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BMC Bioinformatics. 2020 Jan 10;21(1):14. doi: 10.1186/s12859-020-3340-1.

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

Author information

1
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20740, USA.
2
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20892, USA. mitchell.machiela@nih.gov.

Abstract

BACKGROUND:

Linkage disequilibrium (LD)-the non-random association of alleles at different loci-defines population-specific haplotypes which vary by genomic ancestry. Assessment of allelic frequencies and LD patterns from a variety of ancestral populations enables researchers to better understand population histories as well as improve genetic understanding of diseases in which risk varies by ethnicity.

RESULTS:

We created an interactive web module which allows for quick geographic visualization of linkage disequilibrium (LD) patterns between two user-specified germline variants across geographic populations included in the 1000 Genomes Project. Interactive maps and a downloadable, sortable summary table allow researchers to easily compute and compare allele frequencies and LD statistics 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.

CONCLUSIONS:

LDpop is a free and publicly available cross-platform web tool which can be accessed online at https://ldlink.nci.nih.gov/?tab=ldpop.

KEYWORDS:

1000 Genomes Project; Genome-wide association; Geographical visualization; Linkage disequilibrium

PMID:
31924160
PMCID:
PMC6954550
DOI:
10.1186/s12859-020-3340-1
[Indexed for MEDLINE]
Free PMC Article

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