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NHGRI Invests $31.5M into ENCODE for 2012

By Matt Jones

NEW YORK (GenomeWeb News) – The National Human Genome Research Institute has launched the latest phase of its long-term project to fund research to identify all of the functional parts of the human genome with new grant programs that could total around $120 million over the next four years.

The institute has kicked off the upcoming phase of the Encyclopedia of DNA Elements (ENCODE) program with $31.5 million for FY 2012 for three new requests for applications that will support projects to produce more complete human genomic catalogs, make that data accessible to the research community, and analyze the results for applications to human diseases.

GenomeWeb Daily News reported in May that NHGRI approved $123 million to continue the ENCODE project, which began in 2003, with three new RFAs, although the full amount the program receives over the next five years could depend on Congressional appropriations.

"We wanted to expand the ENCODE project to generate as complete catalogs as feasible," ENCODE Program Director at NHGRI Elise Feingold told the National Advisory Council on Human Genome Research in her proposal for the new funding.

"We really wanted to capitalize on the progress that's been made in establishing high-throughput and efficient production pipelines [and to] take advantage of economies of scale, centralized management, and centralized coordination."

In an interview with GWDN late last week Feingold said that the ENCODE project is all about annotating the genome.

"We have the whole genome sequence but we really don't have the punctuation marks to really understand where the genes are, and where the regions of the genome are that regulate gene expression. What we're providing here is a very high detail annotation of the human genome sequence," she said.

"We're pretty good, historically, at finding genes. We've historically been not as good at finding regulatory regions," she added. "So we're providing a high-level annotation of the genes and the regulatory regions. This is going to be used by people who are interested in understanding basic biological questions, understanding chromosome biology, and it's also going to be used by people who are interested in studying diseases."

"We're excited to be able to do this next phase of ENCODE and to really increase the depth of the catalog using more cell types that allow for more coverage of more cell types that are associated with disease," she said.

In one RFA for a program called Expanding the ENCODE in the Human and Model Organisms $23 million will be provided next year to fund between six to eight awards. This research will focus on expanding the maps in a larger number of cells and tissues and across several types of genomic activity, including in all classes of functional RNA molecules, open chromatin, DNA methylation, and transcription factor binding sites, among others.

Feingold said NHGRI wants to "really increase depth of the catalogue using more cell types that allow for more coverage of more cell types that are associated with disease."

The second new program, Computational Analysis of ENCODE Data, will provide $3 million next year for five to eight awards that will develop new analytical methods to improve data analysis and make it more useful in the study of disease.

Feingold said this program also seeks to make data broadly available to the research community to ensure the success of ENCODE.

The third new RFA will provide $.5.5 million to fund two centers, one for a data analysis center that will perform integrated ENCODE analysis, and another that will facilitate data management for ENCODE and disseminate that data.

Feingold said that the goal of these two centers will be to "bring in additional minds to analyze the data... coming up with new ways to analyze the data, visualizing the data, and bringing in disease-type studies."

"One of the long-term goals of this project is not only creating this resource, but understanding what the most informative marks are. If we can come up with a few of the marks that we think are very informative, we think this would be very useful for the rest of the research community," Feingold told GWDN.

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