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The $1,000 genome: the future has arrived


The race for affordable sequencing has been won and with it the promise of a health revolution. Elizabeth Finkel reports.


The rate of innovation in sequencing the human genome has been breathtaking.

This January, the future arrived. The long-running race for the $1,000 genome was finally called with hot favourite Illumina, a San Diego-based company, pulling ahead of competitors like Complete Genomics and Ion Torrent to announce it had “broken the $1,000 barrier”.

When it comes to accurately reading the sequence of billions of letters of DNA faster and cheaper, the rate of innovation has been breathtaking, easily outpacing that suggested by Moore’s Law which observes that computer processing power doubles every two years. It cost $3 billion and took 14 years for a global consortium to read the first human genome in 2000. By 2009 Illumina was charging $48,000. Now its new Hi Seq X ten sequencing machine will read a human genome for $1,000 and process 16 of them in three days.

Many are enthralled by the medical possibilities. “Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine,” said Eric Lander, director of the MIT and Harvard genomics centre at the Broad Institute in Boston.

At $1,000, the cost of having your genome read is not that much more than a lap top computer, and the price will only continue to fall. Moreover, you only have to fork out the expense once. So what can we expect in the era of the $1,000 genome? Are we on the verge of Gattaca, the 1997 movie that envisaged a future where every baby had their genome read, and on the back of it, their destiny ordained?

Maybe.

When it comes to predicting diseases caused by a single malfunctioning gene, we’re getting pretty good at it. In these cases, reading genomes is already having an impact.

Two companies Counsyl and Good Start Genetics will read the genomes of you and your partner and let you know if it’s a good idea. One per cent of all babies are born carrying a genetic defect and DNA tests can so far pick up about 3,000 of them, and the number is going up all the time.

Another company, Verinata, bought by Illumina last year, can detect the defects in a baby’s DNA even before it is born by testing the mother’s blood. So far the company offers tests for particular conditions such as Down’s Syndrome but it probably won’t be long before the company offers a reading of the entire foetal genome.

Genomes are also proving their worth to people living with an undiagnosed genetic disease. According to Richard Gibbs, the Australian-born director of the Human Genome Sequencing Center at Baylor College of Medicine in Texas, a third of patients having their genomes sequenced find the underlying causes. “Genome sequencing is streaming into the clinic in a way that’s blinding,” he says.

Common diseases are complex, meaning they are not
caused by a single gene but many.

Sometimes solving the mystery leads to treatments as in the case of the Beery twins, Noah and Alexis. The children suffered breathing and movement difficulties. Finally at the age of 13 their genomes were read at Baylor College and the underlying cause traced to a mutation in a gene called sepiapterin reductase. That clued the clinicians into realising that the children were in need, not just of dopamine, which they were already receiving, but serotonin. The children are now well, says Gibbs, so well that Alexis wins athletic events.

But while reading genomes is making its mark for rare, severe illnesses, it’s a different story for common diseases. What was always true remains true: common diseases are complex, meaning they are not caused by a single gene but many. Schizophrenia (which affects about one in 100 people), for example, has a large genetic component: whether or not you develop it is 80% determined by the genes you inherit. But according to a paper in Nature Genetics last October by Stephan Ripke and colleagues, there appear to be thousands of schizophrenia-related genes, all coming together in different combinations to cause the disease. For now, that complexity makes the Gattaca scenario unlikely. It is beyond our ability to predict common characteristics from a genome, be it schizophrenia or even a person’s height. But there is one common disease, where reading genomes is leading to useful predictions: cancer. The rampant growth of cancer cells is accelerated by mutations in genes but each cancer can be driven by different genes. Researchers have been reading the genomes of cancers to find out just what those accelerator genes are. And when they find them, they can sometimes pull a drug off the shelf that will turn them off.

This approach is starting to yield dividends for pancreatic cancer, one of the most difficult to treat. Indeed one of the first three customers for Illumina’s $20 million HiSeq X Ten is the Sydney-based Garvan Institute which is part of a global consortium for identifying genes that drive cancer.

We may not be in the world of Gattaca yet but what about the future? Ever cheaper genome sequencing means that millions will be read, and that will bring the possibility of decoding common diseases within reach.

“We can expect major advances in our ability to explain the genetic component of disease risk and thus to predict disease. What we do with that information is a sociological concern with major public health implications, and now is the time to contemplate the implications,” say geneticists Peter Visscher at the University of Queensland and Greg Gibson at Georgia Institute of technology, Atlanta.

The full impact of the $1,000 genome can’t yet be known, but the changes promise to be profound. As sci fi author William Gibson put it, “human social change is more directly driven by technology than by ideology”.

Ella finkel twic.jpg?ixlib=rails 2.1
Elizabeth Finkel is editor-in-chief of Cosmos.
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