ENCODE (the ENCyclopedia Of DNA Elements) is a public research consortium launched by the US National Human Genome Research Institute (NHGRI) in September 2003. The goal is to find all functional elements in the human genome, one of the most critical projects by NHGRI after it completed the successful Human Genome Project. All data generated in the course of the project will be released rapidly into public databases.

Pilot Phase

The project was initiated with a $12 million pilot phase. The aim of this was to evaluate a variety of different methods for use in later stages. Essentially this involved using a number of existing techniques to analyse a portion of the genome equal to about 1% (30mb). The results of these analyses will then be evaluated based on their ability to identify regions of DNA which are known or suspected to contain functional elements. 50% of the sample area selected for study under this phase was manually selected whilst the other 50% was selected at random.^[1] The manually selected regions have been selected based on the presence of well studied genes and the availability of comparative data. Methods currently being evaluated include chromatin immunoprecipitation (ChIP) and quantitative PCR.

The encode pilot project rapidly released all of its data into public databases. This data can be found here. The pilot phase was successfully finished and the result were published in June 2007 in Nature and a special issue of Genome Research.

Technology Phase

The concurrent phase to this is the technology development phase, which aims to investigate and develop new, high throughput techniques and protocols suitable for use in the ENCODE project.

Production Phase

The final phase of the ENCODE project has now been started. It aims to rigorously analyse the entire genome using the best methods and technologies identified in the first two phases. Funding has been granted to seven principal investigators from the U.S. and the U.K. (Bradley Bernstein, Gregory Crawford, Thomas Gingeras, Tim Hubbard, Richard Myers, Michael Snyder, John Stamatoyannopoulos).

Notes

1. ↑ genome.gov | ENCODE Project Target Selection Process and Target Regions

External links

• National Human Genome Research Institute
• NHGRI page on the ENCODE project
• Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature (publication)
• Special Issue with pilot phase results, Genome Research (publication)
• ENCODE project at UCSC

• The modENCODE Project: Model Organism ENCyclopedia Of DNA Elements (modENCODE), continuation of the ENCODE project to model organisms

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