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Review
. 2012 Feb;13(3):343-52.
doi: 10.2217/pgs.11.185.

Computational tools for discovery and interpretation of expression quantitative trait loci

Fred A Wright  1 , Andrey A Shabalin, Ivan Rusyn
Affiliations
Review

Computational tools for discovery and interpretation of expression quantitative trait loci

Fred A Wright et al. Pharmacogenomics. 2012 Feb.

Abstract

Expression quantitative trait locus (eQTL) analysis is rapidly moving from a cutting-edge concept in genomics to a mature area of investigation, with important connections to genome-wide association studies for human disease, pharmacogenomics and toxicogenomics. Despite the importance of the topic, many investigators must develop their own code or use tools not specifically suited for eQTL analysis. Convenient computational tools are becoming available, but they are not widely publicized, and investigators who are interested in discovery or eQTL, or in using them to interpret genome-wide association study results may have difficulty navigating the available resources. The purpose of this review is to help investigators find appropriate programs for eQTL analysis and interpretation.

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References

    1. Rockman MV, Kruglyak L. Genetics of global gene expression. Nat Rev Genet. 2006;7(11):862–872. Key review describing major concepts concerning expression quantitative trait loci (eQTL) and genetical genomics. - PubMed
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    1. Karp CL, Grupe A, Schadt E, et al. Identification of complement factor 5 as a susceptibility locus for experimental allergic asthma. Nat Immunol. 2000;1(3):221–226. - PubMed

Websites

    1. A QTL mapping environment. www.rqtl.org.
    1. eMap. http://bios.unc.edu/~wsun/software.htm.
    1. SNPSTER tool. http://snpster.gnf.org.
    1. snpMatrix. www.bioconductor.org/packages/2.3/bioc/html/snpMatrix.html.
    1. Plink. http://pngu.mgh.harvard.edu/~purcell/plink.

Publication types