LDMAP: The construction of high-resolution linkage disequilibrium maps of the human genome

Methods in Molecular Biology

Volumn 376, Issue , 2007, Pages 47-57

  Kuo, Tai Yue ^a   Lau, Winston ^a   Collins, Andrew R ^a  

^a NONE

Author keywords

Computational load; Human genome; Linkage disequilibrium maps; Relative efficiency; Segmental assembly

Indexed keywords

ALGORITHM; ARTICLE; BASE PAIRING; BIOLOGICAL MODEL; CHROMOSOME 22; CHROMOSOME MAP; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOME; HAPLOTYPE; HUMAN; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; BASE PAIRING; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 22; GENOME, HUMAN; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 36549023860     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-389-7:47     Document Type: Article

References (19)

1. International HapMap Consortium. (2003) The International HapMap Project. Nature 426, 789-796.
2. Maniatis, N., Morton, N. E., Gibson, J., Xu, C. F., Hosking, L. K., and Collins, A. (2005) The optimal measure of linkage disequilibrium reduces error in association mapping of affection status. Hum. Mol. Genet. 14, 145-153.
3. Sabeti, P C., Reich, D. E., Higgins, J. M., et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837.
4. Lonjou, C., Zhang, W., Collins, A., et al. (2003) linkage disequilibrium in human populations. Proc. Natl. Acad. Sci. USA 100, 6069-6074.
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. Tapper, W. J., Maniatis, N., Morton, N. E., and Collins, A. (2003) A metric linkage disequilibrium map of a human chromosome. Ann. Hum. Genet. 67, 487-494.
7. Ke, X., Hunt, S., Tapper, W., et al. (2004) The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum. Mol. Genet. 13, 577-588.
8. Dawson, E., Abecasis, G. R., Bumpstead, S., et al. (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature 418, 544-548.
9. Maniatis, N., Collins, A., Xu, C. F., et al. (2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc. Natl. Acad. Sci. USA 99, 2228-22133.
10. Maniatis, N., Collins, A., Gibson, J., Zhang, W., Tapper, W., and Morton, N. E. (2004) Positional cloning by linkage disequilibrium. Am. J. Hum. Genet. 74, 846-855.
11. Zhang, W., Collins, A., Gibson, J., et al. (2004) Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps. Proc. Natl. Acad. Sci. USA 101, 18,075-18,080.
12. Morton, N. E., Zhang, W., Taillon-Miller, P., Ennis, S., Kwok, P. Y., and Collins, A. (2001) The optimal measure of allelic association. Proc. Natl. Acad. Sci. USA 98, 5217-5221.
13. Malecot, G. (1948) Les Mathematiques de l'Heredite, Maison et Cie, Paris, France.
14. Collins, A. and Morton, N. E. (1998) Mapping a disease locus by allelic association. Proc. Natl. Acad. Sci. USA 95, 1741-1745.
15. Collins, A., Lonjou, C., and Morton, N. E. (1999) Genetic epidemiology of single-nucleotide polymorphisms. Proc. Natl. Acad. Sci. USA 96, 15,173-15,177.
16. Hill, W. G. (1974) Estimation of linkage disequilibrium in randomly mating populations. Heredity 33, 229-239.
17. Gibson, J., Tapper, W., Zhang, W., Morton, N., and Collins, A. (2005) Cosmopolitan linkage disequilibrium maps. Hum. Genomics 2, 20-27.
18. Gomes, I., Collins, A., Lonjou, C., et al. (1999) Hardy-Weinberg quality control. Ann. Hum. Genet. 63, 535-538.
19. Press, W. H., Teukolsky, S. A., Vetterling, W. T., and Flannery, B. P. (1994) Numerical Recipes in C. Cambridge University Press, Cambridge, UK.