The Encyclopedia of DNA Elements (ENCODE) project—a massive undertaking to catalog all the functional bits of human DNA—is expanding, thanks to a $30.3 million grant from the National Human Genome Research Institute (NHGRI) for year one of the next four-year phase of the project.
“When the project was started it wasn’t clear how well the assays would work with primary cells, so there was a strong emphasis on cell lines,” said Pazin. “In the course of the project, we have learned it is reasonable to do [these assays] with tissues and primary cells.”
The next phase will also bring in new experts to develop data analysis tools looking at human disease, basic biology or methods development. These tools will become freely available. “The idea is to stimulate use of the ENCODE resource to show that there are different ways it can be used,” said Pazin.
Getting ENCODE data into researchers’ hands remains an important goal. So far, more than 100 papers using the data have been published by independent researchers. “We’re going to be stepping up our outreach activities and make sure that this catalog is as useful as possible,” said Elise Feingold, program director for ENCODE in NHGRI's Division of Extramural Research.
The ENCODE project will expand analysis of the mouse genome, with the goal of helping researchers annotate the human genome and study mouse models of disease.
In 2003, following the completion of the Human Genome Project, ENCODE was launched with a $55 million grant to test and compare methods by analyzing 1% of the genome. The second phase launched in 2007, cost about $130 million, and involved 442 scientists.
The results from the second phase were reported last month in 30 papers published in a variety of journals, including Nature, Genome Biology, and Genome Research. All told, looking at 147 cell types, the project has given a more complete view of the location and function of regulatory regions in DNA not afforded by individual studies. Its major conclusion was that about 80% of the human genome was functional.
After last month’s publication, some have argued that the consortium’s use of the word “functional”—defined broadly by the consortium as having specific biochemical activity— doesn’t carry much meaning and that the widely reported 80% figure could be misleading to the lay public.
That debate has not changed how ENCODE will be funded or what specific experiments will be done, said Feingold. “It’s just made us a little more careful about how we talk to the press about what we’ve discovered.”