PGP:Genome

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Purpose
The cost of full genome sequencing has reached a point where it is now an affordable option. Complete Genomics Inc. has pushed this technology to its limit by announcing full diploid sequencing with >40x coverage for less than $5,000 per individual by 2010 (Technology and News from their website). Since targeted exon sequencing can be done for far less, it requires exploring the right application for performing full genome sequencing of a large number of individuals, in addition to general association studies of rare genetic polymorphisms.

In collaboration with Complete Genomics, PGP will demonstrate the power of allele-specific gene expression assays in its ability to identify function cis-regulatory sites in the non-coding region of the genome. The non-coding region likely contains many hereto undiscovered and unappreciated regulatory elements responsible for the diversity in human development and diseases #pastinen2005 stranger2007 kristensen2006 degobbi2006. As a pilot study, we will perform full genome sequencing of Phase One PGP volunteers, starting with PGP1 in December 2009.

The resulting full genome sequence will be used in conjunction with many functional expression data using allele-specific gene expression assays in iPS (induced pluripotent stem cell)-derived tissues. This way, we hope to uncover many functional and causative functional variants in the non-coding region (approximately 98.5% of the entire genome), demonstrating the real power of full genome sequencing beyond sampling "reference" individuals.

Collaborators

 * Complete Genomics, Inc.
 * George Church Laboratory (HMS, Boston)
 * Kun Zhang Laboratory (UCSD, San Diego)

Projects

 * PGP1 Full Genome Sequencing
 * Phase One PGP Full Genome Sequencing (PGP2 through PGP10)