Insights into recombination from patterns of linkage disequilibrium in humans

Genetics

Volumn 167, Issue 1, 2004, Pages 387-397

  Ptak, Susan E ^b   Voelpel, Kristian ^a   Przeworski, Molly ^a,c  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; CORRELATION ANALYSIS; GENE CONVERSION; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC RECOMBINATION; GENOTYPE; HOMOLOGOUS RECOMBINATION; HUMAN; MOLECULAR EVOLUTION; PREDICTION; PRIORITY JOURNAL; RELIABILITY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; DATABASES; DEMOGRAPHY; EVOLUTION, MOLECULAR; GENE CONVERSION; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; VARIATION (GENETICS);

EID: 1942511512     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.167.1.387     Document Type: Article

References (44)

1. ANDOLFATTO, P., 2001 Adaptive hitchhiking effects on genome variability. Curr. Opin. Genet. Dev. 11: 635-641.
2. ANDOLFATTO, P., and M. NORDBORG, 1998 The effect of gene conversion on intralocus associations. Genetics 148: 1397-1399.
3. ANDOLFATTO, P., and M. PRZEWORSKI, 2000 A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156: 257-268.
4. CARLSON, C. S., M. A. EBERLE, M. J. RIEDER, J. D. SMITH, L. KRUGLYAK et al., 2003 Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat. Genet. 33: 518-521.
5. CHAKRABORTY, R., and K. M. WEISS, 1988 Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc. Natl. Acad. Sci. USA 85: 9119-9123.
6. COOPER, D. N., and M. KRAWCZAK, 1989 Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum. Genet. 83: 181-188.
7. 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.
8. DE MASSY, B., 2003 Distribution of meiotic recombination sites. Trends Genet. 19: 514-522.
9. FEARNHEAD, P., and P. DONNELLY, 2001 Estimating recombination rates from population genetic data. Genetics 159: 1299-1318.
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. 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,
12. GRIFFITHS, A. J. F., J. H. MILLER, D. T. SUZUKI, R. C. LEWONTIN and W. M. GELBART, 1996 An Introduction to Genetic Analysis, W. H. Freeman, New York.
13. HELGASON, A., B. HRAFNKELSSON, J. R. GULCHER, R. WARD and K. STEFANSSON, 2003 A populationwide coalescent analysis of Icelandic matrilineal and patrilineal genealogies: evidence for a faster evolutionary rate of mtDNA lineages than Y chromosomes, Am. J. Hum. Genet. 72: 1370-1388.
14. HELLMANN, I., I. EBERSBERGER, S. PTAK, S. PAABO and M. PRZEWORSKI, 2003 A neutral explanation for the correlation of diversity with recombination in humans. Am. J. Hum. Genet. 72: 1527-1535.
15. HUDSON, R. R., 1987 Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50: 245-250.
16. HUDSON, R. R., 1990 Oxford Surveys in Evolutionary Biology, pp. 1-44. Oxford University Press, Oxford.
17. HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
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. KONG, A., D. F. GUDBJARTSSON, J. SAINZ, G. M. JONSDOTTIR, S. A. GUDJONSSON et al., 2002 A high-resolution recombination map of the human genome. Nat. Genet. 31: 241-247.
22. KRUGLYAK, L., 1999 Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat. Genet. 22: 139-144.
23. LI, N., and M. STEPHENS, 2003 Modelling linkage disequilibrium and identifying recombination hotspots using SNP data. Genetics 165: 2213-2233.
24. MAY, C. A., A. C. SHONE, L. KALAYDJIEVA, A. SAJANTILA and A. J. JEFFREYS, 2002 Crossover clustering and rapid decay of linkage disequilibrium in the Xp/Yp pseudoautosomal gene SHOX. Nat. Genet. 31: 272-275.
25. MCVEAN, G. A., 2002 A genealogical interpretation of linkage disequilibrium. Genetics 162: 987-991.
26. NACHMAN, M. W., 2001 Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17: 481-485.
27. OHTA, T., and M. KIMURA, 1971 Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics 68: 571-580.
28. PETES, T. D., 2001 Meiotic recombination hot spots and cold spots. Nat. Rev. Genet. 2: 360-369.
29. 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.
30. PITTMANN, D. L., and J. C. SCHIMENTI, 1998 Recombination in the mammalian germ line. Curr. Top. Dev. Biol. 7: 1-35.
31. PRITCHARD, J. K., and M. PRZEWORSKI, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
32. PRZEWORSKI, M., and J. D. WALL, 2001 Why is there so little intragenic linkage disequilibrium in humans? Genet. Res. 77: 143-151.
33. 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.
34. STUMPF, M. P., and D. B. GOLDSTEIN, 2003 Demography, recombination hotspot intensity, and the block structure of linkage disequilibrium. Curr. Biol. 13: 1-8.
35. TISHKOFF, S. A., E. DIETZSCH, W. SPEED, A. J. PAKSTIS, J. R. KIDD et al., 1996 Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271: 1380-1387.
36. WALL, J. D., 2001 Insights from linked single nucleotide polymorphisms: what we can learn from linkage disequilibrium. Curr. Opin. Genet. Dev. 11: 647-651.
37. WALL, J. D., 2003 Estimating ancestral population sizes and divergence times, Genetics 163: 395-404.
38. WALL, J. D., and J. K. PRITCHARD, 2003a Assessing the performance of the haplotype block model of linkage disequilibrium, Am. J. Hum. Genet. 73: 502-515.
39. WALL, J. D., and J. K. PRITCHARD, 2003b Haplotype blocks and the structure of linkage disequilibrium in the human genome. Nat. Genet. Rev. 4: 587-597.
40. WALL, J. D., P. ANDOLFATTO and M. PRZEWORSKI, 2002 Testing models of selection and demography in Drosophila simulans. Genetics 162: 203-216.
41. WALL, J. D., L. A. FRISSE, R. R. HUDSON and A. D. RIENZO, 2003 Comparative linkage disequilibrium analysis of the β-globin hotspot in primates. Am. J. Hum. Genet. 73: 1330-1340.
42. WATTERSON, G. A., 1975 On the number of segregating sites in genetic models without recombination. Theor. Popul. Biol. 7: 256-276.
43. WEBER, J. L., 2002 The Iceland map. Nat. Genet. 31: 225-226.
44. WIUF, C., and J. HEIN, 2000 The coalescent with gene conversion. Genetics 155: 451-462.