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

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 pop...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 21; no. 1; pp. 14 - 4
Main Authors: Alexander, T. A., Machiela, M. J.
Format: Journal Article
Language:English
Published: London BioMed Central 10.01.2020
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
1000 Genomes Project
Algorithms
Alleles
Bioinformatics
Biomedical and Life Sciences
Cancer
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Data visualization
Diseases
Gene Frequency
Gene mapping
Genetic research
Genome-wide association
Genome-Wide Association Study
Genomes
Genomics
Genomics - methods
Geographical visualization
Geography
Haplotypes
Humans
Internet
Life Sciences
Linkage Disequilibrium
Mapping
Microarrays
Operating systems
Polymorphism
Polymorphism, Single Nucleotide
Population
Population (statistical)
Population genetics
Researchers
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Software
Statistics
User-Computer Interface
Visualization
Visualization (Computer)
Web site management software
Webs
United States > US
Genome-wide association
1000 Genomes Project
Linkage disequilibrium
Geographical visualization
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary: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
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-020-3340-1