PILOT PROJECT FOR EXHAUSTIVE DETERMINATION OF FUNCTIONAL ELEMENTS IN THE HUMAN GENOME REQUEST FOR INFORMATION RELEASE DATE: October 9, 2002 NOTICE: NOT-HG-03-001 National Human Genome Research Institute (NHGRI) (http://www.genome.gov) Purpose: The NHGRI is considering establishing a research consortium for a pilot project to develop and evaluate methods for identifying functional elements in the human genome. In order to plan this project, the NHGRI is requesting information from researchers about currently available methods to achieve this goal. Background: In April 2003, the sequence of the human genome will be essentially complete. Although this is 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 will have to be determined. The identity of other functional elements encoded in the DNA sequence, such as promoters and other transcriptional regulatory sequences, along with determinants of chromosome structure and function, such as origins of replication, also remain largely unknown. 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 and to stimulate the development of new ones, the NHGRI proposes 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 (http://www.genome.gov/pages/research/ENCODE). Working together in a highly cooperative effort to rigorously analyze a defined portion of the human genome sequence, investigators with diverse backgrounds and expertise will be able to evaluate the relative merits of each of a diverse set of techniques, technologies, and strategies in identifying all the functional elements in human genomic sequence, to identify gaps in our ability to annotate genomic sequence, and to consider the abilities of such methods to be scaled up for an effort to analyze the entire human genome. Information Requested: To better plan this project, the NHGRI needs more information about the types and uses of available technologies for identifying functional elements in DNA on a large scale. This Request for Information is an attempt to solicit information from the scientific community about what studies are currently being conducted to identify and verify, on a large scale, functional elements in the human genome and what technologies are being developed aimed at establishing the capability to do these types of analyses. Information in the following areas will aid in the design of scope of this pilot study: 1) What experiments, wet bench and/or computational, are your laboratory conducting related to large-scale identification of functional elements in the human sequence? 2) At what scale is this work currently being done? 3) Is the technology being used sufficiently developed for the efficient application to 1% of the genome at this time? This Request for Information is for information and planning purposes only and shall not be construed as a solicitation or as an obligation on the part of the NHGRI. The NHGRI does not intend to award a grant or contract on the basis of responses nor otherwise pay for the preparation of any information submitted or the Government's use of such information. Acknowledgment of receipt of responses will not be made, nor will respondents be notified of the Institute's evaluation of the information received. Responses will be held in a confidential manner. Any proprietary information should be so marked after each response. Comments should be submitted via email to encode@mail.nih.gov by Friday, November 8th, 2002. Direct your questions about scientific/research issues to: Elise Feingold, Ph.D. National Human Genome Research Institute Building 31, Room B2B07 Bethesda, MD 20892-2033 Telephone: (301) 496-7531 FAX: (301) 480-2770 Elise_Feingold@nih.gov Peter Good, Ph.D. National Human Genome Research Institute Building 31, Room B2B07 Bethesda, MD 20892-2033 Telephone: (301) 435-5796 FAX: (301) 480-2770 Peter_Good@nih.gov

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