ENCODE

ENCODE Overview

The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence. The project is being conducted in three phases: a pilot project phase, a technology development phase and a planned production phase.

The pilot phase is testing and comparing existing methods to rigorously analyze a defined portion of the human genome sequence. It is organized as an open consortium (See: ENCODE Participants and Projects) and brings together investigators with diverse backgrounds and expertise to evaluate the relative merits of each of a diverse set of techniques, technologies and strategies. The concurrent technology development phase of the project aims to develop new high throughput methods to identify functional elements. The goal of the first two phases of the ENCODE project is to identify a suite of approaches that will allow the comprehensive identification of all the functional elements in the human genome. Through the ENCODE pilot, NHGRI expects to assess the abilities of different approaches to be scaled up for an effort to analyze the entire human genome and to find gaps in our ability to identify functional elements in genomic sequence.

The ENCODE Pilot Project process involves close interactions between computational and experimental scientists to evaluate a number of methods for annotating the human genome. A set of regions (See: Target Selection Process and Target Regions) representing approximately 1 percent (30 Mb) of the human genome has been selected as the target for this pilot project and is currently being analyzed by all ENCODE Consortium investigators. All data generated by ENCODE participants on these regions will be rapidly released into public databases (See: Accessing ENCODE Data). By initially concentrating on a limited portion of the human genome, the NHGRI hopes that all of those who have experience and insight into the problem will be willing to participate, whether or not their approaches are proprietary or have already generated proprietary data. The ENCODE Consortium is open to all academic, government and private sector scientists interested in participating in an open process to facilitate the comprehensive interpretation of the human genome sequence and who agree to the criteria for participation (See: Criteria for Participation) for the project. The activities of the ENCODE Consortium will be influential in helping to guide the planning for a complete public elucidation of functional elements within the entire human genome.

ENCODE Project Background

In April 2003, the finished sequence of the human genome was announced by the International Human Genome Sequencing Consortium (Finishing the euchromatic sequence of the human genome October 21, 2004, Nature). Although this was a significant achievement, much remains to be done. Before the best use of the information contained in the sequence can be made, the identity and precise location of all of the protein-encoding and non-protein-encoding genes in the human genome will have to be determined, as will the identities and locations of other functional elements including promoters and other transcriptional regulatory sequences and determinants of chromosome structure and function, such as origins of replication. To date, much remains unknown about these functional elements in the human genome. A comprehensive encyclopedia of all of these features is needed to fully utilize the sequence to better understand human biology, to predict potential disease risks, and to stimulate the development of new therapies to prevent and treat these diseases.

To encourage discussion and comparison of existing computational and experimental approaches to annotating the human genome, and to stimulate the development of new ones, the NHGRI proposed to create a highly interactive public research consortium to carry out a pilot project for testing and comparing existing and new methods to identify functional sequences in DNA.

On July 23-24, 2002, the NHGRI organized a workshop, the Comprehensive Extraction of Biological Information from Genomic Sequence, to discuss this proposal. The workshop participants resoundingly supported the concept of a pilot project and made a number of recommendations about the project's goals, organization and implementation, which have now been incorporated into NHGRI's plan.

On March 7, 2003, the NHGRI held a meeting to officially launch the ENCODE Pilot Project Research Consortium and to provide information to potential applications for two RFAs being released.