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. 2020 Jan 8;48(D1):D941-D947.
doi: 10.1093/nar/gkz836.

The International Genome Sample Resource (IGSR) Collection of Open Human Genomic Variation Resources

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Free PMC article

The International Genome Sample Resource (IGSR) Collection of Open Human Genomic Variation Resources

Susan Fairley et al. Nucleic Acids Res. .
Free PMC article

Abstract

To sustain and develop the largest fully open human genomic resources the International Genome Sample Resource (IGSR) (https://www.internationalgenome.org) was established. It is built on the foundation of the 1000 Genomes Project, which created the largest openly accessible catalogue of human genomic variation developed from samples spanning five continents. IGSR (i) maintains access to 1000 Genomes Project resources, (ii) updates 1000 Genomes Project resources to the GRCh38 human reference assembly, (iii) adds new data generated on 1000 Genomes Project cell lines, (iv) shares data from samples with a similarly open consent to increase the number of samples and populations represented in the resources and (v) provides support to users of these resources. Among recent updates are the release of variation calls from 1000 Genomes Project data calculated directly on GRCh38 and the addition of high coverage sequence data for the 2504 samples in the 1000 Genomes Project phase three panel. The data portal, which facilitates web-based exploration of the IGSR resources, has been updated to include samples which were not part of the 1000 Genomes Project and now presents a unified view of data and samples across almost 5000 samples from multiple studies. All data is fully open and publicly accessible.

Figures

Figure 1.
Figure 1.
To support the increased number of populations in IGSR, a map view has been added to the website's data portal. This enables users to explore populations based on sampling location, with colouring indicating superpopulation groupings.
Figure 2.
Figure 2.
The data portal provides various views of key data sets in IGSR. (A) Data can be browsed by sample, population or data collection under different tabs. (B) On the sample and population tabs, different views of the data can be chosen. (C) Filters from multiple categories can be applied to the data. (D) The displayed data can be downloaded as a tab-delimited list. (E) In table views, information is displayed on the left, for samples, this is the sample name, sex and population information. This is followed by indicators, which, in data collection view, show which data collections the sample is present in. (F) The data portal also has search functionality, which can be accessed via the search tab or the search box present throughout the website.
Figure 3.
Figure 3.
An example of a population page, showing the Saami population from the SGDP. (A) Gives some descriptive information. (B) Lists samples present in the population. (C) Tabs at the bottom of the page show which collections the population is found in, here only the SGDP. (D) For each collection, a link is provided to information on how the data may be used. If a population shares samples with another population, this information is presented on this page. In this case, no samples are shared.
Figure 4.
Figure 4.
The page for sample HG01504. (A) Shows details on the sample. This sample belongs to populations in 1000 Genomes and the SGDP. Synonyms for the sample are also shown along with a link to the cell line source, where such exists, in this case Coriell. (B) Lists any known related samples present in IGSR.

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