LDpop: an interactive online tool to calculate and visualize geographic LD patterns

Area of Science:

• Population Genetics
• Genomic Ancestry
• Human Genetic Variation

Background:

• Linkage disequilibrium (LD) describes non-random allele associations at different loci, defining population-specific haplotypes.
• Genomic ancestry influences LD patterns, making population-specific assessments crucial for genetic research.
• Understanding allelic frequencies and LD patterns across diverse ancestral groups enhances insights into population histories and ethnicity-related disease risks.

Purpose of the Study:

• To develop an interactive web module for visualizing linkage disequilibrium (LD) patterns.
• To enable geographic visualization of LD across populations from the 1000 Genomes Project.
• To provide researchers with a tool for computing and comparing allele frequencies and LD statistics.

Main Methods:

• Creation of an interactive web module for LD pattern visualization.
• Integration of data from the 1000 Genomes Project.
• Development of interactive maps and a downloadable summary table for data analysis.

Main Results:

• An interactive web module, LDpop, was developed for geographic visualization of LD patterns.
• The tool allows for quick comparison of allele frequencies and LD statistics across populations.
• Geographic mapping facilitates tracing allelic correlation patterns and identifying population-specific differences.

Conclusions:

• LDpop is a free, publicly available, cross-platform web tool.
• The tool is accessible online at https://ldlink.nci.nih.gov/?tab=ldpop.
• LDpop aids researchers in exploring population-specific genetic variations and LD patterns.