Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies

Genome Research

Volumn 14, Issue 5, 2004, Pages 908-916

  Zhang, Kui ^a,b   Qin, Zhaohui S ^c,d   Liu, Jun S ^d   Chen, Ting ^a   Waterman, Michael S ^a   Sun, Fengzhu ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

^d HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; GENE FREQUENCY; GENE FUNCTION; GENE NUMBER; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; HUMAN GENETICS; POPULATION DENSITY; POPULATION SIZE; PRIORITY JOURNAL; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ALLELES; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 5; COMPUTER SIMULATION; DNA PROBES; GENE FREQUENCY; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; RESEARCH DESIGN; SAMPLE SIZE;

EID: 2442658957     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1837404     Document Type: Article

References (54)

1. Abecasis, G.R. and Cookson, W.O. 2000. GOLD - Graphical overview of linkage disequilibrium. Bioinformatics 16: 182-183.
2. Anderson, E.C. and Novembre, J. 2003. Finding haplotype block boundaries by using the minimum-description-length principle. Am. J. Hum. Genet. 73: 336-354.
3. Cardon, L.R., Ke, X., Lawrence, R., Carter, N., Rogers, J., Stavrides, G., Willey, D., Mullikin, J., Hunt, S., Bentley, D.R., et al. 2003. Towards a fine-scale linkage disequilibrium map of human chromosome 20. Am. J. Hum. Genet. 73 (Suppl): 271.
4. Clark, A.G. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7: 111-122.
5. 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.
6. 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 chromosome 22. Nature 418: 544-548.
7. Douglas, J.A., Boehnke, M., Gillanders, E., Trent, J.M., and Gruber, S.B. 2001. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nat. Genet. 28: 361-364.
8. Dunning, A.M., Durocher, F., Healey, C.S., Teare, M.D,, McBride, S.E., Carlomoahno, F., Xu, C.F., Dawnson, E., Rhodes, S., Ueda, S., et al. 2000. The extent of linkage disequilibrium in four populations with distinct demographic histories. Am. J. Hum. Genet. 67: 1544-1554.
9. Eisenbarth, I., Striedel, A.M., Moschgath, E., Vodel, W., and Assum, G. 2001. Long-range sequence composition mirrors linkage disequilibrium pattern in 1 1.13 MB region of human chromosome 22. Hum. Mol. Genet. 24: 2833-2839.
10. Eskin, E., Halperin, E., and Eskin, E. 2003. Large scale recovery of haplotypes from genotype data using imperfect phylogeny. In Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2003) (eds. W. Miller et al.), pp. 104-113. ACM, New York.
11. Excoffier, L. and Slatkin, M. 1995. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12: 921-927.
12. Fallin, D. and Schork, N. 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.
13. 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.
14. Griffiths, R.C. and Marjoram, P. 1997. An ancestral recombination graph. In Progress in population genetics and human evolution (eds. P. Donnelly and S. Tavaré), pp. 257-270. Springer-Verlag, New York.
15. Gusfield, D. 2001. Inference of haplotypes from samples of diploid populations: Complexity and algorithms. J. Comp. Biol. 8: 305-323.
16. Gusfield, D. 2002. Haplotyping as perfect phylogeny: Conceptual framework and efficient solutions. In Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2002) (eds. G. Myers et al.), pp. 166-175. ACM, New York.
17. Hawley, M.E. and Kidd, K.K. 1995. HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J. Hered. 86: 409-411.
18. Hudson, R.R. 1983. Properties of a neutral-allele model with intragenic recombination. Theor. Popul. Genet. 23: 183-201.
19. Jeffreys, A.J., Kauppi, L., and Neumann, R. 2001. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29: 217-222.
20. Johnson, G.C.L., 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.
21. Kaplan, N.L. and Hudson, R.R. 1985. The use of sample genealogies for studying a selectively neutral m-loci model with recombination. Theor. Popul. Biol. 28: 382-396.
22. Kirk, K.M. and Cardon, L.R. 2002. The impact of genotyping error on haplotype reconstruction and frequency estimation. Eur. J. Hum. Genet. 10: 616-622.
23. 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. Pac. Sym. Biocomput. 8: 502-513.
24. Kruglyak, L. 1999. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22: 139-144.
25. Lewontin, R.C. 1964. The interaction of selection and linkage I. General considerations; heterotic models. Genetics 49: 49-67.
26. Lin, S., Cutler, D.J., Zwick, M.E., and Chakravarti, A. 2002. Haplotype inference in random population samples. Am. J. Hum. Genet. 71: 1129-1137.
27. Long,.J.C., Williams, R.C., and Urbanek, M. 1995. An E-M algorithm and testing strategy for multiple-locus haplotypes. Am. J. Hum. Genet. 56: 799-810.
28. MichlataosBeloin, S., Tishkoff, S.A., Bentley, K.L., Kidd, K.K., and Ruano, G. 1996. Molecular haplotyping of genetic markers 10 kb apart by allelic-specific long-range PCR. Nucleic Acids Res. 24: 4841-4843.
29. Niu, T., Qin, Z., Xu, X., and Liu, J.S. 2002. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am. J. Hum. Genet. 70: 157-159.
30. Nordborg, M. and Tavaré, S. 2002. Linkage disequilibrium: What history has to tell us. Trends Genet. 18: 83-90.
31. Olson, J.M. and Wijsman, E.M. 1994. Design and sample size considerations in the detection of linkage disequilibrium with a disease locus. Am. J. Hum. Genet. 55: 574-580.
32. Papadopolous, N., Leach, F.S., Kinzler, K.W., and Vogelstein, B. 1995. Monoallelic mutation analysis (MAMA) for identifying germline mutations. Nat. Genet. 11: 99-102.
33. 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.
34. Philips, 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.
35. Qin, Z., Niu, T., and Liu, J. 2002. Partitioning-Ligation-Expectation-Maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am. J. Hum. Genet. 71: 1242-1247.
36. Reich, D.E., Schaffner, S.F., Daly, M.J., McVean, G., Mullikin, J.C., Higgins, J.M., Richter, D.J., Lander, E.S., and Altshuler, D. 2002. Human genome sequence variation and the influence of gene history, mutation and recombination. Nat. Genet. 32: 135-142.
37. Risch, N. and Merikangas, K. 1996. The future of genetic studies of complex human diseases. Science 273: 1516-1517.
38. Schneider, J.A., Peto, T.E., Boone, R.A., Boyce, A.J., and Clegg, J.B. 2002. Direct measurement of the male recombination fraction in the human β-globin hot spot. Hum. Mol. Genet. 11: 207-215.
39. Sham, P., Bader, J.S., Craig, I., O'Donovan, M., and Owen, M. 2002. DNA pooling: A tool for larger-scale association studies. Nat. Rev. Genet. 3: 862-871.
40. Spielman, R.S., McGinnis, R.E., and Ewens, W.J. 1993. Transmission test for linkage disequilibrium: The insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52: 506-516.
41. Stephens, M., Smith, N.J., and Donnelly, P. 2001. A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
42. Taillon-Miller, P., Bauer-Sardina, I., Saccone, N.L., Putzel, J., Laitinen, T., Cao, A., Kere, J., Pilia, G., Rice, J.P., and Kwork, P.Y. 2000. Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nat. Genet. 25: 324-328.
43. Thompson, D., Stram, D., Goldgar, D., and Witte, J.S. 2003. Haplotype tagging single nucleotide polymorphisms and association studies. Hum. Hered. 56: 48-55.
44. Tishkoff, S.A., Pakstis, A.J., Ruano, G., and Kidd, K.K. 2000. The accuracy of statistical methods for estimation of haplotype frequencies: An example from the CD4 locus. Am. J. Hum. Genet. 67: 518-522.
45. Wall, J.D. and Pritchard, J.K. 2003. Haplotype blocks and linkage disequilibrium in the human genome. Nat. Rev. Genet. 4: 587-597.
46. Wang, N., Akey, J.M., Zhang, K., Chakraborty, K., and Jin, L. 2002. Distribution of recombination crossovers and the origin of haplotype blocks: The interplay of population history, recombination, and mutation. Am. J. Hum. Genet. 71: 1227-1234.
47. Wang, S., Kidd, K.K., and Zhao, H. 2003. On the use of DNA pooling to estimate haplotype frequencies. Genet. Epidemiol. 24: 74-82.
48. Weiss, K.M. and Clark, A.G. 2002. Linkage disequilibrium and the mapping of complex human traits. Trends Genet. 18: 19-24.
49. Yan, H., Papadopoulos, N., Marra, G., Perrera, C., Jiricny, J., Boland, C.R., Lynch, H.T., Chadwick, R.B., de la Chapelle, A., Berg, K., et al. 2000. Conversion of diploidy to haploidy. Nature. 403: 723-724.
50. Zaykin, D.V., Westfall, P.H., Young, S.S., Karnoub, M.A., Wagner, M.J., and Ehm, M.G. 2002. Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum. Hered. 53: 79-91.
51. Zhang, K., Calabrese, P., Nordborg, M., and Sun, F. 2002a. Haplotype block structure and its applications in association studies: Power and study design. Am. J. Hum. Genet. 71: 1386-1394.
52. Zhang, K., Deng, M., Chen, T., Waterman, M.S., and Sun, F. 2002b. A dynamic programming algorithm for haplotype block partitioning. Proc. Natl. Acad. Sci. 99: 7335-7339.
53. 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.
54. Zhao, H., Zhang, S., Kathleen, R., Merinkangas, K.R., Trixler, M., Wildenauer, D.B., Sun, F., and Kidd, K.K. 2000. Transmission/disequilibrium tests using multiple tightly linked markers. Am. J. Hum. Genet. 67: 936-946.