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PGP Genome Assessment Challenge

October 11, 2012

The Personal Genome Project is working with the Critical Assessment of Genome Interpretation (CAGI) this year to provide a genomic interpretation challenge using PGP data! CAGI’s use of PGP data is a demonstration of how publicly sharing genome & trait data is invaluable to science: because the data is public, the challenge is open to everyone. No restrictions or requirements need to be met to access the data.

How will the challenge work? In the upcoming week or two we will be returning genomes to some participants. Currently genomes automatically become public after 30 days of private access, but participants have the ability to publish a genome immediately should they choose to do so. We’ve added an additional option for CAGI: participants can release the genome to be used as a CAGI genome. When they do this, the genome becomes public — but which participant account the genome belongs to is kept secret. At the end of the challenge genome data will be linked to the specific participant account.

Of course the other half of CAGI is the predictions — we need trait data from participants for the CAGI researchers to try to predict! I’ve been working hard the last couple weeks to make a set of trait surveys for PGP participants. These surveys aren’t just for CAGI, they’re for all participants and they’ll remain open after CAGI is ended. For a genome to be used by CAGI a participant will need to complete all the surveys, but all participants are encouraged to fill them out.

The trait surveys are publicly shared and entirely optional — only choose the items in the survey that you want added to your public profile. You can find the surveys (“PGP Trait & Disease Survey 2012”) at the bottom-center of the screen when you log in to your PGP account.

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