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Population genomics of human gene expression

Nature Genetics volume 39, pages 1217–1224 (2007)Cite this article

Abstract

Genetic variation influences gene expression, and this variation in gene expression can be efficiently mapped to specific genomic regions and variants. Here we have used gene expression profiling of Epstein-Barr virus–transformed lymphoblastoid cell lines of all 270 individuals genotyped in the HapMap Consortium to elucidate the detailed features of genetic variation underlying gene expression variation. We find that gene expression is heritable and that differentiation between populations is in agreement with earlier small-scale studies. A detailed association analysis of over 2.2 million common SNPs per population (5% frequency in HapMap) with gene expression identified at least 1,348 genes with association signals in cis and at least 180 in trans. Replication in at least one independent population was achieved for 37% of cis signals and 15% of trans signals, respectively. Our results strongly support an abundance of cis-regulatory variation in the human genome. Detection of trans effects is limited but suggests that regulatory variation may be the key primary effect contributing to phenotypic variation in humans. We also explore several methodologies that improve the current state of analysis of gene expression variation.

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Figure 1: Associations of SNPs with expression of the gene SPRED2 on chromosome 2.
Figure 2: Comparison of cis associations detected between single- and multipopulation analysis.
Figure 3: Comparison of the direction of shared SNP-gene allelic effects across all pairs of populations.
Figure 4: Properties of significant cis associations as a function of SNP distance from the transcription start site.

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Acknowledgements

We thank the HapMap Consortium for data availability; M. Smith for assistance with software development; and M. Gibbs, J. Orwick and C. Gerringer for technical support. Funding was provided by the Wellcome Trust (to E.T.D. and P.D.), the US National Institutes of Health ENDGAME (to E.T.D. and S.T.), Cancer Research UK (to S.T.), and the Medical Research Council (to M.D.). S.T. is a Royal Society Wolfson Research Merit Award holder.

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Authors and Affiliations

  1. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, Cambridge, UK

    Barbara E Stranger, Alexandra C Nica, Matthew S Forrest, Antigone Dimas, Christine P Bird, Claude Beazley, Catherine E Ingle, Stephen Montgomery, Panos Deloukas & Emmanouil T Dermitzakis

  2. Department of Oncology, University of Cambridge, Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

    Mark Dunning & Simon Tavaré

  3. European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK

    Paul Flicek

  4. Computer Science Department, Gates Building 1A, Stanford University, Stanford, 94305-9010, California, USA

    Daphne Koller

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  1. Barbara E Stranger
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Contributions

B.E.S. performed the majority of the analysis, coordinated the efforts on the project, performed part of the experimental work, and wrote part of the manuscript. E.T.D. and P.D. helped with the analysis, wrote part of the manuscript, and led the project. S.T. and M.D. performed the normalization and helped with statistical analysis. A.C.N., A.D., C.P.B., P.F. and S.M. performed specific parts of the analysis. M.S.F. helped with the analysis and performed part of the experimental work. C.E.I. performed most of the experimental work. C.B. wrote some of the scripts and performed part of the analysis. D.K. provided advice on the permutation analysis.

Corresponding authors

Correspondence to Panos Deloukas or Emmanouil T Dermitzakis.

Supplementary information

Supplementary Text and Figures

Supplementary Figs. 1–6, Supplementary Table 1, and Supplementary Methods (PDF 1606 kb)

Supplementary Table 2

Number and source category of SNPs used in trans analysis. (PDF 833 kb)

Supplementary Table 3

Significant cis- 1Mb associations, linear regression, individual population analysis, 0.001 permutation threshold. (PDF 1406 kb)

Supplementary Table 4

Significant cis- 1 Mb associations, linear regression, multiple population analysis, 0.001 permutation threshold. (PDF 647 kb)

Supplementary Table 5

Significant cis- 1Mb associations, Spearman rank correlation, individual population analysis, 0.001 permutation threshold. (PDF 27 kb)

Supplementary Table 6

Significant trans associations, linear regression, individual population analysis, 0.001 permutation threshold. (PDF 44 kb)

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Stranger, B., Nica, A., Forrest, M. et al. Population genomics of human gene expression. Nat Genet 39, 1217–1224 (2007). https://doi.org/10.1038/ng2142

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