News Release

Thursday, February 2, 2017

NIH to expand critical catalog for genomics research

Image of a folding paper genome The genome in three dimensions folds up, forming loops and other shapes, to fit inside the nucleus.Ernesto Del Aguila, NHGRI

The National Institutes of Health plans to expand its Encyclopedia of DNA Elements (ENCODE) Project, a genomics resource used by many scientists to study human health and disease. Funded by the National Human Genome Research Institute (NHGRI), part of NIH, the ENCODE Project is generating a catalog of all the genes and regulatory elements — the parts of the genome that control whether genes are active or not — in humans and select model organisms. With four years of additional support, NHGRI builds on a long-standing commitment to developing freely available genomics resources for use by the scientific community.

“ENCODE has created high-quality and easily accessible sets of data, tools and analyses that are being used extensively in studies to interpret genome sequences and to understand the consequence of genomic variation,” said Elise Feingold, Ph.D., a program director in the Division of Genome Sciences at NHGRI. “These awards provide the opportunity to strengthen this foundation by expanding the breadth and depth of the resource.”

Since launching in 2003, ENCODE has funded a network of researchers to develop and apply methods for mapping candidate functional elements in the genome, and to analyze the enormous database of generated genomic information. The data and tools generated by ENCODE are organized by two groups: a data coordinating center, which houses the data and provides access to the resource through an open-access portal, and a data analysis center, which synthesizes the data into an encyclopedia for use by the research community.

Pending the availability of funds, NHGRI plans to commit up to $31.5 million in fiscal year 2017 for these awards. With this funding, ENCODE will expand the scope of these efforts to include characterization centers, which will study the biological role that candidate functional elements may play and develop methods to determine how they contribute to gene regulation in a variety of cell types and model systems. Additionally, the project will enhance the ENCODE catalog by developing a way to incorporate data provided by the research community, and will use biological samples from research participants who have explicitly consented for unrestricted sharing of their genomic data.

At its core, ENCODE is about enabling the scientific community to make discoveries by using basic science approaches to understand genomes at the most fundamental level. Its catalog of genomic information can be used for a variety of research projects – for example, generating hypotheses about what goes wrong in specific diseases or understanding the processes that determine how the same genome sequence is used in different parts of the body to make cells with specialized functions. More than 1,600 scientific publications by the research community have used ENCODE data or tools.

“We found that many of the people that are using the ENCODE resource are doing so for disease studies, and this attests to its translational value,” said Mike Pazin, Ph.D., a program director in NHGRI’s Division of Genome Sciences.

For more information about the ENCODE Project, go to: https://www.genome.gov/10005107/encode-project.

Recipients of the awards are:

Mapping Centers

  • Bradley Bernstein, M.D., Ph.D. and Chad Nusbaum, Ph.D.; Broad Institute, Cambridge, Massachusetts
  • Erez Lieberman Aiden, Ph.D.; Baylor College of Medicine, Houston
  • Mats Ljungman, Ph.D.; University of Michigan, Ann Arbor
  • Richard Myers, Ph.D. and Eric Mendenhall, Ph.D.; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; University of Alabama in Huntsville
  • Yijun Ruan, Ph.D.; The Jackson Laboratory, Bar Harbor, Maine
  • Michael Snyder, Ph.D.; Stanford University, California
  • John Stamatoyannopoulos, M.D.; Altius Institute for Biomedical Sciences, Seattle
  • Barbara Wold, Ph.D. and Ali Mortizavi, Ph.D.; California Institute of Technology, Pasedena; University of California, Irvine

Characterization Centers

  • Nadav Ahituv, Ph.D. and Jay Shendure, M.D., Ph.D.; University of California, San Francisco; University of Washington, Seattle
  • William Greenleaf, Ph.D. and Michael Bassik, Ph.D.; Stanford University
  • John Lis, Ph.D. and Haiyuan Yu, Ph.D.; Cornell University, Ithaca, New York
  • Len Pennacchio, Ph.D. and Axel Visel, Ph.D.; University of California, Lawrence Berkeley National Laboratory, Berkeley, California
  • Yin Shen, Ph.D. and Bing Ren, Ph.D.; University of California, San Francisco; Ludwig Institute for Cancer Research/University of California, San Diego School of Medicine

Computational Analysis

  • Michael Beer, Ph.D.; Johns Hopkins University, Baltimore
  • Christina Leslie, Ph.D.; Sloan Kettering Institute for Cancer Research, New York City
  • Alkes Price, Ph.D. and Soumya Raychaudhuri, M.D., Ph.D.; Harvard University, Cambridge, Massachusetts; Brigham and Women's Hospital, Boston
  • Jonathan Pritchard, Ph.D.; Stanford University
  • Ting Wang, Ph.D., Barak Cohen, Ph.D. and Cedric Feschotte, Ph.D.; Washington University, St. Louis; University of Utah, Salt Lake City
  • Xinshu Grace Xiao, Ph.D.; University of California, Los Angeles

Data Coordinating Center

  • J. Michael Cherry, Ph.D.; Stanford University

Data Analysis Center

  • Zhiping Weng, Ph.D. and Mark Gerstein, Ph.D.; University of Massachusetts, Amherst; Yale University, New Haven, Connecticut

NHGRI is one of the 27 institutes and centers at the National Institutes of Health. The NHGRI Extramural Research Program supports grants for research, and training and career development at sites nationwide. Additional information about NHGRI can be found at www.genome.gov.

About the National Institutes of Health (NIH): NIH, the nation's medical research agency, includes 27 Institutes and Centers and is a component of the U.S. Department of Health and Human Services. NIH is the primary federal agency conducting and supporting basic, clinical, and translational medical research, and is investigating the causes, treatments, and cures for both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.

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