Article abstract

Nature Genetics 39, 1202 - 1207 (2007)
Published online: 16 September 2007 | doi:10.1038/ng2109

A genome-wide association study of global gene expression

Anna L Dixon1,2,6, Liming Liang3,6, Miriam F Moffatt1,6, Wei Chen3, Simon Heath4, Kenny C C Wong1, Jenny Taylor2, Edward Burnett5, Ivo Gut4, Martin Farrall2, G Mark Lathrop4, Gonçalo R Abecasis3 & William O C Cookson1

We have created a global map of the effects of polymorphism on gene expression in 400 children from families recruited through a proband with asthma. We genotyped 408,273 SNPs and identified expression quantitative trait loci from measurements of 54,675 transcripts representing 20,599 genes in Epstein-Barr virus–transformed lymphoblastoid cell lines. We found that 15,084 transcripts (28%) representing 6,660 genes had narrow-sense heritabilities (H2) > 0.3. We executed genome-wide association scans for these traits and found peak lod scores between 3.68 and 59.1. The most highly heritable traits were markedly enriched in Gene Ontology descriptors for response to unfolded protein (chaperonins and heat shock proteins), regulation of progression through the cell cycle, RNA processing, DNA repair, immune responses and apoptosis. SNPs that regulate expression of these genes are candidates in the study of degenerative diseases, malignancy, infection and inflammation. We have created a downloadable database to facilitate use of our findings in the mapping of complex disease loci.

  1. National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK.
  2. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
  3. Center for Statistical Genetics, Department of Biostatistics, School of public Health, Ann Arbor, Michigan 48109-2029, USA.
  4. Centre National de Génotypage, Institut Génomique, Commissariat à l'Énergie Atomique, 91057 Evry, France.
  5. European Collection of Cell Cultures (ECACC), Porton Down, SP4 0JG, UK.
  6. These authors contributed equally to this work.

Correspondence to: William O C Cookson1 e-mail:


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