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The PGP 10: The first 10 volunteers in the Personal Genome Project are currently having the coding regions of their genomes sequenced; a small piece of sequence is shown for those whose data is posted online. The sequence data will be stored in a public database, along with the volunteers’ medical records and other information, such as their facial morphology (as measured by the forehead tapes). Scientists will use the database, which is expected eventually to include 100,000 people, to search for links between genes and diseases or other characteristics.

Harvard Medical School geneticist George Church, who has been working on sequencing technology since his PhD research at Harvard in the early 1980s, aims to speed that process along. Three years ago Church launched the Personal Genome Project (PGP), which aims to collect genetic and medical data from thousands of people over the next five years. The project indicates not just the technical and scientific challenges that might be posed by large-scale sequencing of human genomes, but the ethical issues as well.

In the pilot phase, the project will focus on 10 volunteers, including Church, Harvard psychologist Steven Pinker, and entrepreneur Esther Dyson. To start, it will sequence the coding regions of their genomes–the 1 percent of DNA that directs the production of proteins. That information, along with the participants’ medical histories (including prescription regimens) and information about their height, weight, handedness, and other traits, will be deposited in a public database. Church’s team hopes that this database will serve as a resource for scientists, or even members of the public, who want to search for links between specific genetic variations and diseases or other traits.

The first set of data–released to participants in October–hints at both the promise of sequencing and the current limitations of genetic analysis. John Halamka, CIO of Harvard Medical School and another one of the 10 original volunteers, learned that he carries a mutation for Charcot Marie-Tooth disease, an inherited neurological disorder. This rare variation would not have been found with existing SNP arrays. But since Halamka survived childhood unscathed, and only three other people in the world have been shown to carry that particular mutation, it’s hard to know what impact, if any, it has had on his health. Perhaps many people carry the variation with no ill effect, and the link between the disease and the mutation has been overstated. Or perhaps the gene has a broader impact than expected, raising the risk of other neurological diseases. (Or, as George Church notes, the finding may simply be an error.)

The greater the number of entries in the database, the easier it will be to understand a finding like Halamka’s. And in April 2008, Church’s team received approval from Harvard to expand the project from 10 to 100,000 participants. (Church plans to scale up slowly, multiplying the number of subjects by 10 each year.) This next phase will seriously test both the technology used to sequence the genomes and the strategies used to interpret the resulting data. As of November, about a year into the project, PGP scientists had gotten only about a fifth of the way through sequencing the coding regions of the original volunteers’ genomes. (Church plans to expand the PGP to the entire genome once sequencing becomes cheap enough.) If they’re to sequence thousands more genomes, sequencing technology will need to become as fast and robust as Church believes it can be.

Too Much Information
Making use of the data from the PGP will pose problems of its own. First, Church and his team will need to figure out the best way to give the larger group of volunteers their results. The first 10 received one-on-one genetic counseling from Joseph ­Thakuria, the project’s medical director and a clinical geneticist at Harvard Medical School. But Thakuria won’t be able to counsel the thousands of new subjects. Given the shortage of geneticists and genetic counselors with appropriate training, that problem is almost certain to be echoed much more broadly as personal genomics becomes more accessible.

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Credits: Justin Fantl, courtesy of
Video by Conrad Warre

Tagged: Biomedicine, Pacific Biosciences

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