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Levels of interpopulation differentiation among different functional classes of immunologically important genes

Genes & Immunity volume 7, pages 179–183 (2006)Cite this article

Abstract

It has been postulated that gene function may influence the degree to which allele frequencies differ among populations. In order to evaluate this effect, genotypic data from resequencing studies of genes classified as cytokines, cytokine receptors, cell adhesion molecules, Toll-like receptors and coagulation proteins were analysed for genetic differentiation (FST) between population samples of European and African descent. FST values did not differ statistically among functional groups when all polymorphic sites were included in the analyses. However, analysis based on nonsynonymous SNPs alone suggested weak heterogeneity among functional classes (P=0.0424). Particularly high levels of differentiation were shown by individual nonsynonymous SNPs at some genes, most notably ICAM1 and some Toll-like receptors. These genes interact directly with pathogens, and may therefore have been subject to geographically localised natural selection. Such loci warrant particular attention in studies of genetic disease risk and local adaptation to environmental conditions.

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Acknowledgements

We thank Arun Mankan and Matthew Lawless, Trinity College Dublin and Tony Fitzgerald, The Haughton Institute, St James's Hospital, Dublin for helpful discussion, and the SeattleSNPs and Innate Immunity teams for making their data public. Funding from Hitachi Corporation, Europe, The Wellcome Trust, the Health Research Board and the Higher Education Authority Programme for Research in Third Level Institutions (PRTLI) is gratefully acknowledged. RMM is a Wellcome Trust/Health Research Board lecturer.

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Authors and Affiliations

  1. Department of Clinical Medicine, Trinity College, Trinity Centre for Health Sciences, St James's Hospital, Dublin, Ireland

    A W Ryan, D Kelleher & R McManus

  2. Institute of Molecular Medicine, Dublin Molecular Medicine Centre, Trinity Centre for Health Sciences, St James's Hospital, Dublin, Ireland

    A W Ryan, J Mapp, S Moyna, V Mattiangeli, D Kelleher & R McManus

  3. Smurfit Institute of Genetics, Trinity College, Dublin, Ireland

    V Mattiangeli & D G Bradley

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  1. A W Ryan
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  3. S Moyna
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Correspondence to A W Ryan.

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Ryan, A., Mapp, J., Moyna, S. et al. Levels of interpopulation differentiation among different functional classes of immunologically important genes. Genes Immun 7, 179–183 (2006). https://doi.org/10.1038/sj.gene.6364266

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