FastMap

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 10(5) and 10(5)-10(6), 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.

FastMap: fast eQTL mapping in homozygous populations.

FastMap is a software tool designed to quickly and accurately identify gene expression quantitative trait loci (eQTL) in homozygous inbred populations with binary allele calls. It is organized into a Hamming distance-based tree that reduces the necessary calculations to determine the association between an SNP and its parent SNP, allowing for single marker mapping and haplotype association mapping over an m-SNP window. This structure also enables permutation-based significance testing.

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