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

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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

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Most cited references 3

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Linkage disequilibrium in the human genome.

D. E. Reich, M Cargill, S Bolk … (2001)

With the availability of a dense genome-wide map of single nucleotide polymorphisms (SNPs), a central issue in human genetics is whether it is now possible to use linkage disequilibrium (LD) to map genes that cause disease. LD refers to correlations among neighbouring alleles, reflecting 'haplotypes' descended from single, ancestral chromosomes. The size of LD blocks has been the subject of considerable debate. Computer simulations and empirical data have suggested that LD extends only a few kilobases (kb) around common SNPs, whereas other data have suggested that it can extend much further, in some cases greater than 100 kb. It has been difficult to obtain a systematic picture of LD because past studies have been based on only a few (1-3) loci and different populations. Here, we report a large-scale experiment using a uniform protocol to examine 19 randomly selected genomic regions. LD in a United States population of north-European descent typically extends 60 kb from common alleles, implying that LD mapping is likely to be practical in this population. By contrast, LD in a Nigerian population extends markedly less far. The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked demographic event about 27,000-53,000 years ago.

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LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation

Stephen J. Chanock, Oliver Stegle, Mitchell J Machiela (2018)

Motivation Existing approaches to plot association results from genome-wide association studies (GWAS) are in the form of static Manhattan plots and often lack data integration with rich databases on variant regulatory potential as well as population-specific linkage disequilibrium patterns. Summary We created an intuitive web module for uploading and efficiently exploring GWAS association results. Interactive plots and sortable tables allow researchers to query genomic regions of interest, facilitating the integration of data on linkage disequilibrium, variant regulatory potential and potential target genes. External links allow for visualization of association results in the UCSC genome browser as well as easy access to publically available databases (e.g. dbSNP and RegulomeDB). Through improved visualization and data integration, LDassoc offers genomic researchers a specialized environment to examine association signals and suggests variants for functional investigation. Availability and implementation LDassoc is a free and publically available web tool which can be accessed online at https://analysistools.nci.nih.gov/LDlink/? tab=ldassoc .

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Is Open Access

Visualizing the geography of genetic variants

Joseph Marcus, John Novembre (2016)

Summary: One of the key characteristics of any genetic variant is its geographic distribution. The geographic distribution can shed light on where an allele first arose, what populations it has spread to, and in turn on how migration, genetic drift, and natural selection have acted. The geographic distribution of a genetic variant can also be of great utility for medical/clinical geneticists and collectively many genetic variants can reveal population structure. Here we develop an interactive visualization tool for rapidly displaying the geographic distribution of genetic variants. Through a REST API and dynamic front-end, the Geography of Genetic Variants (GGV) browser (http://popgen.uchicago.edu/ggv/) provides maps of allele frequencies in populations distributed across the globe. Availability and Implementation: GGV is implemented as a website (http://popgen.uchicago.edu/ggv/) which employs an API to access frequency data (http://popgen.uchicago.edu/freq_api/). Python and javascript source code for the website and the API are available at: http://github.com/NovembreLab/ggv/ and http://github.com/NovembreLab/ggv-api/. Contact: jnovembre@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

M. J. Machiela:

ORCID: https://orcid.org/0000-0001-6538-9705

mitchell.machiela@nih.gov

Journal

Journal ID (nlm-ta): BMC Bioinformatics

Journal ID (iso-abbrev): BMC Bioinformatics

Title: BMC Bioinformatics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2105

Publication date (Electronic): 10 January 2020

Publication date PMC-release: 10 January 2020

Publication date Collection: 2020

Volume: 21

Electronic Location Identifier: 14

Affiliations

[1 ]ISNI 0000 0001 0941 7177, GRID grid.164295.d, Center for Bioinformatics and Computational Biology, , University of Maryland, ; College Park, MD 20740 USA

[2 ]ISNI 0000 0004 1936 8075, GRID grid.48336.3a, Division of Cancer Epidemiology and Genetics, National Cancer Institute, ; Rockville, MD 20892 USA

Author information

T. A. Alexander https://orcid.org/0000-0002-0083-3657

M. J. Machiela https://orcid.org/0000-0001-6538-9705

Article

Publisher ID: 3340

DOI: 10.1186/s12859-020-3340-1

PMC ID: 6954550

PubMed ID: 31924160

SO-VID: ef55257b-50e7-4181-92ce-b384acd5787c

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 20 September 2019

Date accepted : 3 January 2020

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100011541, Division of Cancer Epidemiology and Genetics, National Cancer Institute;

Award ID: Intramural Research Program

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ScienceOpen disciplines: Bioinformatics & Computational biology

Keywords: linkage disequilibrium,genome-wide association,geographical visualization,1000 genomes project

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ScienceOpen disciplines: Bioinformatics & Computational biology

Keywords: linkage disequilibrium, genome-wide association, geographical visualization, 1000 genomes project

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

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Most cited references 3

Linkage disequilibrium in the human genome.

LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation

Visualizing the geography of genetic variants

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