Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus

Abstract

Summary: Often in human genetic analysis, multiple tables of single nucleotide polymorphism (SNP) statistics are shown alongside a Haploview style correlation plot. Readers are then asked to make inferences that incorporate knowledge across these multiple sets of results. To better facilitate a collective understanding of all available data, we developed a Ruby-based web application, LD-Plus, to generate figures that simultaneously display physical location of SNPs, binary SNP attributes (such as coding/non-coding or presence on genotyping platforms), common haplotypes and their frequencies and continuously scaled values (such as Fst, minor allele frequency, genotyping efficiency or P-values), all in the context of the D′ and r2 linkage disequilibrium structures. Combining these results into one comprehensive figure reduces dereferencing between figures and tables, and can provide unique insights into genetic features that are not clearly seen when results are partitioned across multiple figures and tables. Availability: LD-Plus is freely available for non-commercial research institutions. For full details see http://chgr.mc.vanderbilt.edu/ritchielab/ldplus. Contact: ritchie@chgr.mc.vanderbilt.edu © The Author(s) 2010. Published by Oxford University Press.