transcript. SPOT considers all known SNP/gene transcript associations, and selects the one with the highest priority to ensure no biologically promising association signal is missed. Furthermore, when genes overlap, SPOT will take into account specific genes prioritized by the user. Finally, the task of checking for LD proxies while taking into account all of the previous elements is not only a complex algorithm to implement, but requires the processing of an enormous amount of information (our LD database alone contains data on 343 million pairs of SNPs) that must be implemented on a genome-wide scale when applied to GWAS data. While we are planning to incorporate additional biological information into future implementations of SPOT, researchers should find SPOT useful even with this relatively limited amount of information.
