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Bioinformatics Advance Access originally published online on December 17, 2008
Bioinformatics 2009 25(4):482-489; doi:10.1093/bioinformatics/btn648
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

FastMap: Fast eQTL mapping in homozygous populations

Daniel M. Gatti 1,{dagger}, Andrey A. Shabalin 2,{dagger}, Tieu-Chong Lam 1, Fred A. Wright 3, Ivan Rusyn 1,* and Andrew B. Nobel 2,3,*

1Department of Environmental Sciences and Engineering, 2Department of Statistics and Operations Research and 3Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina 27599, USA

*To whom correspondence should be addressed.


  Abstract

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{at}unc.edu; nobel{at}email.unc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Olga Troyanskaya

Received on July 25, 2008; revised on December 8, 2008; accepted on December 15, 2008

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