GWAS catalog explained

The GWAS catalog is a free online database that compiles data of genome-wide association studies (GWAS), summarizing unstructured data from different literature sources into accessible high quality data. It was created by the National Human Genome Research Institute (NHGRI) in 2008 and have become a collaborative project between the NHGRI and the European Bioinformatics Institute (EBI) since 2010.[1] As of September 2018, it has included 71,673 SNP–trait associations in 3,567 publications.[2]

A GWAS identifies genetic loci associated with common traits and disease through the analysis of categorized variants across the genome and the catalog provides information from all published GWAS results that meet its criteria.[3] The catalog contains publication information, study groups information (origin, size) and SNP-disease association information (including SNP identifier, P-value, gene and risk allele).[4] Over the years, the GWAS catalog has enhanced its data release frequency by adding features such as graphical user interface, ontology-supported search functionality and a curation interface.[5]

The GWAS catalog is widely used to identify causal variants and understand disease mechanisms by biologists, bioinformaticians and other researchers.[6] [7] [8] Some GWAS identified common genomic loci that are associated diseases include: cardiovascular disease, inflammatory bowel disease, type 2 diabetes and breast cancer.[9]

Accessibility of data

The public can gain access to the GWAS Catalog’ s data in three ways:[4]

  1. The NHGRI web interface’s search: provide information on traits and study publication and an tab-delimited file that is available for download.
  2. Interactive interface: provide a visualization of all SNP-associated traits in the GWAS catalog as well as SNPs’ positions on human chromosomes. And all SNPs are associated with a particular trait are displayed with web links to related literature from different databases.
  3. Ensembl, the UCSC Genome Browser, the PheGenI and other data portals provide access to the GWAS catalog through providing web links.

Applications

Some current applications of the GWAS Catalog include the use of studies on the genetics of human diseases [10] and the heritability of human traits. The GWAS catalog data can also be used as a pool of markers for SNP studies.

Notes and References

  1. Web site: About the GWAS Catalog . GWAS Catalog . 2019-06-17.
  2. Buniello A, MacArthur JA, Cerezo M, Harris LW, Hayhurst J, Malangone C, McMahon A, Morales J, Mountjoy E, Sollis E, Suveges D, Vrousgou O, Whetzel PL, Amode R, Guillen JA, Riat HS, Trevanion SJ, Hall P, Junkins H, Flicek P, Burdett T, Hindorff LA, Cunningham F, Parkinson H . 6 . The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019 . Nucleic Acids Research . 47 . D1 . D1005–D1012 . January 2019 . 30445434 . 6323933 . 10.1093/nar/gky1120 .
  3. MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H . 6 . The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) . Nucleic Acids Research . 45 . D1 . D896–D901 . January 2017 . 27899670 . 5210590 . 10.1093/nar/gkw1133 .
  4. Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H . 6 . The NHGRI GWAS Catalog, a curated resource of SNP-trait associations . Nucleic Acids Research . 42 . Database issue . D1001-6 . January 2014 . 24316577 . 3965119 . 10.1093/nar/gkt1229 .
  5. MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H . 6 . The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) . Nucleic Acids Research . 45 . D1 . D896–D901 . January 2017 . 27899670 . 5210590 . 10.1093/nar/gkw1133 .
  6. Loos RJ, Yeo GS . The bigger picture of FTO: the first GWAS-identified obesity gene . Nature Reviews. Endocrinology . 10 . 1 . 51–61 . January 2014 . 24247219 . 4188449 . 10.1038/nrendo.2013.227 .
  7. López-Cortegano E, Caballero A . Inferring the Nature of Missing Heritability in Human Traits Using Data from the GWAS Catalog . Genetics . 212 . 3 . 891–904 . July 2019 . 31123044 . 6614893 . 10.1534/genetics.119.302077 . 7 Nov 2019 .
  8. Pal LR, Moult J . Genetic Basis of Common Human Disease: Insight into the Role of Missense SNPs from Genome-Wide Association Studies . Journal of Molecular Biology . 427 . 13 . 2271–89 . July 2015 . 25937569 . 4893807 . 10.1016/j.jmb.2015.04.014 .
  9. MacArthur J, Bowler E, Cerezo M, Gil L, Hall P, Hastings E, Junkins H, McMahon A, Milano A, Morales J, Pendlington ZM, Welter D, Burdett T, Hindorff L, Flicek P, Cunningham F, Parkinson H . 6 . The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog) . Nucleic Acids Research . 45 . D1 . D896–D901 . January 2017 . 27899670 . 5210590 . 10.1093/nar/gkw1133 .
  10. Morales J, Welter D, Bowler EH, Cerezo M, Harris LW, McMahon AC, Hall P, Junkins HA, Milano A, Hastings E, Malangone C, Buniello A, Burdett T, Flicek P, Parkinson H, Cunningham F, Hindorff LA, MacArthur JA . 6 . A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog . Genome Biology . 19 . 1 . 21 . February 2018 . 29448949 . 5815218 . 10.1186/s13059-018-1396-2 . free .

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