Paper Info
Title
FastMap: Fast eQTL mapping in homozygous populations.
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 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.
Year
DOI
Venue
2009
10.1093/bioinformatics/btn648
BIOINFORMATICS
Keywords
Field
DocType
quantitative trait loci,genotype,genome,gene expression profiling,algorithms
Population,Association mapping,Quantitative trait locus,Biology,Haplotype,Single-nucleotide polymorphism,Bioinformatics,Expression quantitative trait loci,Genetics,SNP,Gene expression profiling
Journal
Volume
Issue
ISSN
25
4
1367-4803
Citations 
PageRank 
References 
8
1.34
5
Authors
6
Name
Order
Citations
PageRank
Daniel M. Gatti182.69
Andrey A Shabalin21038.38
Tieu-Chong Lam381.34
Fred A. Wright412712.81
Ivan Rusyn5276.69
Andrew B Nobel625421.11