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Geography of Genetic Variants Browser

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Genetic Variant Browser

The Geography of Genetic Variants Browser uses graphics and mapping utilities to generate maps showing the geographic distribution of a genetic variant. You can query different datsets.  An API that has been developed, allows querying of  allele frequencies by chromosome and position, by reference SNP identifier or randomly  sampled SNPs.  This information can be especially useful because it provides a highly visual way for learners to understand human genetic variation. If you study genetic variants or are just curious, check out this article and this new Genetic Variants Browser.

Abstract from the Article: “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 distribution of a genetic variant  can also be of great utility for medical/clinical geneticists. Collectively the geographic distribution of 10 many genetic variants can reveal population structure. As a result, visual inspection of geographic maps  for genetic variants is common practice in genetic studies. 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 provides maps of allele frequencies  in populations distributed across the globe.”

What is the Genetic Variants Browser?

From the Article: “The Geography of Genetic Variants browser (GGV) uses the scalable vector graphics and mapping utilities of D3.js (Bostock et al., 2011) to generate interactive frequency maps, allowing for quick and dynamic displays of the geographic distribution of a genetic variant. The front-end provides legends for the map and various configuration boxes to allow users to query different datasets or choose visualization options.  In order to allow for easy access to commonly used public genomic datasets, such as the 1000 Genomes  project (The 1000 Genomes Project Consortium, 2015) or Human Genome Diversity project (Li et al., 64 2008), we have developed a REST API (Grinberg, 2014) for accessing data. The API allows querying of  allele frequencies by chromosome and position, by reference SNP identifier (Sherry et al., 2001), or randomly  sampled SNPs. While many applications require inspection of the distribution of a specific variant, from our  experience, it can be very helpful to view the geographic distribution of several randomly chosen variants to  quickly gain a sense of structure in a dataset. We find this to be especially useful in teaching contexts, as it provides a highly visual way for learners to understand human genetic variation. After a query, the GGV displays the allele frequencies for a set of populations as a collection of pie charts where each represents the minor and major allele frequency in a single population. Pie charts are displayed as points at a latitude and longitude associated with a population and the map boundaries are chosen based off of the geographic configuration of populations in a given dataset.”

Read the entire Journal Article here.

bioRxiv preprint first posted online Aug. 9, 2016; doi: http://dx.doi.org/10.1101/068536. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.

https://creativecommons.org/licenses/by-nc/4.0/

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