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Scientists announce the completion of the ENCODE project, a massive genome encyclopedia

Updated 11:30 AM: Nature has provided a very interesting interactive graphic of the research that includes a link to each of the relevant papers and highlights the common themes, or 'threads,' between each line of research.


10:02 AM: More than 400 researchers around the world, including Stanford geneticist Michael Snyder, PhD, announced this morning the completion of the multimillion dollar ENCODE project. The project, which was funded by the National Human Genome Research Institute (NHGRI), serves as an encyclopedia of DNA elements. These functional portions of the human genome will play a vital role in personalized medicine and in biological research for decades to come. According to our release:

The completion of the human genome sequencing project in 2003 revealed what many scientists already knew to be true: more than 90 percent of the newly sequenced DNA had no known function. In fact, only about 1.5 percent encodes instructions for proteins that do the work of the cell.

Now a five-year collaboration of more than 440 scientists in 32 labs around the world has pulled back the curtain on this so-called “junk DNA” to reveal a complex interplay among regulatory regions, proteins and RNA molecules that governs when and how genes are expressed.

“Until now, we had only the nucleotide sequence,” said Stanford geneticist Michael Snyder, PhD, one of the leaders of the mammoth effort, which was funded and coordinated by the National Human Genome Research Institute. “Now we have the beginnings of a regulatory network, or wiring diagram, for a human being. This global overview will help us understand how changes in the genome cause disease, and also to see how an individual’s unique genetic code may affect his or her health in meaningful ways.” In fact, more than 80 percent of so-called “junk DNA” was found to have some type of biological function.

Together, the researchers performed more than 1600 complex, genome-wide experiments on about 150 different cell types to identify about four million regulatory switches peppered throughout the genome. The prevalence of useful information in the genome shocked even experienced scientists, who had been expecting to find important regulatory elements in only five or ten percent of the total DNA sequence. Again, from our release:

Their results paint a picture of a genome that, rather than existing as a static sequence of nucleotides, is instead as complex and as busy as our nation’s largest airports. Casual observers will notice first the airplanes taking off and landing, but a closer inspection reveals the planes’ activities are dependent on myriad other workers, from air traffic controllers, to ticketing agents, baggage cart drivers and all the other support systems that keep things running smoothly.

Four scientists, including Snyder, participated in a media briefing conference call this morning in advance of the simultaneous publication of the more than 30 papers in several journals, including Nature, Science and Genome Research, detailing results from the five-year collaboration. The transcript from the conversation, which highlights the scientists' excitement about their findings, will be available later this afternoon on the NHGRI website.  According to Snyder:

This project will have a profound impact on personal genomics. If you were to have your genome sequenced, you'd find that there are four million differences between you and the person sitting next to you. But many of these variants do not occur in known protein-coding regions. ENCODE can now help us see what these variants mean; and how a particular variant affects the control of nearby genes and puts people at risk for certain diseases or controls how they respond to drugs. [...] In a world where genomic sequencing is becoming commonplace, this will be very useful for preventive medicine and therapeutic treatments.

Previously Open-source of human genome's functional elements in the works
Photo by Stewart

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