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A one-in-a-thousand genome
ASHLAND, Ore.—The Alan and Priscilla Oppenheimer Foundation announced at the start of November that, in collaboration with the Personal Genome Project (PGP), it has begun the process of sequencing the first full human genome in the next major phase of that project, the PGP-1K.
In concert with the PGP, the Oppenheimer Foundation has chosen Complete Genomics Inc., a life sciences company that provides an end-to-end outsourced DNA sequencing service, to provide the first of 1,000 PGP-1K sequences. Complete Genomics expects to deliver the data from that sequence in February.
More than 1,000 people have already gone through the enrollment process to participate in PGP-1K, but the individual whom Complete Genomics will sequence was specifically picked for certain traits that PGP and the Oppenheimer Foundation thought were interesting and unique to get the ball rolling, notes foundation President Alan Oppenheimer.
In keeping with the goals of the PGP, although the genome and associated physical traits will be published, the participant's identity may not be revealed, the foundation and PGP note.
The initial Human Genome Project required 10 years and more than $1 billion to sequence a single human's genome, but the first PGP-1K genome is expected to take only three months and cost an estimated $10,000, according to Oppenheimer and Dr. George M. Church, founder and principal investigator of the PGP—as well as a professor of Genetics at Harvard Medical School and director of the Center for Computational Genetics.
"As we had hoped, the price of sequencing a full human genome has come down to the point where a small foundation like ours can actually spearhead a sequencing effort," Oppenheimer says. "We look forward to all we're going to learn from the effort and to how it will help the PGP meet its long-term goals."
Although the PGP-1K may sound a lot like the 1000 Genomes Project just based on numbers and the kind of work being performed, Oppenheimer does note that there are differences.
"The 1000 Genomes Project is collecting a lot of data and useful stats but has certain populations it is focusing on," he notes. "We're a more open study with PGP-1K, though, as I see it, and we will be doing trait associations, which I think also makes it novel."
The PGP had already sequenced and published the genomes of its first 10 participants, the PGP-10, but scaling up to 1,000 for this second project isn't the end of the process. PGP plans to eventually sequence 100,000 genomes, though Oppenheimer admits that significantly more infrastructure and processes will need to be put in place before that can occur.
"We do hope to be involved throughout that process as well, though," Oppenheimer says, noting that the initial sequence data being provided by the foundation will be key to building the infrastructure, understanding the necessary processes and gaining more support for the continuation of PGP-1K and ramp-up to future stages.
Other work that has been carried out by the foundation in support of the sequencing efforts has included the development of an online study guide to help people participate in the PGP, sponsorship of the first Genomes, Environments and Traits Conference and production of a documentary related to the PGP's efforts.
"We're a very small family foundation, and had been looking for an important area we could contribute to and really make an impact. About four years ago when I went to an MIT reunion, my wife and I met with Dr. Church, and he was very welcoming to us and sat down to explain what they were doing, and it seemed like a good fit," Oppenheimer says. "My wife and I are both computer scientists, not life science researchers, but the project had a lot of appeal to us. DNA is a lot like computer code, when you get down to it."
The foundation was launched in 2007, with the goal of leveraging the knowledge and resources the Oppenheimers accumulated over 25 years in the computer industry. As Alan Oppenheimer notes, they saw the growing interdependency among science, computers, and the Internet standing out as providing a number of opportunities for that leverage, so they have made a goal of focusing on the fields of genetics, molecular biology and computer science—and the intersections of these fields.
The mission of the PGP is to encourage the development of personal genomics technology and practices that are effective, informative, and responsible; yield identifiable and improvable benefits at manageable levels of risk; and are broadly available for the good of the general public. Church has emphasized that the PGP's mission is best served by soliciting input and promoting openness and collaboration from the very start to ensure that the different threads of personal genomics are all individually addressed and reinforce each other as they come together.