LDpop Plots Linkage Disequilibrium by Ancestry or Geographic Location

March 26, 2019, by DCEG Staff

Enlarge

Differences in patterns of linkage disequilibrium (LD) by population ancestry are important for understanding population genetics and have relevance for the genetic architecture of disease. Current genetic tools do not plot LD by ancestry or geographic location.

To address this gap, investigators in DCEG created an interactive web module to quickly generate visualizations of geographic linkage equilibrium patterns between two user-specified germline variants across populations included in the 1000 Genomes Project. Interactive maps and a downloadable, sortable summary table allow researchers to easily compare allele frequencies and LD statistics (D' or R²) of dbSNP-catalogued variants. The geographic mapping of each SNP’s allele frequencies by population as well as visualization of LD statistics allows the user to easily trace geographic allelic correlation patterns and examine population-specific differences.

LDpop is a free and publicly available cross-platform web tool.