With the anticipated deluge of data from various personal genome projects, all drawing from a large human population, it will be be practical for a single institution or a company to deal with all the data at the pre-consumption level. One of the models that Personal Genome Project (PGP) has embraced is the open source model, in which various interested parties, whether they be interested individuals, academic labs, or for profit entities, contribute to laying down an integrated and highly networked infrastructure for independently collecting, analyzing, and distributing genomics data to end-users (i.e. patients, researchers, pharmaceutical companies).
The PGP group, headed by John Aach and assisted by Jay Lee, Sasha Wait and Jason Bobe, and the GQ group, Phil Robidoux and Richard Resnick, met in Novermeber 2008 for an introductory meeting. It was followed by several conversations regarding the present need and the anticipated needs/capablities of both PGP and GQ. PGP had released 8 out 10 preliminary exome data to public in October 2008, and PGP was preparing methods for releasing the rest of its data to the scientific community and to public in early 2009. In order to see how the GQ group could contribute, the PGP group and the GQ group initiated a pilot study looking at a subset of PGP volunteers.
The purpose of this pilot is to demonstrate the feasibility of a working relationship between the PGP team and the GQ team, and to demonstrate the ability of the GQ platform. It is encouraged that the participants interested in this pilot interact through OpenWetWare wiki, in order to communicate with the entire teams and also to log our progress. With this first pilot, GQ and PGP groups will work out the best combination of sensitivity and specificity parameters to be used in the alignment, assembly and SNP detection. For this, we will focus on PGP2 only, and extend to the rest of PGP10 later as the PGP data release pipeline becomes finalized.