How Will Genetic Sequencing Technology Play Globally?

Posted by Brian Buntz on November 12, 2012

Image from Flickr: http://www.flickr.com/photos/95135261@N00/116028995/sizes/s/in/photostream/Noninvasive prenatal testing is “an unbelievable test case” for how genetic sequencing technology can influence human healthcare, said John Stuelpnagel, DVM, executive chairman of Ariosa Diagnostics (San Jose) and co-founder of Illumina (San Diego) at a panel discussion held on November 8 in San Francisco. Over the course of the next 10 years, sequencing technology will likely be used for a quickly growing number of healthcare applications, Stuelpnagel predicted. As the technology gets faster and less expensive, new markets for sequencing technology open up. “It will probably start with very serious illnesses [such as those] associated with early childhood disease and cancer where these people are very sick and they have exhausted a lot of their diagnostic testing options,” he said. “It will influence their healthcare very quickly” and profoundly alter the course of human health testing.

Genetic sequencing technology is advancing so quickly, that it is outstripping even Moore’s Law. To get a sense of the scale, consider that sequencing the first human genome cost roughly $3 billion. That amount is roughly the cost of sending up the Mars Rover, explained Gregory Heath, PhD, senior vice president and general manager, diagnostics at Illumina. “Imagine if in about 10 years you could send up a Mars lander for about $10,000,” he said. “People would be doing that in their backyard.” The costs of genetic sequencing have fallen by an order of magnitude in the past decade, he pointed out. Just last year, Illumina began offering human whole-genome sequencing services at $4,000 for projects of 50 samples or more.

A picture of the panel discussion, in which the panelists (shown on the right-hand side of the table) asked questions from journalists. Picture from @HarmonyPrenatal

Other panelists at the event included Jay Shendure, PhD of the University of Washington; and Mary Norton, MD, professor of obstetrics and gynecology at Stanford University. The panel was moderated by Ken Song, MD, CEO of Ariosa Diagnostics.

Genetic sequencing ultimately is poised to become a pervasive technology like PCR with a broad scope of applications. Heath divided the applications of genetic sequencing technology into four broad groups: detecting genetic disease—reproductive genetics in particular; cancer; infectious disease; and transplantation.  

“Cancer is probably the sweet spot where you have got great alignment of performance characteristics around the technology to the parameters of the disease,” Heath added. “There are a lot of commonalities between cancer and prenatal testing.”

The technology has recently become sufficiently fast and cheap that it could be soon used for infectious disease applications. “Certain things like fungal infections are very difficult to culture and you can sequence through them,” he explained.

“A transplant decision from a donor for an organ is made within 24 hours. For bone marrow, it has got to be a little bit cheaper,” he said. “You’ve got more time to match people up but you still need to be relatively inexpensive.”

Ultimately, genetic sequencing could become similar to blood testing in terms of how common it is. “If sequencing cost five dollars, every time you go into the hospital, you are going to get sequenced,” Heath said. “You might even use it at home to see if, say, this milk is still good,” he joked.

In the shorter term, there could be surge in the applications for the technology in reproductive genetics. Related to that point, Illumina recently acquired UK-based Blue Gnome, a firm that plays in the in vitro fertilization space. "One of the applications of what they do is pre-implantation genetic screening. They are actually testing embryos before implantation," Heath said. The testing could be used to determine which embryos are best suited for implantation and which should be discarded because they would likely result in a miscarriage.

Where Does Sequencing Technology End Up?

In terms of scaling globally, currently the vast majority of all of the clinically relevant tests operate through a CLIA laboratory. They are centralized laboratories that have to be validated, Ken Song, MD pointed out. So the question becomes: how close does sequencing need to be to patients?

“My own belief is that the application tells us where it should be done,” Stuelpnagel said. “The applications for infectious disease and preimplantation genetics require very quick turnaround and probably have a rationale for very near patient testing. For other things like whole genome testing for cancer diagnostics of [...] and non-invasive prenatal testing—a turnaround time of three to seven days makes no clinical difference and so the economies of scale and the ability to reduce cost are greater drivers towards centralization.”

Another consideration is sample prep—“the upfront part of getting a tube of blood and getting into a condition that you can pipette onto a sequencer,” Heath said. “That part is still pretty labor intensive.” Another factor is the relative scarcity of medical technologists, which is increasing the need for automated prepping.

The other consideration is the interpretation of the massive amounts of data generated through sequencing. “Again, we don’t have enough bioinformatics experts out there. If I was in college, I would try to major in that,” he added. “We are going to have cheap sequencing. We are going to have relatively inexpensive and quick sample prep but [the lack of bioinformatics] is going to burden,” he predicted.

Acknowledging these hurdles, the global uptake of genetic sequencing technology will likely be rapid, Heath predicted. “The rate genomics technology is adopted clinically could be helped by automation technology and the broader tech field. Companies like Illumina are essentially taking biological information and digitizing it, Heath said. “And there are a lot of people who know how to deal with digital information.”

Brian Buntz is the editor-at-large at UBM Canon's medical group. Follow him on Twitter at @brian_buntz.