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This article is part of the supplement: Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci

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Identifying cis- and trans-acting single-nucleotide polymorphisms controlling lymphocyte gene expression in humans

Pingzhao Hu1, Hui Lan12, Wei Xu34, Joseph Beyene35 and Celia MT Greenwood13*

Author Affiliations

1 Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, 15-706 TMDT, 101 College Street, Toronto, Ontario, M5G 1L7, Canada

2 Department of Computer Science, University of Toronto, 10 Kings College Road, Toronto, Ontario, M5S 3G4, Canada

3 Department of Public Health Sciences, University of Toronto, 155 College Street, Toronto, Ontario, M5T 3M7, Canada

4 Department of Biostatistics, Princess Margaret Hospital, Toronto, Ontario, M5G 2M9, Canada

5 Program in Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, 555 University Ave, Toronto, Ontario, M5G 1X8, Canada

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BMC Proceedings 2007, 1(Suppl 1):S7  doi:

Published: 18 December 2007


Assuming multiple loci play a role in regulating the expression level of a single phenotype, we propose a new approach to identify cis- and trans-acting loci that regulate gene expression. Using the Problem 1 data set made available for Genetic Analysis Workshop 15 (GAW15), we identified many expression phenotypes that have significant evidence of association and linkage to one or more chromosomal regions. In particular, six of ten phenotypes that we found to be regulated by cis- and trans-acting loci were also mapped by a previous analysis of these data in which a total of 27 phenotypes were identified with expression levels regulated by cis-acting determinants. However, in general, the p-values associated with these regulators identified in our study were larger than in their studies, since we had also identified other factors regulating expression. In fact, we found that most of the gene expression phenotypes are influenced by at least one trans-acting locus. Our study also shows that much of the observable heritability in the phenotypes could be explained by simple single-nucleotide polymorphism associations; residual heritability was reduced and the remaining heritability may represent complex regulation systems with interactions or noise.