The idea of creating resources for interpreting genetic variation is far from new. Indeed, there are a great many valuable existing resources such as dbSNP, dbGaP, PharmGKB, GeneTests, OMIM which are detailed on the resources page of this site.

There have been efforts to amalgamate these and the hundreds of Locus Specific Databases, such as MutationView. The HGMD probably has the largest array of mutations tabularly annotated; however, in order to support its continued maintenance, its authors have restricted full access to those who pay license fees and prohibited redistribution. As we enter the era of personal genomes there is a profound new impetus for suitable open resources.

There had been an effort a decade ago with several goals in common with the Genome Commons, though of narrower scope, called the Mutation Database Initiative. This initiative held promise, and had been offered considerable funds. Its foundering has been reported and analyzed. From the ashes of this program has arisen the Human Genome Variation Society and the Human Variome Project, about which Nature Genetics had a special issue. This project’s 2006 meeting developed 96 recommendations for how to proceed. One step towards this is building The WayStation, which has failed to attract financial support.

Numerous groups have developed systems for mapping variation on to various instances of the genome. For example, GBrowse maps HapMap variation onto the NCBI human genome build.

The Genome Commons does not specifically address the process by which we obtain personal genomes and all of the privacy issues associated with those genomes. One source of information about this is George Church’s Personal Genome Project. He has also written about this in a Scientific American article. There is an active blog about personal genomics.

The Genome Commons musings also do not specifically address the incredible difficulty of integrating and interpreting multiple variants in an individual, each associated with a given trait. I believe that addressing this challenge requires a resource like the Genome Commons and workable Navigators as prerequisites.