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Low-cost personal DNA readings are on the way

by Peter AldhousNew Scientist
September 6th, 2007

"GENETICS is about to get personal." So proclaims the website of 23andMe, a Californian company that is gearing up to offer people a guided tour of their own DNA. For the superstars of genetics, it has already got personal. Earlier this week, genomics pioneer Craig Venter revealed an almost complete sequence of his genome, while that of James Watson, co-discoverer of DNA's double-helix structure, has been available on the web since late June.

Given that Watson's genome took almost $1 million to read, most of us won't immediately be following in his and Venter's footsteps. It isn't necessary to read your entire genome, however, to browse many of the genetic variations that may influence your health. According to George Church, a geneticist at Harvard Medical School in Boston, the most pertinent information could be gleaned by sequencing the 1 per cent of the genome that codes for proteins. Thanks to the advances in sequencing technology, that might be done for as little as $1000 per person. "DNA chips", meanwhile, can scan your genome for common "spelling mistakes" for just a few hundred dollars. At that price, the era of personalised genomics is already dawning. "This is the year," claims Church.

To push the field forward, Church has launched the Personal Genome Project (PGP), in which he and nine other volunteers have signed up to have the protein-coding regions of their genome made available on the web, along with their medical records, photographs of facial features and the results of a questionnaire about their health and personal habits. Within a few months, he aims to start scaling up to 100,000 volunteers.

Church is also an adviser to both 23andMe - named for the number of chromosome pairs in the human genome - and Cambridge Genomics, two of the firms hoping to turn personalised genomics into big business. But is the world ready for their services? As well as raising questions about the protection of personal genetic data, there are concerns about how people will use information that, at this stage, even trained medical geneticists find extremely difficult to interpret.

"The really big thing is for medicine and biology to catch up," says Michael Egholm of 454 Life Sciences in Branford, Connecticut, which provided the technology used to read Watson's genome. "We're going to have routine genome sequencing long before physicians know how to make any sense of it."

Church's PGP is intended in part as a resource to help researchers investigate the biological consequences of individual DNA sequence variation. To facilitate this, the relevant genetic, medical and lifestyle information will be placed in a public database. Church does not intend to include the names of the 100,000 volunteers, but he will warn them that it may be possible for them to be identified from the information that they provide.

For this reason, the PGP is drawing up procedures for obtaining informed consent, detailing ways in which participants' personal information might, in theory, be misused. These range from discrimination in employment or insurance to more fanciful scenarios such as someone synthesising DNA that matches part of your genome, then planting it at a crime scene. The project will even have an entrance examination to ensure that people understand the potential risks of participating. Further raising the motivational bar, volunteers may be asked to pay up to 20 per cent of the cost of sequencing their DNA.

Even so, some observers have reservations about the motivations of those who may take part. "Putting your DNA out there for the whole world to see appeals to people who have a molecular exhibitionist streak," suggests Kathy Hudson, who heads the Genetics and Public Policy Center in Washington DC. She and other experts consulted by New Scientist nevertheless agree that the PGP should be a valuable project. "On balance, I applaud what George is doing," says Richard Gibbs, director of the Human Genome Sequencing Center at Baylor College of Medicine in Houston, Texas.

Roadmap to health?

More controversial is the idea of companies providing paying customers with access to information about their own genomes. 23andMe - co-founded by Anne Wojcicki, wife of Google mogul Sergey Brin - is the best known. Based in Mountain View, California, the company plans to launch by the end of the year, and until then is keeping quiet about exactly what services it will provide. Informed sources expect it to concentrate initially on scanning customers' genomes for common genetic variants called SNPs - single-letter variations in our personal genetic code that are sometimes associated with disease. 23andMe's customers will also be able to share genetic information via web-based social networking - likely to appeal to people interested in using genetic data to help trace their family trees.

Navigenics, based just a short distance away in Redwood City, also intends to analyse customers' SNPs, but is more clearly focused on medical applications. "Your genes offer a roadmap to optimal health," claims its website, which includes a video explaining how customers can submit saliva samples and receive a read-out of their genome in return, with an explanation of what it means.

Massachusetts-based Cambridge Genomics, meanwhile, intends to move directly into DNA sequencing. Initially, customers can expect to pay around $40,000 for sequences of regions thought to be most relevant for health, rising to more than $1 million for a high-quality sequence of their entire genome. These costs will come down as sequencing technology continues to improve (see "Towards the $1000 genome"). Other companies are focusing on different aspects of "genome health", such as variations in our ability to repair DNA (see "Chromosome repairs").

Unlike Church's PGP, personalised genomics companies promise to keep prying eyes away from customers' genetic information - so one challenge lies in protecting the data from hackers. But the bigger concern, say geneticists, is how personal genomic information will be presented to customers, given our limited ability to interpret it at present (New Scientist, 19 August 2006, p 28).

Venter's genome, described in detail in PLoS Biology (DOI: 10.1371/journal.pbio.0050254), shows how far we have to go to fully understand the consequences of individual genetic variation. Researchers at the J. Craig Venter Institute in Rockville, Maryland, found 4.1 million differences between their boss's genome and the "reference" human sequence held by the US National Center for Biotechnology Information - around 30 per cent of which were new to science. Most of Venter's departures from the reference sequence were SNPs, but 22 per cent involved larger deletions, insertions, or other rearrangements of DNA.

The biological significance of most of these variants is unknown, and even looking at those that have been associated with definite traits (see Table) gives a confusing picture. For instance, SNPs in the gene LCT indicate that Venter should be able to tolerate the sugar lactose. In fact, he suffers from lactose intolerance, which is presumably due to the modifying effects of other genes, or to environmental influences.

Nevertheless, Venter is pleased with what he learned from his sequence. For instance, certain SNPs may put him at increased risk of cardiovascular disease and Alzheimer's. This, coupled with the knowledge that his father died of sudden heart failure, has led Venter to start taking a statin drug, which can help prevent both conditions.

Venter is in a privileged position when it comes to interpreting his personal genetics. "I could see that the information could have a very different impact on a less well-informed person," he says. Some people might panic on learning that they possess genetic variants that increase the risk of Alzheimer's disease, for example.

This is no reason to hold back the tide of personalised genomics, Venter argues. "I think people, if they want to know, have a right to know," he says. "But with that goes a responsibility to provide the most complete and accurate information."

That responsibility falls most heavily on the companies now preparing to enter the field. "We're caveating everything we say, and we're trying to turn it into English that everyone can understand," says Ari Kiirikki of Cambridge Genomics. Venter argues that experts in genomics must share the task of educating the public about what they can learn from poring over their own books of life. Gibbs agrees. "We don't want to develop a culture of giving people half-baked genetic information," he says.

From issue 2620 of New Scientist magazine, 06 September 2007, page 8-11


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