Journal Article

FastMap: Fast eQTL mapping in homozygous populations

Daniel M. Gatti, Andrey A. Shabalin, Tieu-Chong Lam, Fred A. Wright, Ivan Rusyn and Andrew B. Nobel

in Bioinformatics

Volume 25, issue 4, pages 482-489
Published in print February 2009 | ISSN: 1367-4803
Published online December 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn648

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Motivation: Gene expression Quantitative Trait Locus (eQTL) mapping measures the association between transcript expression and genotype in order to find genomic locations likely to regulate transcript expression. The availability of both gene expression and high-density genotype data has improved our ability to perform eQTL mapping in inbred mouse and other homozygous populations. However, existing eQTL mapping software does not scale well when the number of transcripts and markers are on the order of 105 and 105–106, respectively.

Results: We propose a new method, FastMap, for fast and efficient eQTL mapping in homozygous inbred populations with binary allele calls. FastMap exploits the discrete nature and structure of the measured single nucleotide polymorphisms (SNPs). In particular, SNPs are organized into a Hamming distance-based tree that minimizes the number of arithmetic operations required to calculate the association of a SNP by making use of the association of its parent SNP in the tree. FastMap's tree can be used to perform both single marker mapping and haplotype association mapping over an m-SNP window. These performance enhancements also permit permutation-based significance testing.

Availability: The FastMap program and source code are available at the website: http://cebc.unc.edu/fastmap86.html

Contact: iir@unc.edu; nobel@email.unc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6124 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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