HVP Beijing: dealing with variation

December 11, 2011

The Human Variome Project (HVP) Beijing Meeting has officially ended (though a number of delegates will be busy tomorrow at the Advisory Council meeting). The energy and commitment towards better understanding and treatment of heritable diseases displayed by both the speakers and participants was great to see. Peter Taschner’s talk on the Leiden Open (source) Variation Database (LOVD) system was very well received, and a number of  other speakers were using LOVD for their locus-specific databases. I enjoyed Peter Robinson’s presentation on phenotype ontology and representation in gene and disease specific databases. He discussed his free differential diagnosis tool Phenomizer, which integrates OMIM and the Orphanet rare disease nosology (Orphanet was also the subject of an earlier talk by Mariana Jovanovic).

Ethics and curation were recurring themes at this HVP meeting as well. Many of the ethical issues concerning the sharing of  human genetic data were raised by Sue Povey and Carol Isaacson Barash: consent; the tradeoff regarding the release of a carrier’s  or affected individual’s geographical and ethnic information, which is both potentially identifying and of great scientific use; the impact of culture on the idea of genetic privacy; and the use of databases for diagnosis and treatment decisions. They are all thorny issues that will be discussed again and again as the field continues to change.

I was very impressed by the universal recognition of the value of curation. Most presentations discussed curation procedures and the various challenges of curating potentially sensitive and potentially diagnostic human genetic, genomic and medical data. Arleen Auerbach’s talk on the Fanconi Anemia Mutation Database (which now uses LOVD) dealt with curation issues exclusively. Anthony Brookes spoke on the technical standards and data models necessary for system interoperability, which fit well with the mood of the audience who wanted to share data without enforcing a one-system rule. The open access software Cafe Variome for sharing the existence of data, but not necessarily the data itself, that he described generated a lot of interest. Mauno Vihinen introduced VariO, an ontology for varation at the DNA and RNA level, and took the curation discussion in a different direction; Vihinen proposed an independent evaluation and rating system for human gene variation databases akin to hotel stars or Michelin stars.

The meeting ended with a brainstorming session for new recommendations for action by the Human Variome Project. It sounds like the HVP group has ambitious plans to start on before they meet again in Paris this spring!