Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics

Volumn 165, Issue 4, 2003, Pages 2213-2233

  Li, Na ^a   Stephens, Matthew ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE;

ARTICLE; BIOLOGY; CHROMOSOME NOR; DNA POLYMORPHISM; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENE STRUCTURE; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; POPULATION; POPULATION STRUCTURE; PRIORITY JOURNAL; STATISTICAL MODEL;

ALGORITHMS; ATP-BINDING CASSETTE TRANSPORTERS; CHROMOSOME MAPPING; COMPUTER SIMULATION; GENETIC HETEROGENEITY; GENETICS, POPULATION; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DENSITY; RECOMBINATION, GENETIC;

EID: 0347361674     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (42)

1. BESAG, J., 1974 Spatial interaction and the statistical analysis of lattice systems. J. R. Stat. Soc. Ser. B 36: 192-236.
2. CLARK, A. G., 1990 Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7 (2): 111-122.
3. CLARK, A. G., K. M. WEISS, D. A. NICKERSON, S. L. TAYLOR, A. BUCHANAN et al., 1998 Haplotype structure and population genetics inferences from nucleotide-sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63: 595-612.
4. 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.
5. EWENS, W. J., 1972 The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 3: 87-112.
6. FEARNHEAD, P. N., and P. DONNELLY, 2001 Estimating recombination rates from population genetic data. Genetics 159: 1299-1318.
7. FEARNHEAD, P., and P. DONNELLY, 2002 Approximate likelihood methods for estimating local recombination rates. J. R. Stat. Soc. Ser. B 64: 657-680.
8. FRISSE, L., R. R. HUDSON, A. BARTOSZEWICZ, J. D. WALL, J. DONFACK et al., 2001 Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet. 69: 831-843.
9. GRIFFITHS, R. C., and P. MARJORAM, 1996 Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3: 479-502.
10. HAMMER, M. C., T. KARAFET, A. RASANAYAGAM, E. T. WOOD, T. K. ALTHEIDE et al., 1998 Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Mol. Biol. Evol. 15 (4): 427-441.
11. HARDING, R. M., S. M. FULLERTON, R. C. GRIFFITHS, J. BOND, M.J. COX et al., 1997 Archaic African and Asian lineages in the genetic ancestry of modern humans. Am. J. Hum. Genet. 60: 772-789.
12. HEY, J., and J. WAKELEY, 1997 A coalescent estimator of the population recombination rate. Genetics 145: 833-846.
13. HUDSON, R. R., 1983 Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23: 183-201.
14. HUDSON, R. R., 1987 Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50: 245-250.
15. HUDSON, R. R., 2001 Two-locus sampling distribution and their application. Genetics 159: 1805-1817.
16. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
17. 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.
18. JEFFREYS, A.J., and R. NEUMANN, 2002 Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot. Nat. Genet. 31: 267-271.
19. JEFFREYS, A. J., A. RITCHIE and R. NEUMANN, 2000 High resolution analysis of haplotype diversity and meiotic crossover in the human TAP2 recombination hotspot. Hum. Mol. Genet. 9: 725-733.
20. JEFFREYS, A.J., L. KAUPPI and R. NEUMANN, 2001 Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet, 29: 217-222.
21. JOHNSON, G. C. L., L. ESPOSlTO, B.J.B.A.N. SMITH, J. HEWARD, G. D. GENOVA et al., 2001 Haplotype tagging for the identification of common disease genes. Nat. Genet. 29: 233-235.
22. KINGMAN, J. F. C., 1982 The coalescent. Stoch. Proc. Appl. 13: 235-248.
23. KRUGLYAK, L., 1999 Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22:139-144.
24. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 2000 Maximum likelihood estimation of recombination rates from population data. Genetics 156: 1393-1401.
25. LIU, J. S., C. SABATTI, J. TENG, B.J. KEATS and N. RISCH, 2001 Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Res. 11: 1716-1724.
26. 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.
27. MCVEAN, G., P. AWADALLA and P. FEARNHEAD, 2002 A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
28. MORRIS, A. P., J. C. WHITTAKER and D. J. BALDINC., 2000 Bayesian fine-scale mapping of disease loci, by hidden Markov models. Am. J. Hum. Genet. 67: 155-169.
29. NICKERSON, D. A., S. L. TAYLOR, K. M. WEISS, A. G. CLARK, R. G. HUTCHINSON et al., 1998 DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nat. Genet. 19: 233-240.
30. NIELSEN, R., 2000 Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154: 931-942.
31. OLIVIER, M., V. I. BUSTOS, M. R. LEVY, G. A. SMICK, I. MORENO et al., 2001 Complex high-resolution linkage disequilibrium and haplotype patterns of single-nucleotide polymorphisms in 2.5 Mb of sequence on human chromosome 21. Genomics 78: 64-72.
32. PRESS, W. H., S. A. TEUKOLSKY, W. T. VETTERLING and B. P. FLANNERY, 1992 Numerical Recipes in C: The Art of Scientific Computing. Cambridge University Press, New York.
33. PRITCHARD, J. K., and M. PRZEWORSKI, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
34. PRITCHARD, J. K., M. STEPHENS and P. DONNELLY, 2000 Inference of population structure using multilocus genotype data. Genetics 155:945-959.
35. RABINER, L. R., 1989 A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77: 257-286.
36. STEPHENS, M., and P. DONNELLY, 2000 Inference in molecular population genetics. J. R. Stat. Soc. Ser. B 62: 605-655.
37. STEPHENS, M., N. J. SMITH and P. DONNELLY, 2001 A new statistical Anewstatistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
38. TEMPLETON, A. R., A. G. CLARK, K. M. WEISS, D. A. NICKERSON, E. BOERWINKLE et al., 2000 Recombination and mutation at the LPL locus. Am. J. Hum. Genet. 66: 69-83.
39. UEBERHUBER, C. W., 1997 Numeric Computation: Methods, Software, and Analysis, Vol. I. Springer-Verlag, Berlin-Heidelberg, Germany.
40. WAKELEY, J., 1997 Using the variance of pairwise differences to estimate the recombination rate. Genet. Res. 69: 45-48.
41. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
42. WANG, N., J. M. AKEY, K. ZHANG, R. CHAKRABORTY and L. JIN, 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.