Application of coalescent methods to reveal fine-scale rate variation and recombination hotspots

Genetics

Volumn 167, Issue 4, 2004, Pages 2067-2081

  Fearnhead, Paul ^a   Harding, Rosalind M ^b,c   Schneider, Julie A ^b,d   Myers, Simon ^c   Donnelly, Peter ^c  

^a LANCASTER UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GLOBIN;

ARTICLE; DEMOGRAPHY; DNA SEQUENCE; GENE CLUSTER; GENE MAPPING; GENETIC DISTANCE; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME; HUMAN; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SPERM; STATISTICAL MODEL;

DNA; GENOME; GLOBINS; HAPLOTYPES; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; RECOMBINATION, GENETIC; VARIATION (GENETICS);

EID: 4644362514     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.021584     Document Type: Article

References (49)

1. ABECASIS, G. R., E. NOGUCHI, A. HEINZMANN, J. A. TRAHERNE, S. BHATTACHARYYA et al., 2001 Extent and distribution of linkage disequilibrium in three genomic regions. Am. J. Hum. Genet. 68: 191-197.
2. CARGILL, M., D. ALTSHULER, J. IRELAND, P. SKLAR, K. ARDLIE et al., 1999 Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22: 231-238.
3. CHAKRAVARTI, A., K. H. BUETOW, S. E. ANTONARAKIS, P. G. WABER, C. D. BOEHM et al., 1984 Nonuniform recombination within the human β-globin gene cluster. Am. J. Hum. Genet. 36: 1239-1258.
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. 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.
6. FEARNHEAD, P., 2003 Consistency of estimators of the population-scaled recombination rate. Theor. Popul. Biol. 64: 67-79.
7. FEARNHEAD, P., and P. DONNELLY, 2001 Estimating recombination rates from population genetic data. Genetics 159: 1299-1318.
8. FEARNHEAD, P., and P. DONNELLY, 2002 Approximate likelihood methods for estimating local recombination rates (with discussion). J. R. Stat. Soc. Ser. B 64: 657-680.
9. FLINT, J., R. M. HARDING and J. B. CLEGG, 1998 The population genetics of the haemoglobinopathies. Baillieres Clin. Haematol. 11: 1-51.
10. 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.
11. GRIFFITHS, R. C., and P. MARJORAM, 1996a Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3: 479-502.
12. GRIFFITHS, R. C., and P. MARJORAM, 1996b An ancestral recombination graph, pp. 257-270 in IMA Volume on Mathematical Population Genetics, edited by P. DONNELLY and S. TAVARÉ. Springer-Verlag, Berlin/Heidelberg, Germany/New York.
13. GRIFFITHS, R. C., and S. TAVARÉ, 1994 Unrooted genealogical tree probabilities in the infinitely-many-sites model. Math. Biosci. 127: 77-98.
14. 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.
15. HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
16. HUDSON, R. R., and N. KAPLAN, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
17. JEFFREYS, A. J., and C. A. MAY, 2004 Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat. Genet. 36: 151-156.
18. JEFFREYS, A. J., and R. NEUMANN, 2002 Reciprocal crossover asymmetry and meiotic drive in a human recombination hotspot. 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. JORDE, L. B., 2000 Linkage disequilibrium and the search for complex disease genes. Genome Res. 10: 1435-1444.
22. KONG, A., D. F. GUBDJARTSSON, J. SAINZ, G. M. JONSDOTTIR, S. A. GUDJONSON et al., 2002 A high-resolution recombination map of the human genome. Nat. Genet. 31: 241-247.
23. KRUGLYAK, L., 1999 Prospects for whole-genome linkage disequilibrium mapping of common diseases. Nat. Genet. 22: 139-144.
24. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 1995 Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
25. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 2000 Maximum likelihood estimation of recombination rates from population data. Genetics 156: 1393-1401.
26. LI, N., and M. STEPHENS, 2003 Modelling LD, and identifying recombination hotspots from SNP data. Genetics 165: 2213-2233.
27. LI, W. H., and L. SADLER, 1991 Low nucleotide diversity in man. Genetics 129: 513-523.
28. MCVEAN, G. A. T., P. AWADALLA and P. FEARNHEAD, 2002 A coalescent method for detecting recombination from gene sequences. Genetics 160: 1231-1241.
29. MYERS, S. R., and R. C. GRIFFITHS, 2003 Bounds on the minimum number of recombination events in a sample history. Genetics 163: 375-394.
30. NACHMAN, M. W., 2002 Variation in recombination rate across the genome: evidence and implications. Curr. Opin. Genet. Dev. 12: 657-663.
31. NORDBORG, M., 2001 Coalescent theory, pp. 179-212 in Handbook of Statistical Genetics, edited by D. J. BALDING, M. BISHOP and C. CANNINGS. John Wiley & Sons, Chichester, England.
32. OTT, J., 2000 Predicting the range of linkage disequilibrium. Proc. Natl. Acad. Sci. USA 97: 2-3.
33. PETES, T. D., 2001 Meiotic recombination hot spots and cold spots. Nat. Rev. Genet. 2: 360-369.
34. PRITCHARD, J. K., and M. PRZEWORSKI, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
35. PRZEWORSKI, M., and J. D. WALL, 2001 Why is there so little intragenic linkage disequilibrium in humans? Genet. Res. 77: 143-151.
36. PRZEWORSKI, M., R. R. HUDSON and A. DIRIENZO, 2000 Adjusting the focus on human variation. Trends Genet. 16: 296-302.
37. REICH, D. E., M. CARGILL, S. BOLK, J. IRELAND, P. C. SABETI et al., 2001 Linkage disequilibrium in the human genome. Nature 411: 199-204.
38. ROGERS, A. R., and L. B. JORDE, 1995 Genetic evidence on modern human origins. Hum. Biol. 67: 1-36.
39. SCHNEIDER, J. A., T. E. A. PETO, R. A. BOONE, A. J. BOYCE and J. B. CLEGG, 2002 Direct measurement of the male recombination fraction in the human beta-globin hot spot. Hum. Mol. Genet. 11: 207-215.
40. SHERRY, S. T., A. R. ROGERS, H. HARPENDING, H. SOODYALL, T. JENKINS et al., 1994 Mismatch distribution of mtDNA reveals recent human population expansions. Hum. Biol. 66: 761-775.
41. SMITH, R. A., P. J. Ho, J. B. CLEGG, J. R. KIDD and S. L. THEIN, 1998 Recombination breakpoints in the human β-globin gene cluster. Blood 92: 4415-4421.
42. STEPHENS, M., and P. DONNELLY, 2000 Inference in molecular population genetics (with discussion). J. R. Stat. Soc. Ser. B 62: 605-655.
43. STEPHENS, M., and P. DONNELLY, 2003 A comparison of Bayesian methods for haplotype reconstruction. Am. J. Hum. Genet. 70: 1162-1169.
44. STEPHENS, M., N.J. SMITH and P. DONNELLY, 2001 A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
45. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
46. WALL, J. D., and J. K. PRITCHARD, 2003 Haplotype blocks and LD in the human genome. Nat. Rev. Genet. 4: 587-597.
47. WALL, J. D., L. A. FRISSE, R. R. HUDSON and A. Di RIENZO, 2003 Comparative linkage-disequilibrium analysis of the beta-globin hotspot in primates. Am. J. Hum. Genet. 73: 1330-1340.
48. WEATHERALL, D. J., and J. B. CLEGG, 1996 Thalassemia - a global public health problem. Nat. Med. 2: 847.
49. WEBSTER, M. T., J. B. CLEGG and R. M. HARDING, 2003 Common 5′ β-globin RFLP haplotypes harbour a surprising level of ancestral sequence mosaicism. Hum. Genet. 113: 123-139.