openSNP--a crowdsourced web resource for personal genomics

Abstract

Genome-Wide Association Studies are widely used to correlate phenotypic traits with genetic variants. These studies usually compare the genetic variation between two groups to single out certain Single Nucleotide Polymorphisms (SNPs) that are linked to a phenotypic variation in one of the groups. However, it is necessary to have a large enough sample size to find statistically significant correlations. Direct-To-Consumer (DTC) genetic testing can supply additional data: DTC-companies offer the analysis of a large amount of SNPs for an individual at low cost without the need to consult a physician or geneticist. Over 100,000 people have already been genotyped through Direct-To-Consumer genetic testing companies. However, this data is not public for a variety of reasons and thus cannot be used in research. It seems reasonable to create a central open data repository for such data. Here we present the web platform openSNP, an open database which allows participants of Direct-To-Consumer genetic testing to publish their genetic data at no cost along with phenotypic information. Through this crowdsourced effort of collecting genetic and phenotypic information, openSNP has become a resource for a wide area of studies, including Genome-Wide Association Studies. openSNP is hosted at http://www.opensnp.org, and the code is released under MIT-license at http://github.com/gedankenstuecke/snpr.

Figure 1. Growth of openSNP-user-accounts.

The increase in numbers for users from 27.09.2011 to 27.10.2012 is shown.

Figure 2. Growth of available genotypings.

The increase in numbers for genotyping-files from 27.09.2011 to 27.10.2012 is shown.

Figure 3. Development of unique phenotypes and phenotypic information over time.

The x-axis shows the time-frame from start of the project until October 2012, the left y-axis shows how many unique phenotypes have been entered, and the right y-axis shows the amount of phenotypes users entered.

Figure 4. Distribution of annotation-sources at openSNP.

Currently, SNP-annotations from SNPedia, PLOS, Mendeley, the GET Evidence System and the NHGRI GWAS Catalog are being collected.

Figure 5. Ratio of open access Publications.

Green pieces are open access. The NHGRI GWAS Catalog doesn't give information about the open access status.

Figure 6. Flow of data inside openSNP.

External databases and user-provided data are used as input. Output of data is done using the website, the Distributed Annotation System and a JSON-API.