Defining haplotype blocks and tag single-nucleotide polymorphisms in the human genome

Human Molecular Genetics

Volumn 13, Issue 3, 2004, Pages 335-342

  Schulze, Thomas G ^a,b,c   Zhang, Kui ^d,e   Chen, Yu Sheng ^c   Akula, Nirmala ^b,c   Sun, Fengzhu ^d   McMahon, Francis J ^b,c  

^a CENTRAL INSTITUTE OF MENTAL HEALTH   (Germany)

^b NATIONAL INSTITUTE OF MENTAL HEALTH   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

^d UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^e UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC ALGORITHM; GENETIC PARAMETERS; GENETIC RECOMBINATION; HAPLOTYPE; HUMAN; HUMAN GENOME; INTERMETHOD COMPARISON; METHODOLOGY; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; GENE FREQUENCY; GENETIC MARKERS; GENOME, HUMAN; HAPLOTYPES; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 1042280308     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddh035     Document Type: Article

References (38)

1. Risch, N. (2000) Searching for genes in complex diseases: lessons from systemic lupus erythematosus. J. Clin. Invest, 105, 1503-1506.
2. Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J. and Lander, E.S. (2001) High-resolution haplotype structure in the human genome. Nat. Genet., 29, 229-232.
3. Taillon-Miller, P., Bauer-Sardina, I., Saccone, N.L., Putzel, J., Laitinen, T., Cao, A., Kere, J., Pilia, G., Rice, J.P. and Kwok, P.Y. (2000) Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nat. Genet., 25, 324-328.
4. Zhang, K., Calabrese, P., Nordborg, M. and Sun, F. (2002) Haplotype block structure and its applications to association studies: power and study designs. Am. J. Hum. Genet., 71, 1386-1394.
5. 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.
6. 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.
7. Koivisto, M., Perola, M., Varilo, T., Hennah, W., Ekelund, J., Lukk, M., Peltonen, L., Ukkonen, E. and Mannila, H. (2003) An MDL method for finding haplotype blocks and for estimating the strength of haplotype block boundaries. Pacific Symposium on Biocomputing, pp. 502-513.
8. Mannila, H., Koivisto, M., Perola, M., Varilo, T., Hennah, W., Ekelund, J., Lukk, M., Peltonen, L. and Ukkonen, E. (2003) Minimum description length block finder, a method to identify haplotype blocks and to compare the strength of block boundaries. Am. J. Hum. Genet., 73, 86-94.
9. 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.
10. 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.
11. Zhang, K. and Jin, L. (2003) HaploBlockFinder: haplotype block analyses. Bioinformatics, 19, 1300-1301.
12. Schwartz, R., Halldorsson, B.V., Bafna, V., Clark, A.G. and Istrail, S. (2003) Robustness of inference of haplotype block structure. J. Comput. Biol., 10, 13-19.
13. Phillips, M.S., Lawrence, R., Sachidanandam, R., Morris, A.P., Balding, D.J., Donaldson, M.A., Studebaker, J.F., Ankener, W.M., Alfisi, S.V., Kuo, F.S. et al. (2003) Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat. Genet., 33, 382-387.
14. Zhang, W., Collins, A., Maniatis, N., Tapper, W. and Morton, N.E. (2002) Properties of linkage disequilibrium (LD) maps. Proc. Natl Acad. Sci. USA, 99, 17004-17007.
15. 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.
16. Collins, F.S. and Green, E.D. (2003) A vision for the future of genomics research. Nature, 422, 835-847.
17. 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.
18. Goldstein, D.B. (2001) Islands of linkage disequilibrium. Nat. Genet., 29, 109-111.
19. Jeffreys, A.J., Kauppi, L. and Neumann, R. (2001) Intensely punctuate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet., 29, 217-222.
20. Jeffreys, A.J., Ritchie, A. and Neumann, R. (2000) High resolution analysis of haplotype diversity and meiotic crossover in the human TAP2 recombination hotspot. Hum. Mol. Genet., 9, 725-733.
21. Zhang, K., Akey, J.M., Wang, N., Xiong, M., Chakraborty, R. and Jin, L. (2003) Randomly distributed crossovers may generate block-like patterns of linkage disequilibrium: an act of genetic drift. Hum. Genet, 113, 51-59.
22. Stumpf, M.P. and Goldstein, D.B. (2003) Demography, recombination hotspot intensity, and the block structure of linkage disequilibrium. Curr. Biol., 13, 1-8.
23. Judson, R., Salisbury, B., Schneider, J., Windemuth, A. and Stephens, J.C. (2002) How many SNPs does a genome-wide haplotype map require? Pharmacogenomics, 3, 379-391.
24. Shifman, S., Kuypers, J., Kokoris, M., Yakir, B. and Darvasi, A. (2003) Linkage disequilibrium patterns of the human genome across populations. Hum. Mol. Genet., 12, 771-776.
25. Risch, N. and Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science, 273, 1516-1517.
26. McGinnis, R., Shifman, S. and Darvasi, A. (2002) Power and efficiency of the TDT and case-control design for association scans. Behav. Genet., 32, 135-144.
27. 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.
28. Cardon, L.R. and Abecasis, G.R. (2003) Using haplotype blocks to map human complex trait loci. Trends Genet., 19, 135-140.
29. Dawson, E., Abecasis, G.R., Bumpstead, S., Chen, Y., Hunt, S., Beare, D.M., Pabial, J., Dibling, T., Tinsley, E., Kirby, S. et al. (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature, 418, 544-548.
30. Chen, X., Levine, L. and Kwok, P.Y. (1999) Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res., 9, 492-498.
31. Akula, N., Chen, Y.S., Hennessy, K., Schulze, T.G., Singh, G. and McMahon, F.J. (2002) Utility and accuracy of template-directed dye-terminator incorporation with fluorescence-polarization detection for genotyping single nucleotide polymorphisms. Biotechniques, 32, 1072-1076.
32. Lewontin, R.C. (1964) The interaction of selection and linkage. I. general considerations; heterotic models. Genetics, 49, 49-67.
33. Abecasis, G.R. and Cookson, W.O. (2000) GOLD - graphical overview of linkage disequilibrium. Bioinformatics, 16, 182-183.
34. Dempster, A.P., Laird, N.M. and Rubin, D.B. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc., Ser. B, 39, 1-38.
35. Excoffier, L. and Slatkin, M. (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol., 12, 921-927.
36. Qin, Z.S., Niu, T. and Liu, J.S. (2002) Partition-ligation expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am. J. Hum. Genet, 71, 1242-1247.
37. Zapata, C., Alvarez, G. and Carollo, C. (1997) Approximate variance of the standardized measure of gametic disequilibrium D′. Am. J. Hum. Genet., 61, 771-774.
38. Kim, S.K., Zhang, K. and Sun, F. (2004) A comparison of different strategies for computing confidence intervals of the linkage disequilibrium measure D′. Pacific Symposium on Biocomputing (in press).