The extent of linkage disequilibrium and haplotype sharing around a polymorphic site

Genetics

Volumn 165, Issue 1, 2003, Pages 437-444

  Innan, Hideki ^a,b   Nordborg, Magnus ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CHROMOSOME; GENE LINKAGE DISEQUILIBRIUM; GENE MUTATION; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; HAPLOTYPE; MODEL; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

DATA INTERPRETATION, STATISTICAL; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; PHYLOGENY; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC;

EID: 0141789996     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (31)

1. ANDOLFATTO, P., J. D. WALL and M. KREITMAN, 1999 Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153: 1297-1311.
2. DALY, M. J., J. D. RIOUX, S. F. SCHAFFNER, T. J. HUDSON and E. S. LANDER, 2001 High-resolution haplotype structure in the human genome. Nat. Genet. 29: 229-232.
3. DAWSON, E., G. R. ABECASIS, S. BUMPSTEAD, Y. CHEN, S. HUNT et al., 2002 A first-generation linkage disequilibrium map of human chromosome 22. Nature 418: 544-548.
4. GABRIEL, S. B., S. F. SCHAFFNER, H. NGUYEN, J. M. MOORE, J. ROY et al., 2002 The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
5. GRIFFITHS, R. C., and S. TAVARÉ, 1998 The age of a mutant in a general coalescent tree. Stoch. Models 14: 273-295.
6. GRIFFITHS, R. C., and S. TAVARÉ, 1999 The ages of mutations in gene trees. Ann. Appl. Prob. 9: 567-590.
7. HUDSON, R. R., 1983 Testing the constant-rate neutral allele model with protein sequence data. Evolution 37: 203-217.
8. HUDSON, R. R., and N. L. KAPLAN, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
9. INNAN, H., and F. TAJIMA, 1997 The amounts of nucleotide variation within and between allelic classes and the reconstruction of the common ancestral sequence in a population. Genetics 147: 1431-1444.
10. INNAN, H., and F. TAJIMA, 1999 The effect of selection on the amounts of nucleotide variation within and between allelic classes. Genet. Res. 73: 15-28.
11. INNAN, H., B. PADHUKASAHASRAM and M. NORDBORG, 2003 The pattern of polymorphism on human chromosome 21. Genome Res. 13: 1158-1168.
12. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The "hitch-hiking" effect revisited. Genetics 123: 887-899.
13. KAPLAN, N. L., W. G. HILL and B. S. WEIR, 1995 Likelihood methods for locating disease genes in nonequilibrium populations. Am. J. Hum. Genet. 56: 18-32.
14. KINGMAN, J. F. C., 1982 The coalescent. Stoch. Proc. Appl. 13: 235-248.
15. LEWONTIN, R. C., 1964 The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49: 49-67.
16. LIU, J. S., C. SABATTI, J. TENG, B. J. B. KEATS and N. RISCH, 2001 Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res. 11: 1716-1724.
17. MARUYAMA, T., 1977 Stochastic Problems in Population Genetics. Springer-Verlag, Berlin.
18. MCPEEK, M. S., and A. STRAHS, 1999 Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping. Am. J. Hum. Genet. 65: 858-875.
19. MORRIS, A. P., J. C. WHITTAKER and D. J. BALDING, 2000 Bayesian fine-scale mapping of disease loci, by hidden Markov models. Am. J. Hum. Genet. 67: 155-169.
20. MORRIS, A. P., J. C. WHITTAKER and D. J. BALDING, 2002 Fine-scale mapping of disease loci via shattered coalescent modeling of genealogies. Am. J. Hum. Genet, 70: 686-707.
21. NORDBORG, M., 2001 Coalescent theory, pp. 179-212 in Handbook of Statistical Genetics, edited by D. J. BALDING, M. J. BISHOP and C. CANNINGS. John Wiley & Sons, Chichester, UK.
22. NORDBORG, M., and S. TAVARÉ, 2002 Linkage disequilibrium: what history has to tell us. Trends Genet. 18: 83-90.
23. PATIL, N., A. J. BERNO, D. A. HINDS, W. A. BARRETT, J. M. DOSHI et al., 2001 Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294: 1719-1723.
24. PHILLIPS, M. S., R. LAWRENCE, R. SACHIDANANDAM, A. P. MORRIS, D. J. BALDING et al., 2003 Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat. Genet. 33: 382-387.
25. SABETI, P. C., D. E. REICH, J. M. HIGGINS, H. Z. P. LEVINE, D. J. RICHTER et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
26. SAUNDERS, I. W., S. TAVARÉ and G. A. WATTERSON, 1984 On the genealogy of nested subsamples from a haploid population. Adv. Appl. Prob. 16: 471-491.
27. SLATKIN, M., and G. BERTORELLE, 2001 The use of intraallelic variability for testing neutrality and estimating population growth rate. Genetics 158: 865-874.
28. TAJIMA, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
29. THOMPSON, E. A., and J. V. NEEL, 1997 Allelic disequilibrium and allele frequency distribution as a function of social and demographic history. Am. J. Hum. Genet. 60: 197-204.
30. WIUF, C., and P. DONNELLY, 1999 Conditional genealogies and the age of a neutral mutant. Theor. Popul. Biol. 56: 183-201.
31. WRIGHT, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.