Prospects for association mapping in classical inbred mouse strains.

The collection of classical inbred mouse strains displays heritable variation in a large number of complex traits. Many generations of historical recombination have contributed to the panel of classical strain genomes, raising the possibility that quantitative trait loci could be located with high resolution by correlating strain genotypes and phenotypes. Although this association mapping framework has been successful in several empirical applications, its expected performance remains unclear. We used computer simulations based on a publicly available, dense single-nucleotide polymorphism (SNP) map to measure the power and false-positive rate of association mapping on a genomic scale across 30 commonly used classical inbred strains. Expected power is (i) often low for phenotypic effect sizes that are realistic for complex traits, (ii) highly variable across the genome, and (iii) correlated with linkage disequilibrium, aspects of the allele frequency distribution, and haplotype characteristics, as predicted by theory. Simulations also demonstrate clear potential for spurious associations to be generated by unequal relatedness among the strains. These findings suggest that association mapping in the classical strains is best applied in combination with other procedures, such as QTL mapping.