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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.

Pilot Phase

The project is currently in a $12 million pilot phase. The aim of this is to evaluate a variety of different methods for use in later stages. Essentially this involves 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 releases all of its data into public databases. This data can be found here.

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 will be a planned production phase, which will rigorously analyse the entire genome using the best methods and technologies identified in the first two phases.


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