Efficiency and consistency of haplotype tagging of dense SNP maps in multiple samples

Human Molecular Genetics

Volumn 13, Issue 21, 2004, Pages 2557-2565

  Ke, Xiayi ^a   Durrant, Caroline ^a   Morris, Andrew P ^a   Hunt, Sarah ^b   Bentley, David R ^b   Deloukas, Panos ^b   Cardon, Lon R ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ARTICLE; CAUCASIAN; CHROMOSOME; CONTROLLED STUDY; DATA BASE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC MARKER; GENOTYPE; HAPLOTYPE; HUMAN; HUMAN CHROMOSOME; HUMAN GENOME; PRIORITY JOURNAL; SAMPLE; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED KINGDOM;

AFRICAN AMERICANS; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 20; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENETIC MARKERS; GREAT BRITAIN; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MATHEMATICS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 8444223091     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddh294     Document Type: Article

References (36)

1. Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P. et al. (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719-1723.
2. Ke, X., Hunt, S., Tapper, W., Lawrence, R., Stavrides, G., Ghori, J., Whittaker, P., Collins, A., Morris, A.P., Bentley, D. et al. (2004) The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum. Mol. Genet., 13, 577-588.
3. Nickerson, D.A., Taylor, S.L., Weiss, K.M., Clark, A.G., Hutchinson, R.G., Stengard, J., Salomaa, V., Vartiainen, E., Boerwinkle, E. and Sing, C.F. (1998) DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nat. Genet., 19, 233-240.
4. Nickerson, D.A., Taylor, S.L., Fullerton, S.M., Weiss, K.M,, Clark, A.G., Stengard, J.H., Salomaa, V., Boerwinkle, E. and Sing, C.F. (2000) Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene. Genome Res., 10, 1532-1545.
5. Subrahmanyan, L., Eberle, M.A., Clark, A.G., Kruglyak, L. and Nickerson, D.A. (2001) Sequence variation and linkage disequilibrium in the human T-cell receptor beta (TCRB) locus. Am. J. Hum. Genet., 69, 381-395.
6. Crawford, D.C., Carlson, C.S., Rieder, M.J., Carrington, D.P., Yi, Q., Smith J.D., Eberle, M.A., Kruglyak, L. and Nickerson, D.A. (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.
7. Gibbs, R.A., Belmont, J.W., Hardenbol, P., Willis, T.D., Yu, F., Yang, H., Ang, L., Huang, W., Liu, B., Shen, Y. et al. (2003) The International HapMap project. Nature, 426, 789-796.
8. Johnson, G.C., Esposito, L., Barratt, B.J., Smith, A.N., Heward, J., Di Genova, G., Ueda, H., Cordell, H.J., Eaves, I.A., Dudbridge, F. et al. (2001) Haplotype tagging for the identification of common disease genes. Nat. Genet., 29, 233-237.
9. Goldstein, D.B., Ahmadi, K.R., Weale, M.E. and Wood, N.W. (2003) Genome scans and candidate gene approaches in the study of common diseases and variable drug responses. Trends Genet., 19, 615-622.
10. Zhang, K., Sun, F., Waterman, M.S. and Chen, T. (2003) Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. Am. J. Hum. Genet., 73, 63-73.
11. Zhang, K., Deng, M., Chen, T., Waterman, M.S. and Sun, F. (2002) A dynamic programming algorithm for haplotype block partitioning. Proc. Natl Acad. Sci. USA, 99, 7335-7339.
12. Weale, M.E., Depondt, C., Macdonald, S.J., Smith, A., Lai, P.S., Shorvon, S.D., Wood, N.W. and Goldstein, D.B. (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.
13. Ke, X. and Cardon, L.R. (2003) Efficient selective screening of haplotype tag SNPs. Bioinformatics, 19, 287-288.
14. Meng, Z., Zaykin, D.V., Xu, C.F., Wagner, M. and Ehm, M.G. (2003) Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am. J. Hum. Genet., 73 115-130.
15. Sebastiani, P., Lazarus, R., Weiss, S.T., Kunkel, L.M., Kohane, I.S. and Ramoni, M.F. (2003) Minimal haplotype tagging. Proc. Natl Acad. Sci. USA, 100, 9900-9905.
16. Cousin, E., Genin, E., Mace, S., Ricard, S., Chansac, C., del Zompo, M. and Deleuze, J.F. (2003) Association studies in candidate genes: strategies to select SNPs to be tested. Hum. Hered., 56 151-159.
17. Wiuf, C., Laidlaw, Z. and Stumpf, M.P. (2003) Some notes on the combinatorial properties of haplotype tagging. Math. Biosci., 185, 205-216.
18. Barratt, B.J., Payne, F., Rance, H.E., Nutland, S., Todd, J.A. and Clayton, D.G. (2002) Identification of the sources of error in allele frequency estimations from pooled DNA indicates an optimal experimental design. Ann. Hum. Genet., 66, 393-405.
19. Carlson, C.S., Eberle, M.A., Rieder, M.J., Yi, Q., Kruglyak, L. and Nickerson, D.A. (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet., 74, 106-120.
20. Chapman, J.M., Cooper, J.D., Todd, J.A. and Clayton, D.G. (2003) Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum. Hered., 56, 18-31.
21. Goldstein, D.B., Tate, S.K. and Sisodiya, S.M. (2003) Pharmacogenctics goes genomic. Nat. Rev. Genet., 4, 937-947.
22. Lowe, C.E., Cooper, J.D., Chapman, J.M., Barratt, B.J., Twells, R.C., Green, E.A., Savage, D.A., Guja, C., Ionescu-Tirgoviste, C., Tuomilehto-Wolf, E. et al. (2004) Cost-effective analysis of candidate genes using htSNPs: a staged approach. Genes Immun., 5 301-305.
23. Zhang, K., Qin, Z.S., Liu, J.S., Chen, T., Waterman, M.S. and Sun, F. (2004) Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res., 14, 908-916.
24. Schulze, T.G., Zhang, K., Chen, Y.S., Akula, N., Sun, F. and McMahon, F.J. (2004) Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome. Hum. Mol. Genet., 13, 335-342.
25. Deloukas, P., Matthews, L.H., Ashurst, J., Burton, J., Gilbert, J.G., Jones, M., Stavrides, G., Almeida, J.P., Babbage, A.K., Bagguley, C.L. et al. (2001) The DNA sequence and comparative analysis of human chromosome 20. Nature, 414, 865-871.
26. Cavalli-Sforza, L.L., Menozzi, P. and Piazza, A. (1994) History and Geography of Human Genes. Princeton University Press, Princeton.
27. Zondervan, K.T. and Cardon, L.R. (2004) The complex interplay among factors that influence allelic association. Nat. Rev. Genet., 5, 89-100.
28. Abecasis, G.R., Cookson, W.O. and Cardon, L.R. (2001) The power to detect linkage disequilibrium with quantitative traits in selected samples. Am. J. Hum. Genet., 68, 1463-1474.
29. Muller-Myhsok, B. and Abel, L. (1997) Genetic analysis of complex diseases. Science, 275, 1328-1329.
30. Tu, I.P. and Whittemore. A,S. (1999) Power of association and linkage tests when the disease alleles are unobserved. Am. J. Hum. Genet., 64, 641-649.
31. Zhang, W., Collin, A. and Morton, N. (2004) Does haplotype diversity predict power for association mapping of disease susceptibility? Hum. Genet., 115, 157-164.
32. Kong, A., Gudbjartsson, D.F., Sainz, J., Jonsdottir, G.M., Gudjonsson, S.A., Richardsson, B., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G. et al. (2002) A high-resolution recombination map of the human genome. Nat. Genet., 31, 242-247.
33. Ardlie, K.G., Kruglyak, L. and Seielstad, M. (2002) Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet., 3, 299-309.
34. Carlson, C.S., Eberle, M.A., Rieder, M.J., Smith, J.D., Kruglyak, L. and Nickerson, D.A. (2003) Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat. Genet., 33, 518-521.
35. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel. B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M. et al. (2002) The structure of haplotype blocks in the human genome. Science, 296, 2225-2229.
36. Fallin, D. and Schork, N.J. (2000) Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am. J. Hum. Genet., 67, 947-959.