The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health, has announced the recipients of up to $31.5 million in fiscal grant funding in 2017. The funding is dedicated to the expansion of NHGRI’s Encyclopedia of DNA Elements (ENCODE) programme, a project launched in 2003 to identify all functional elements within the human genome and to make the resulting data freely accessible and interpretable. 

New Funding for NHGRI’s ENCODE

Illustration by Frits

The programme is currently split in two main elements: a data coordinating centre which houses the data and allows access to the resources through an open-access portal, and a data analysis centre which orders the data into a useable encyclopedia for the research community.

Last year, the NHGRI announced that it was seeking grant applications for five new initiatives: expanding the current catalogue, creating a general understanding of the role of these genomic elements in different contexts, developing strategies to apply their findings to disease study and treatment, increasing the number of participating researchers, and developing new analytical tools. The new funding streams generally reflect these outlined goals.

The first parts of the programme to benefit are the mapping centres. These centres are made up of researchers aiming to pinpoint the location of certain genes and their regulatory regions within the genome. The new funding will allow the centres to access a broader diversity of biological samples, including samples from individuals with a variety of diseases, and highly specialised cells which can enhance the catalogue. “In the past, ENCODE has focused on identifying functional elements in healthy individuals; but gene expression may be regulated differently in people that are unhealthy versus those that are healthy,” said Dr. Mike Pazin, a programme director in NHGRI’s Division of Genome Sciences. “Diseased tissues may help with the detection of new functional elements.”

The awards have also helped the mapping centres to recruit new researchers from a range of institutions and organisations, including the California Institute of Technology and the Broad Institute.

ENCODE will also now be able to establish five characterisation centres that will focus on examining how genomic elements function in different biological environments. “We want to try and breathe life into the functional aspects of the catalogue that ENCODE has created,” said Dr. Will Greenleaf, assistant professor at Stanford University and one of the new ENCODE investigators who will run a characterisation centre. His research involves working in collaboration with another Stanford group to use methods such as CRISPR-Cas9 to alter various regulatory elements and then characterising cell growth under different conditions.

The third arm of the ENCODE expansion is focused on developing statistical and computational tools that will allow the catalogue to become more useful to researchers. Working with big data sets like those contained within the ENCODE programme requires many different computational tools to make the data accessible and to allow researchers to analyse their results.

“As a community resource, ENCODE data must be rapidly and freely available to researchers so they can immediately put it to use in their own work. This is where the data coordinating centre and data analysis centre play such critical roles,” said Dr. Dan Gilchrist, program director in NHGRI’s Division of Genome Sciences. “Thanks to these centres, ENCODE data are findable, accessible, interoperable and reusable – maximizing their utility to the research community.”

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