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 [1, 2, 3, 4]. 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

Projects

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

Publications

References

  1. Pastinen T and Hudson TJ. Cis-acting regulatory variation in the human genome. Science. 2004 Oct 22;306(5696):647-50. DOI:10.1126/science.1101659 | PubMed ID:15499010 | HubMed [pastinen2005]
  2. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P, and Dermitzakis ET. Population genomics of human gene expression. Nat Genet. 2007 Oct;39(10):1217-24. DOI:10.1038/ng2142 | PubMed ID:17873874 | HubMed [stranger2007]
  3. Kristensen VN, Edvardsen H, Tsalenko A, Nordgard SH, Sørlie T, Sharan R, Vailaya A, Ben-Dor A, Lønning PE, Lien S, Omholt S, Syvänen AC, Yakhini Z, and Børresen-Dale AL. Genetic variation in putative regulatory loci controlling gene expression in breast cancer. Proc Natl Acad Sci U S A. 2006 May 16;103(20):7735-40. DOI:10.1073/pnas.0601893103 | PubMed ID:16684880 | HubMed [kristensen2006]
  4. De Gobbi M, Viprakasit V, Hughes JR, Fisher C, Buckle VJ, Ayyub H, Gibbons RJ, Vernimmen D, Yoshinaga Y, de Jong P, Cheng JF, Rubin EM, Wood WG, Bowden D, and Higgs DR. A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science. 2006 May 26;312(5777):1215-7. DOI:10.1126/science.1126431 | PubMed ID:16728641 | HubMed [degobbi2006]
All Medline abstracts: PubMed | HubMed