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Nucleotide diversity of the TNF gene region in an African village

Genes & Immunity volume 2, pages 343–348 (2001)Cite this article

Abstract

The wide variety of disease associations reported at the TNF locus raises the question of how much variation exists within a single population. To address this question, we sequenced the entire TNF gene in 72 chromosomes from healthy residents of a village in The Gambia, West Africa. We found 12 polymorphisms in 4393 nucleotides, of which five have not been previously described, giving an estimated nucleotide diversity (θ) of 5.6 × 10−4. A significantly higher frequency of polymorphisms was found in the promoter region than in the coding region (8/1256 vs 0/882 nucleotides, P = 0.02). All polymorphisms with the exception of one rare allele were found to be present in Malawi, which is both geographically and genetically distant from The Gambia. Genotyping of 424 Gambian and 121 Malawian adults showed a significant frequency difference between the two populations for eight of the 12 polymorphisms, but the average fixation index across the variable sites was relatively low (FST = 0.007). We conclude that, at the TNF locus, the nucleotide diversity found within a single African village is similar to the global value for human autosomal genes sampled across different continents.

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Acknowledgements

We thank the inhabitants of Sukuta for making this study possible, and Simon Correa, Idi Sambou, Yaya Dibba and Isatou Drammeh for excellent technical help and field work. FS-J is a WHO Training Fellow.

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Authors and Affiliations

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

    A Richardson, H Ackerman & D Kwiatkowski

  2. MRC Laboratories, Fajara, The Gambia

    F Sisay-Joof, S Usen & M Pinder

  3. Wellcome Trust Research Laboratories and Malawi Project, College of Medicine, University of Malawi, Blantyre, Malawi

    P Katundu, T Taylor & M Molyneux

Authors
  1. A Richardson
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  2. F Sisay-Joof
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  3. H Ackerman
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  4. S Usen
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  7. M Molyneux
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  8. M Pinder
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  9. D Kwiatkowski
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Corresponding author

Correspondence to D Kwiatkowski.

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This work was funded by the Medical Research Council.

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Richardson, A., Sisay-Joof, F., Ackerman, H. et al. Nucleotide diversity of the TNF gene region in an African village . Genes Immun 2, 343–348 (2001). https://doi.org/10.1038/sj.gene.6363789

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  • DOI: https://doi.org/10.1038/sj.gene.6363789

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