A Sequencer for Every Clinic?


The Heliscope Single Molecule Sequencer

The Heliscope Single Molecule Sequencer

An idea that may be close to jumping from the world of science fiction to your local hospital is the concept of full, individualized genome scans – a personal genetic profile that could, at least in theory, help a doctor assess your risk for certain diseases and prescribe more effective treatment. That’s the prize a number of biotechnology engineers are currently chasing, producing a scientific race to invent quick, cheap and accurate sequencing machines that could open up a new world of genetic research and medicine. An important step was announced in that race this week, as a group based out of Stanford University detailed the sequencing of the 8th full human genome using a new machine with the delightfully sci-fi name of the Heliscope Single Molecule Sequencer.

The ultimate goal, laid out by the Genomics X Prize , is to invent a method that can sequence 100 human genomes in 10 days, at an average cost of no more than $10,000 per genome. The HSMS scan of Stephen R. Quake, one if the machine’s inventors, published in Nature Biotechnology this week, is said to have taken about two weeks and cost roughly $50,000 – still far from the X Prize standard. But by contrast, the sequencing of James Watson’s DNA in 2007 took 2 months and cost $2 million.

Kevin White, a professor of human genetics at the University of Chicago, said by e-mail that the HSMS demonstration was a ” a powerful demonstration of what can be done with the current technologies,” but points out that the Helicos sequencer is one of several machines, each with their own innovation that speeds up sequencing, to have hit the market recently. It’s also not a new effort: first proposed in a 2003 paper, the refrigerator-sized machine (which costs about $1 million) was used to sequence a viral genome last year.

However, White notes that even these new technologies are limited by the enzymes they use to indirectly deduce the ingredients of the DNA molecule. For the technology to truly achieve the speed and affordability necessary to be a clinical game-changer, White said, they must be capable of directly “reading” the base-pair language of DNA. 

“This ‘ultimate’ machine is what many of us are looking forward to, but in the meantime the current batch of next generation sequencers is enabling a vast array of new research to be performed by individuals or small teams of researchers who otherwise would not have access to genome sequencing,” White wrote. “Because of this, more focused and often more interesting questions are being asked than the days when genome sequencing was dominated by just a few centers. ”

[A very technical, but excellent, comparison of the HSMS with other sequencing technologies on the cutting edge can be found at the Genetic Future blog.]

In the meantime, doctors and patients have more time to grapple with a more abstract question: do we actually want to know what lurks in our genes?

In March, Quake did a blog post on the New York Times website about his reasons for sequencing his own genome, and this week told the newspaper that he had found a genetic variant associated with heart disease.

“You have to have a strong stomach when you look at your own genome,” Quake told reporter Nicholas Wade.

When personal genome scans become cheap enough to perform regularly for patients (an option experts estimate could only be a few years away), there is no doubt it will revolutionize medical care. The growing field of pharmacogenetics, where a patient’s genes are used to determine what drugs will be most effective for that particular person in treating their disease, would benefit immensely from fast, inexpensive genetic profiles of patients. 

But in an environment where many people already have difficulty finding affordable health insurance due to pre-existing medical conditions, the idea of giving insurers a genetic tip sheet for potential future illness – pre-existing medical conditions of a different sort – troubles many. Advances in genetic sequencing have also taught scientists that the links between genes and disease are not always clear cut, with only relatively rare diseases showing obvious genetic origins. Even if sequencing one’s genome becomes affordable in the next few years, it may be much longer before we understand that information well enough to make common medical decisions based on that data.

Such issues are thankfully already being discussed and even legislated – the Genetic Information Nondiscrimination Act, which forbids employment or insurance decisions based on genetics, was passed and signed by President George W. Bush last year. But as the Heliscope Single Molecule Sequencer signals that the promise of sequencing technology is accelerating, so too are the excitement and concerns surrounding personalized genetics on the fast track.

(For an excellent essay on the oddity of sequencing one’s own genome and the issues that personal genomics will soon create, read Steven Pinker’s article on his involvement with the Personal Genome Project from the NYT magazine in January.)

About Rob Mitchum (525 Articles)
Rob Mitchum is communications manager at the Computation Institute, a joint initiative between The University of Chicago and Argonne National Laboratory.
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