What is Cafe Variome?

Diagnostics laboratories routinely assess DNA samples from patients with various inherited disorders, and so produce a great wealth of data on the genetic basis of disease. Unfortunately, those data are not usually shared with others. To address this gross deficiency, a novel system has been developed that aims to facilitate the automated transfer of diagnostic laboratory data to the wider community, via an internet based Cafe for routinely exchanging genetic variation data.

The flow of research data concerning the genetic basis of health and disease is critical to understanding and developing treatments for a range of genetic diseases. Overall, the project aims to lower the barriers and provide incentives for a willing community to share data, and thereby facilitate the broader exploitation of diagnostic laboratory data. Cafe Variome aims to address the above data flow problems by:

  1. Minimising the effort required to publish variant data
  2. Ensuring attribution for data creators working in diagnostic laboratories

Key elements of the project strategy are:

a)  Data publication will be automated by endowing standard analysis tools used by laboratories with an online "data submission" function. Submissions will be received by a central Internet depot, which will serve as a place where published datasets are advertised, and subsequently discovered by diverse 3rd parties.

b)  Each dataset will be unambiguously linked with the data submitter's identity, and systems devised to facilitate citation of published variant datasets so they can be cited in the literature. Data creators will thus be credited for their contributions.

Cafe Variome should not be thought as a database but instead as a 'shop window' for what exists in various data sources. It is designed to enable users to ask the question 'where can certain data be found?', seeking to access those data under one of three models, as stipulated by the data submitter:

  1. Open Access: variant records are publicly available for access
  2. Restricted Access: variants can be downloaded only after having sought and received specific permission from the data submitter/owner
  3. Linked Access: only the variant's existence is reported, with a link to the original data source

Data submitters can use Cafe Variome to simply announce or publicise their data to the world. To enable this, only core, non-identifiable data is submitted to the central repository, enabling users to search and discover records of interest in the source repository. The data are not automatically handed on to the user (unless intended by the submitters). Hence, the concept is used to deal with the challenge of maximally sharing data whilst fully respecting ethico-legal considerations.