GWAS Central

GWAS Central

From the website:

GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. We actively gather datasets from public domain projects, and encourage direct data submission from the community.

GWAS Central is built upon a basal layer of Markers that comprises all known SNPs and other variants from public databases such as dbSNP and the DBGV. Allele and genotype frequency data, plus genetic association significance findings, are added on top of the Marker data, and organised the same way that investigations are reported in typical journal manuscripts. Critically, no individual level genotypes or phenotypes are presented in GWAS Central – only group level aggregated (summary level) data. The largest unit in a data submission is a Study, which can be thought of as being equivalent to one journal article. This may contain one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. Sample Panels may be characterised in terms of various Phenotypes, and they also may be combined and/or split into Assayed Panels. The Assayed Panels are used as the basis for reporting allele/genotype frequencies (in Genotype Experiments) and/or genetic association findings (in ‘Analysis Experiments’). Environmental factors are handled as part of the Sample Panel and Assayed Panel data structures.

Although I mentioned GWAS some time ago, I saw it mentioned in Christophe Lalanne’s Bag of Tweets for March 2012 and on taking a another look, thought I should mention it again.

In part because as the project reports above, this is an aggregation level site, not one that reaches into the details of studies, that may or may not be important for some researchers. That aggregation leaves a gap for aggregation or analysis of the underlying data, plus mapping it to other data!