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NHGRI Unveils Second Phase of ENCODE Project With $80M in Grants

NEW YORK (GenomeWeb News) — The National Human Genome Research Institute has fired up the second phase of its Encyclopedia of DNA Elements project by doling out $80 million in new grants over four years in hopes of building a “parts list of biologically functional elements” in the entire human genome.
The new ENCODE initiative, which comes four months after the program’s pilot project released its data, are aimed at investigating some of the questions left hanging by the pilot program.
The pilot project, which looked at 1 percent of the human genome, “produced findings that are reshaping many long-held views about our genome,” NHGRI Director Frances Collins said in a statement today. The research will now move forward “with a full-scale initiative to build a parts list of biologically functional elements in the human genome.”
The scaled-up ENCODE project plans to “build a comprehensive catalog of the components of the human genome that are crucial to biological function,” Elise Feingold, program director for ENCODE in the NHGRI Division of Extramural Research, said in a statement.
The data generated from the ENCODE project will be dropped into public databases as soon as they are verified, according to Peter Good, the NHGRI’s extramural research director for genome informatics.
"Free and rapid access to this data will enable researchers around the world to pose new questions and gain new insights into how the human genome functions,” Good said.
Receiving funding for the scale-up phase will be:
  • Bradley Bernstein of the Broad Institute of the Massachusetts Institute of Technology and Harvard University, who will use $4.8 million to investigate chromatin immunoprecipitation followed by high-throughput DNA sequencing to map modifications of histones in various human cells;


  • Gregory Crawford of Duke University’s Institute for Genome Sciences and Policy, who will use $6.5 million to identify and characterize regions of open chromatin through DNase I hypersensitivity assays, formaldehyde-assisted isolation of regulatory elements, and chromatin immunoprecipitation;
  • Thomas Gingeras of Affymetrix, who will use $10.2 million to identify protein-coding and non-protein-coding RNA transcripts using microarrays, high-throughput sequencing, sequenced paired-end ditags, and sequenced cap analysis of gene-expression tags;
  • Tim Hubbard of the Wellcome Trust Sanger Institute, who will use $8.5 million to use “computational methods, manual annotation, and targeted experiments … to annotate gene features in the human genome;”
  • Richard Myers of Stanford University, who received $14.6 million to study global annotation of regulatory elements in the human genome, and will use high-throughput sequencing to determine the methylation status of CpG-rich regions in the human genome; 
  • Michael Snyder of Yale University, who will use $11.5 million to start a production center for global mapping of regulatory elements;
  • John Stamatoyannopoulos of the University of Washington, Seattle, who will use $9.7 million to map and classify DNase I hypersensitive sites across major human cell lineages;
  • Scott Tenenbaum of the State University of New York at Albany, who received $2.2 million for research aimed at comprehensively identifying ENCODE RNA-based Cis-regulatory elements; 
  • Zhiping Weng of Boston University, who will use $1.5 million to identify transcriptional factor-binding sites in human promoters; and 
  • W. James Kent of the University of California, Santa Cruz, who will use $5 million to establish the UCSC ENCODE Data Coordination Center, which will collect, organize, store, manage, and provide access to data from ENCODE projects.
  • Additional information can be found here.

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