March 3, 2017

Public personal genomes; open-access, open-source, open-ended?

Over at Genomes Unzipped yesterday, 12 named individuals, molecular biologists in the main, released their genomes into the public domain, generating some press interest. These exponents of molecular naturism are the latest in a growing line, including Craig (first, of course) Venter, James Watson, and the PGP-10 featuring George Church. Alongside DIY genomics, a prominant thread in the genomics blogosphere right now is increasing angst over how to interpret the encroaching genomics data deluge. Bringing these two together, cynics may say that, if the funded bodies can't afford the analysis, then what chance have the hobbyists? Sure, a line-by-line approach using Excel is just about feasible for a single genome (hats off to Anne West) but is hardly scalable in the context of the 100,000 genomes that the Personal Genomics Project aim to collect. In this context, it is interesting that the Genomes Unzipped effort considers software development from the start, open-source of course, and the first piece of software is a genome browser. The Genomes Unzipped software also comes complete with a RESTful API. So what is the overall scientific vision of the DIYers? For instance, should a matched set of privacy-advocating scientists be genotyped to test the hypothesis that genome exhibitionism is associated with some impared/enhanced molecular pathway? No - it is very clear that the aim of this effort is to stimulate thought and generate novel genomics-related theories. In the Genomes Unzipped post, Daniel MacArthur's first justification for the project is to;

"help [the participants] get access to their own genetic data, and create a platform for them to talk about what they found".

Is he advocating a community-developed content management system for personal genomics? Excellent; this is exactly the type of software that is desperately needed as a defence against the encroaching genomics data tsunami, so that's that circle closed. And one final thought: In his post, MacArthur stated that a major risk being taken by the participants is that of unknown unknowns; risks that no-one knows about yet. Recall also that a significant goal of the whole effort is to generate novel hypotheses - to unearth these unknown unknowns. Public personal genomes, therefore; simply a highly intellectual game of Russian Roulette?

Topics: Bioinformatics, Blog, genome, genome browser, open access, Open source, personal genomes