PGP:Research

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About

The Personal Genome Project is an on-going effort to collect phenotype, genome sequences and functional genomics data on 100,000 volunteers [1]. PGP and its multiple collaborators will generate data both on the genetics and the cellular level, and this site will serve as a portal for various early efforts taking place within and outside of PGP.

Area of Research Interest

Various efforts are now underway to study the relationship between human genetics and phenotypes/diseases, including several large GWAS studies using high-density arrays and soon with next generation sequencing [2, 3, 4, 5]. Similarly, PGP and Church laboratory at Harvard Medical School is developing technologies and methods for affordable sequencing of human genome/epigenome and haplotyping.

In parallel, PGP is actively pursuing large-scale functional genomics studies in human volunteers, in order to look at cis-regulatory logic and polymorphisms in human development and diseases at the level of gene expression, miRNA and methylation. In addition to our genetic determinants of individual variations, we are collecting microbial flora from multiple sites from a subset of PGP volunteers as well as examining the individual- and environment-specific sequence profile of VDJ-recombination events in millions of B- and T-lymphocytes at a single cell level.

While PGP is engaged in these and several other research efforts, the majority of functional genomics will be carried out by our collaborators. Many labs, industry partners and other entities have expressed keen interest in participating in this large collaborative, 'open-source' effort. PGP's current research focus includes, but is not limited to:


  • Targeted genome sequencing (i.e. Exons, CpG)
  • Cis-regulatory polymorphisms in human development and disease
  • Functional genomics and automated cellular biology assay platforms
  • Derivation and characterization of induced pluripotent stem cells from a human population
  • Epigenetics as a determinant of gene expression polymorphisms
  • Susceptibility and resistance determinants of human microbiome
  • Evolution of immunoglobulin sequences after an antigenic/environmental exposure
  • Open-source sequencing hardware/software platforms for next generation sequencing
  • Impact of full genome sequencing on medical genetics and common medical disorders
  • Ethics and science of open consent and sharing of personal genetic information
  • Open and secure storage, management and distribution of personal genome data

Selected Research Groups and Partners

Selected Recent Publications

  1. Lunshof JE, Chadwick R, Church GM (2008) Hippocrates revisited? Oldideals and new realities. Genomic Med. 2(1-2):1-3.
  2. Sommer MO, Dantas G, Church GM. (2008) The human-associated microbiome is a mobilizable reservoir of antibiotic resistance (submitted)
  3. Lunshof JE, Chadwick R, Vorhaus DB, Church GM. From genetic privacy to open consent. Nat Rev Genet. 2008
  4. Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Yuan Gao Y, Church GM, Shendure, J (2007) Multiplex amplification of large sets of human exons. Nat Methods. 2007 Nov;4(11):931-6.] (Supplement)

References

  1. Church GM. The personal genome project. Mol Syst Biol. 2005;1:2005.0030. DOI:10.1038/msb4100040 | PubMed ID:16729065 | HubMed [church2005]
  2. Kruglyak L. The road to genome-wide association studies. Nat Rev Genet. 2008 Apr;9(4):314-8. DOI:10.1038/nrg2316 | PubMed ID:18283274 | HubMed [Kruglyak2008]
  3. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007 Jun 7;447(7145):661-78. DOI:10.1038/nature05911 | PubMed ID:17554300 | HubMed [GWAS2007]
  4. Cheung VG, Spielman RS, Ewens KG, Weber TM, Morley M, and Burdick JT. Mapping determinants of human gene expression by regional and genome-wide association. Nature. 2005 Oct 27;437(7063):1365-9. DOI:10.1038/nature04244 | PubMed ID:16251966 | HubMed [Cheung2005]
  5. Couzin J and Kaiser J. Genome-wide association. Closing the net on common disease genes. Science. 2007 May 11;316(5826):820-2. DOI:10.1126/science.316.5826.820 | PubMed ID:17495150 | HubMed [Couzin2007]
All Medline abstracts: PubMed | HubMed