identification of common disease genes. Nat Genet 2001;29:233-237.
10. Stram DO, Haiman CA, Hirschhorn JN, Altshuler D, Kolonel LN, Henderson BE, Pike MC: Choosing haplotype-tagging SNPs based on unphased genotype data from a preliminary sample of unrelated subjects with an example from the Multiethnic Cohort Study. Hum Hered 2003;55:27-36.
11. Génin E: Selection of single nucleotide polymorphisms for association studies in candidate genes. Genet Epidemiol 2001;21(suppl 1):S614-S619.
12. Schlesselman JJ: Case-control studies: design, conduct, analysis. Oxford University Press, New York, 1982.
13. Poirier J, Delisle MC, Quirion R, Aubert I, Farlow M, Lahiri D, Hui S, Bertrand P, Nalbantoglu J, Gilfix BM, Gauthier S: Apolipoprotein E4 allele as a predictor of cholinergic deficits and treatment outcome in Alzheimer disease. Proc Natl Acad Sci USA 1995;92:12260-12264.
14. Nickerson DA, Taylor SL, Fullerton SM, Weiss KM, Clark AG, Stengård JH, Salomaa V, Boerwinkle E, Sing CF: Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene. Genome Res 2000;10:1532-1545.
15. Fullerton SM, Clark AG, Weiss KM, Nickerson DA, Taylor SL, Stengard JH, Salomaa V, Vartiainen E, Perola M, Boerwinkle E, Sing CF: Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism. Am J Hum Genet 2000;67:881-900.
16. Devlin B, Risch N: A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995;29:311-322.
17. Lewis C: Selecting informative SNP subsets for association studies. Association Studies in Genomic Analysis, Henry Stewart Conference Studies 2002.
18. Almasy L, Terwilliger JD, Nielsen D, Dyer TD, Zaykin D, Blangero J: GAW12: Simulated genome scan, sequence, and family data for a common disease. Genet Epidemiol 2001;21(suppl 1):S332-S338.
19. Bourgain C, Genin E, Quesneville H, Clerget-Darpoux F: Search for multifactorial disease susceptibility genes in founder populations. Ann Hum Genet 2000;64:255-265.
20. Zhang K, Calabrese P, Nordborg M, Fengzhu S: Haplotype block structure and its applications to association studies: Power and study designs. Am J Hum Genet 2002;71:1386-1394.