Relationship between SNP density and analysis strategy for eQTL data. The current state of computer hardware allows little if any consideration of joint effects of markers when millions of SNPs are considered for tens of thousands of expression traits. Simple univariate tests or expert knowledge are often employed to reduce the number of considered SNPs to a range where mapping methods may be used and increased attention may be given to the interplay between loci. In the optimal case, successful application of mapping methods in many populations will yield an explicit model of the expression trait in terms of a smaller number of genetic loci, optionally including environmental effects.
Michaelson et al. BMC Genomics 2010 11:502 doi:10.1186/1471-2164-11-502