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Population-specific patterns of linkage disequilibrium in the human 5q31 region

Genes & Immunity volume 6, pages 723–727 (2005)Cite this article

Abstract

Linkage disequilibrium across the human genome is generally lower in West Africans than Europeans. However in the 5q31 region, which is rich in immune genes, we find significantly more examples of apparent nonrecombination between distant marker pairs in West Africans. Much of this effect is due to SNPs that are absent in Europeans, possibly reflecting recent positive selection in the West African population.

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References

  1. Hinds DA, Stuve LL, Nilsen GB et al. Whole-genome patterns of common DNA variation in three human populations. Science 2005; 307: 1072–1079.

    Article  CAS  Google Scholar 

  2. Ahmadi KR, Weale ME, Xue ZY et al. A single-nucleotide polymorphism tagging set for human drug metabolism and transport. Nat Genet 2005; 37: 84–89.

    Article  CAS  Google Scholar 

  3. Daly MJ, Rioux JD, Schaffner SF et al. High-resolution haplotype structure in the human genome. Nat Genet 2001; 29: 229–232.

    Article  CAS  Google Scholar 

  4. Rihet P, Traore Y, Abel L et al. Malaria in humans: Plasmodium falciparum blood infection levels are linked to chromosome 5q31–q33. Am J Hum Genet 1998; 63: 498–505.

    Article  CAS  Google Scholar 

  5. Marquet S, Abel L, Hillaire D et al. Genetic localization of a locus controlling the intensity of infection by Schistosoma mansoni on chromosome 5q31–q33. Nat Genet 1996; 14: 181–184.

    Article  CAS  Google Scholar 

  6. Ansel KM, Lee DU, Rao A . An epigenetic view of helper T cell differentiation. Nat Immunol 2003; 4: 616–623.

    Article  CAS  Google Scholar 

  7. Lee GR, Fields PE, Griffin TJ et al. Regulation of the Th2 cytokine locus by a locus control region. Immunity 2003; 19: 145–153.

    Article  CAS  Google Scholar 

  8. Ardlie KG, Kruglyak L, Seielstad M . Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 2002; 3: 299–309.

    Article  CAS  Google Scholar 

  9. Bamshad M, Wooding SP . Signatures of natural selection in the human genome. Nat Rev Genet 2003; 4: 99–111.

    Article  CAS  Google Scholar 

  10. Sabeti PC, Reich DE, Higgins JM et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 2002; 419: 832–837.

    Article  CAS  Google Scholar 

  11. Luoni G, Verra F, Arca B et al. Antimalarial antibody levels and IL4 polymorphism in the Fulani of West Africa. Genes Immun 2001; 2: 411–414.

    Article  CAS  Google Scholar 

  12. Zhang K, Jin L . HaploBlockFinder: haplotype block analyses. Bioinformatics 2003; 19: 1300–1301.

    Article  CAS  Google Scholar 

  13. Rioux JD, Daly MJ, Silverberg MS et al. Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat Genet 2001; 29: 223–228.

    Article  CAS  Google Scholar 

  14. Noguchi E, Nukaga-Nishio Y, Jian Z et al. Haplotypes of the 5′ region of the IL-4 gene and SNPs in the intergene sequence between the IL-4 and IL-13 genes are associated with atopic asthma. Hum Immunol 2001; 62: 1251–1257.

    Article  CAS  Google Scholar 

  15. Howard TD, Whittaker PA, Zaiman AL et al. Identification and association of polymorphisms in the interleukin-13 gene with asthma and atopy in a Dutch population. Am J Resp Cell Mol Biol 2001; 25: 377–384.

    Article  CAS  Google Scholar 

  16. Stephens M, Smith NJ, Donnelly P . A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001; 68: 978–989.

    Article  CAS  Google Scholar 

  17. Ackerman H, Usen S, Mott R et al. Haplotypic analysis of the TNF locus by association efficiency and entropy. Genome Biol 2003; 4: R24.

    Article  Google Scholar 

  18. Mott R . Marker selection by maximum entropy. http://www.well.ox.ac.uk/~rmott/SNPS/2003.

  19. Gabriel SB, Schaffner SF, Nguyen H et al. The structure of haplotype blocks in the human genome. Science 2002; 296: 2225–2229.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was funded by a Marie Curie fellowship (GL), a Wellcome Trust research training fellowship (JF) and the Medical Research Council.

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Author notes

  1. G Luoni: Deceased

  2. M Jallow and E Sadighi Akha: These authors made an equal contribution.

Authors and Affiliations

  1. Wellcome Trust Centre for Human Genetics, Oxford, UK

    G Luoni, J Forton, E Sadighi Akha, N Hanchard, M Kimber, R Mott, K Rockett & D Kwiatkowski

  2. University Department of Paediatrics, Oxford, UK

    J Forton, N Hanchard, M Herbert, J Hull & D Kwiatkowski

  3. MRC Laboratories, Fajara, The Gambia

    M Jallow, F Sisay-Joof & M Pinder

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  1. G Luoni
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  2. J Forton
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  3. M Jallow
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  4. E Sadighi Akha
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  5. F Sisay-Joof
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  9. M Kimber
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  10. R Mott
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  11. J Hull
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  12. K Rockett
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  13. D Kwiatkowski
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Corresponding author

Correspondence to D Kwiatkowski.

Additional information

Supplementary information accompanies the paper on Genes and Immunity website (http://www.nature.com/gene).

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Luoni, G., Forton, J., Jallow, M. et al. Population-specific patterns of linkage disequilibrium in the human 5q31 region. Genes Immun 6, 723–727 (2005). https://doi.org/10.1038/sj.gene.6364250

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  • DOI: https://doi.org/10.1038/sj.gene.6364250

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