An intrepid group of volunteers will be granted a glimpse at their genomes today as part of the first release of data from the Personal Genome Project (PGP).
Headed by Harvard University genomics pioneer George Church, the project aims to capitalize on rapid improvements in gene-sequencing technologies to better understand human health and disease. The PGP will serve as both a technological and an ethical test bed, assessing new methods of reading, sorting, and analyzing DNA, and highlighting societal issues that could spring up in the era of personal genomics–most notably, the privacy of genetic information.
Over the past year, the first 10 volunteers, including the linguist Steven Pinker, the entrepreneur Esther Dyson, and Church himself, have surrendered blood and skin samples, subjected themselves to medical examinations, and filled out extensive personal and medical questionnaires. Scientists have since gone to work sequencing their DNA, and an initial analysis of a portion of their genomes will be released today.
The data will be deposited into a database that Church and his collaborators hope will serve as a public resource for personal-genomics research, allowing other scientists to search for specific genetic variations linked to diseases and other traits. The researchers aim to grow the database rapidly and are now enrolling the next wave of volunteers, possibly as many as 100,000 participants. They are also creating cell lines from participants’ tissue samples, which they will make available for research.
Church envisioned the PGP as a way to explore the ongoing revolution in gene-sequencing technology. Over the past 10 years, the cost of sequencing has plummeted: current estimates for a human-genome sequence are approximately $100,000, compared with the $3 billion price tag for the Human Genome Project. By some reckoning, the price could fall to between $5,000 and $10,000 per genome within the next six months. Church and others predict that the capacity to sequence thousands and then millions of human genomes could transform not only medicine but also society. “We went from complete ignorance of computers in the 1970s to complete dependence today,” says Church. “You can imagine something analogous for DNA.”
To date, most large-scale studies of the genomics of disease have focused on specific portions of the genome, uncovering hundreds of variations that raise the risk of common ailments, including diabetes, heart disease, and schizophrenia. But these variations account for only a small increased risk. Scientists hope that sequencing entire genomes will allow them to identify much rarer, disease-linked variations that have not been detected previously.
The PGP is focusing first on the coding regions of the genome (the portions that direct the production of proteins), which accounts for about 1.5 percent of the entire sequence and covers 20,000 genes. Joseph Thakuria, the PGP’s medical director and a clinical geneticist at Massachusetts General Hospital, in Boston, says that the sequencing of 20,000 genes in a patient is remarkable. With current clinical diagnostics, it’s possible to test only about 1,370 genes, and patients get at most two or three, he says.
Perhaps the biggest challenge for the project will be interpreting differences in individual genomes. Human genomes are about 99.5 percent identical, and variations in the rest can have a range of effects, from lethal to benign. In preparation, Thakuria and his colleagues pored over the only two full human-genome sequences that are publicly available: those of Craig Venter, who led the private sector’s race to sequence the human genome, and James Watson, codiscoverer of the structure of DNA. Thakuria’s analysis and that of others have found that each man has about three million base-pair changes out of the three billion chemical letters that make up their genomes.
The first 10 PGP volunteers are unlikely to receive any shocking news in their initial analyses. According to medical records available on the PGP site, they are a largely healthy group. Narcolepsy, asthma, depression, and basal cell carcinoma are some of the more serious conditions suffered by the so-called PGP 10. And at ages ranging from 44 to 59, none have suffered serious, early-onset genetic diseases.
The participants are more likely to learn that they are at a modestly increased risk of some common diseases. John Halamka, chief information officer at Harvard Medical School, got an early peek at his genomic information and discovered that he has double the average risk of obesity. “Even with this imperfect screening tool, if someone had told me 10 years ago I was at twice the risk of obesity, I would have stopped the cheeseburger, doughnut, and two lattes a day habit much earlier,” says Halamka. (The now slim physician was inspired to make lifestyle changes several years ago for other reasons, and is now a vegan who makes his own tofu and weighs 100 pounds less than he did at his heaviest weight.)
Open access to medical information is one of the most unique aspects of the PGP. The project website carries stripped-down versions of each of the PGP 10’s medical records. “It shows my height, my weight, every drug I’m on,” says Halamka. While the records are currently anonymized, it is fairly easy to deduce from birth dates and other details the identity of each individual.
The participants will decide today whether they want to make their genetic information and complete medical records public on the PGP website. “We might be called medical exhibitionists, pioneers, or cavalier,” says Halamka. Steven Pinker’s record already includes his name. For those who are curious about the world-famous linguist, professor Pinker has a pulse rate of 51 and is prone to “occasional swelling and blistering of toes after winter walks.”
Because participants’ medical records are collected along with their DNA, scientists will be able to search the database for links between genotype and phenotype. Other whole genome sequencing projects, by contrast, such as the internationally funded 1000 Genomes Project, will collect only genetic information. That project is intended to compare different sequencing technologies and document just the baseline variation in the human genome.
Church has emphasized open access throughout the development of the PGP. He argues that it is difficult to promise research subjects anonymity when the data being collected includes genetic information–the ultimate personal identifier–and medical records, which can often be used to identify an individual.
Not everyone thinks that the PGP model is the best approach to personal-genomics research, however. “It’s interesting and thought provoking,” says Francis Collins, former director of the National Human Genome Research Institute. “It’s one thing to get people more comfortable with the idea [of having their genomic information made public], but it’s another to ask them to give up any shred of privacy.”
Still, the project seems to have captured the public’s attention. Researchers have already received thousands of letters of interest for the next phase of the project. Volunteers will have to pass an online test assessing their knowledge of genetics, of the experiment, and of its potential risks. Participants will also be asked to help with fund-raising for the project by partially subsidizing their sequencing with a $1,000 donation.