VALID: visualization of association study results and linkage disequilibrium.
Promising findings from genetic association studies are commonly presented with two distinct figures: one gives the association study results and the other indicates linkage disequilibrium (LD) between genetic markers in the region(s) of interest. Fully interpreting the results of such studies requires synthesizing the information in these figures, which is generally done in a subjective and unsystematic manner. Here we present a method to formally combine association results and LD and display them in the same figure; we have developed a freely available web-based application that can be used to generate figures to display the combined data. To demonstrate this approach we apply it to fine mapping data from the prostate cancer 8q24 loci. Combining these two sources of information in a single figure allows one to more clearly assess patterns of association, facilitating the interpretation of genome-wide and fine mapping data and improving our ability to localize causal variants.
Jorgenson
Eric
E
Department of Biopharmaceutical Sciences, University of California, San Francisco, San Francisco, California 94143-0794, USA. Eric.Jorgenson@ucsf.edu
Kvale
Mark
M
Witte
John S
JS
D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D003627:Data Interpretation, Statistical; D016678:Genome; D055106:Genome-Wide Association Study; D006801:Humans; D020407:Internet; D015810:Linkage Disequilibrium; D008297:Male; D008957:Models, Genetic; D015233:Models, Statistical; D017720:Molecular Epidemiology; D020641:Polymorphism, Single Nucleotide; D011471:Prostatic Neoplasms / Q000235:genetics*