Human Molecular Genetics Advance Access originally published online on August 11, 2009
Human Molecular Genetics 2009 18(22):4296-4303; doi:10.1093/hmg/ddp382
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Expression quantitative trait loci detected in cell lines are often present in primary tissues
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1 Department of Ecology and Evolution and 2 Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA and 3 Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
* To whom correspondence should be addressed at: 920 E. 58th Street, CLSC 325C, Chicago, IL 60637, USA. Tel: +1 7737028507; Fax: +1 7738348470; Email: gilad{at}uchicago.edu
Received July 9, 2009; Accepted August 6, 2009
Expression quantitative trait loci (eQTL) mapping is a powerful tool for identifying genetic regulatory variation. However, at present, most eQTLs in humans were identified using gene expression data from cell lines, and it remains unknown whether these eQTLs also have a regulatory function in other expression contexts, such as human primary tissues. Here we investigate this question using a targeted strategy. Specifically, we selected a subset of large-effect eQTLs identified in the HapMap lymphoblastoid cell lines, and examined the association of these eQTLs with gene expression levels across individuals in five human primary tissues (heart, kidney, liver, lung and testes). We show that genotypes at the eQTLs we selected are often predictive of variation in gene expression levels in one or more of the five primary tissues. The genotype effects in the primary tissues are consistently in the same direction as the effects inferred in the cell lines. Additionally, a number of the eQTLs we tested are found in more than one of the tissues. Our results indicate that functional studies in cell lines may uncover a substantial amount of genetic variation that affects gene expression levels in human primary tissues.
Previous address: Department of Human Genetics, University of Chicago, Chicago 60637, USA.