Tag SNP selection for association studies

Genetic Epidemiology

Volumn 27, Issue 4, 2004, Pages 365-374

  Stram, Daniel O ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Candidate gene analysis; Case control studies; Haplotypes; ht SNP; Linkage disequilibrium; Tag SNP

Indexed keywords

ACCURACY; CASE CONTROL STUDY; CHROMOSOME 2; CHROMOSOME ANALYSIS; COMPUTER PROGRAM; CORRELATION ANALYSIS; DATA ANALYSIS; DENSITY; GENE FREQUENCY; GENE MAPPING; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC MARKER; GENETIC RISK; GENETIC SELECTION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; PREDICTION; REVIEW; RISK ASSESSMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 10044235010     PISSN: 07410395     EISSN: None     Source Type: Journal    
DOI: 10.1002/gepi.20028     Document Type: Review

References (33)

1. Barzuza T, Beckman J, Shamir R, Pe'er I. 2004. Computational problems in perfect phylogeny haplotyping: Xor-genotypes and tagSNPs. In: Sahinalp S, Muthukrishnan S, Dogrusoz U, editors. Proceedings of the Fifteenth Annual Symposium on Combinatorial Pattern Matching, Lecture notes in Computer Science, Vol 3109, Istanbul. New York: Springer-Verlag. 2004. p 15-27.
2. Bonnen PE, Wang PJ, Kimmel M, Chakraborty R, Nelson DL. 2002. Haplotype and linkage disequilibrium architecture for human cancer-associated genes. Genome Res 1212:1846-1853.
3. Botstein D, Risch N. 2003. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33(Suppl): 228-237.
4. 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. 1999. Sequence diversity in 36 candidate genes for cardiovascular disorders. Am J Hum Genet 65:183-191.
5. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. 2004. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74:106-120.
6. Chapman JM, Cooper JD, Todd JA, Clayton DG. 2003. Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum Hered 56:18-32.
7. Crawford DC, Carlson CS, Rieder MJ, Carrington DP, Yi Q, Smith JD, Eberle MA, Krugylak L, Nickerson DA. 2004. Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am J Hum Genet 74:610-622.
8. Daly MJ, Rioux J, Schaffner S, Hudson T, Lander E. 2001. High-resolution haplotype structure in the human genome. Nature Genet 29:229-232.
9. Excoffier L and Slatkin M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927.
10. Fullerton SM, Buchanan AV, Sonpar VA, Taylor SL, Smith JD, Carlson CS, Salomaa V, Stengard JH, Boerwinkle E, Clark AE, Nickerson DA, Weiss KM. 2004. The effects of scale: variation in the APOA1/C3/A4/A5 gene cluster. Hum Genet 115:36-56.
11. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. 2002. The structure of haplotype blocks in the human genome. Science 296:2225-2229.
12. Haiman CA, Stram DO, Pike MC, Kolonel LN, Burtt NP, Altshuler D, Hirschhorn J, Henderson BE. 2003. A comprehensive haplotype analysis of CYP19 and breast cancer risk: the multiethnic cohort study. Hum Mol Genet 12:2679-2692.
13. International HapMap Consortium. 2003. The International HapMap Project. Nature 426:789-796.
14. Jeffreys AJ, Kauppi L, Neumann R. 2001. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 29:217-222.
15. Jeffreys AJ, Holloway JK, Kauppi L, May CA, Neumann R, Slingsby MT, Webb AJ. 2004. Meiotic recombination hot spots and human DNA diversity. Philos Trans R Soc Lond B Biol Sci 359:141-152.
16. Johnson GC, 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. 2001. Haplotype tagging for the identification of common disease genes. Nat Genet 29:233-237.
17. Kauppi L, Sajantila A, Jeffreys AJ. 2003. Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. Hum Mol Genet 12:33-40.
18. Kauppi L, Jeffreys AJ, Keeney S. 2004. Where the crossovers are: recombination distributions in mammals. Nat Rev Genet 5:413-424.
19. Ke X, Cardon LR. 2003. Efficient selective screening of haplotype tag SNPs. Bioinformatics 19:287-288.
20. Kolonel LN, Henderson BE, Hankin JH, Nomura AM, Wilkens LR, Pike MC, Stram DO, Monroe KR, Earle ME, Nagamine FS. 2000. A multiethnic cohort in Hawaii and Los Angeles: baseline characteristics. Am J Epidemiol 151:346-357.
21. McVean GA, Myers SR, Hunt S, Deloukas P, Bentley DR, Donnelly P. 2004. The fine-scale structure of recombination rate variation in the human genome. Science 304:581-584.
22. Qin ZS, Niu T, Liu JS. 2002. Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet 71:1242-1247.
23. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. 2001. Linkage disequilibrium in the human genome. Nature 411:199-204.
24. Risch N, Merikangas K. 1996. The future of genetic studies of complex human diseases. Science 273:1516-1517.
25. Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. 2002. Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70:425-434.
26. Stram D, Haiman C, Hirschhorn JN, Altshuler D, Kolonel L, Henderson B, Pike M. 2003. Choosing haplotype-tagging SNPs based on unphased genotype data from a preliminary sample of unrelated subjects with an example from the Multiethnic Cohort Study. Human Hered 55:27-36.
27. Terwilliger JD, Weiss KM. 1998. Linkage disequilibrium mapping of complex disease: fantasy or reality? Curr Opin Biotechnol 9:578-594.
28. Wall JD, Pritchard JK. 2003. Assessing the performance of the haplotype block model of linkage disequilibrium. Am J Hum Genet 73:502-515.
29. Weale ME, Depondt C, Macdonald SJ, Smith A, Lai PS, Shorvon SD, Wood NW, et al. 2003. Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibrium gene mapping. Am J Hum Genet 73:551-565.
30. Weiss KM, Clark AG. 2002. Linkage disequilibrium and the mapping of complex human traits. Trends Genet 18:19-24.
31. Zaykin DV, Westfall PH, Young SS, Karnoub MA, Wagner MJ, Ehm MG. 2002. Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum Hered 53:79-91.
32. Zhang K, Deng M, Chen T, Waterman MS, Sun F. 2002. A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci U S A 99:7335-7339.
33. Zhang K, Qin ZS, Liu JS, Chen T, Waterman MS, Sun F. 2004. Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res 14:908-916.