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Gloria Oh/MEDILL

Northwestern University's genetics community offers insight into the $1,000 genome and dropping costs as well its its implications on clinical application.

Beyond the thousand-dollar human genome

by Gloria Oh
Jan 12, 2012


National Human Genome Research Institute

Data presented by the National Human Genome Research Institute reveals that the cost of DNA sequencing is falling at a faster rate than Moore's Law.

Life Torrent

Gloria Oh/MEDILL

Northwestern University's Genomics Core Facility lab uses various DNA sequencers, including this one made by the same company developing the Ion Proton Sequencer.

A U.S.-based biotech company has developed technology to sequence the human genome in a day for the long-awaited thousand-dollar benchmark. But prices will continue to drop over time, a strong marker that the road to democratizing the genetic revolution is fast under way, experts say.

Ion Torrent, the startup company acquired by Life Technologies Corp., unveiled the Benchtop Ion Proton Sequencer, at the Consumer Electronics Show in Las Vegas Tuesday. The chip in the Ion Proton is 1,000 times more powerful than its predecessor, said Jonathan Rothberg, the founder and CEO of the Ion Torrent division.

“It was a nice surprise,” said Nadereh Jafari, director for Genomics Core Facility of Northwestern University’s Feinberg School of Medicine, which uses rival sequencing equipment from Illumina and SOLiD systems. “We were waiting for something to come out from other companies.”

True to Moore’s Law, a concept derived by Gordon Moore, co-founder of Intel, the price of whole-genome sequencing has inevitably fallen as higher hardware capacity leads to reduced costs. Moore stated that the number of semiconductor parts on a chip doubles around every two years, so prices go down.

But perhaps even more telling of the road to a genetically enabled future is data presented by the National Human Genome Research Institute, a division of the National Institutes of Health. According to the agency, data from its large-scale genome sequencing program showed that a threshold had been found in which the cost of genome sequencing was falling at a faster rate than Moore’s Law (see chart).

“I think we’ll eventually head to a zero-dollar genome,” said Atul Butte, associate professor and division chief of systems medicine in the department of pediatrics at Stanford University School of Medicine. “You could imagine a negative genome in the future, where the insurance pays for your genome sequence.”

He compared plummeting DNA sequencing costs to receiving lower car insurance rates when taking preventative measures such as a driver’s course.

Clifford Reid, chairman, president and CEO of Complete Genomics, a rival company in Mountain View, Calif., said that the announcement of a $1,000 genome was somewhat misleading. “There are four major costs in DNA sequencing,” he said. They include DNA consumables cost – including the chip that will be used on the sequencer as well as DNA preparation – as well as the cost of the instrument, labor and overhead.

“One thousand dollars is the cost of the consumable just on the instrument. It doesn’t represent the total cost of sequencing a genome,” he said. Assuming that all other aspects of sequencing were incorporated, it would cost a grand. “The problem is everything else isn’t free.”

Yet Reid said he believes that whole-genome sequencing is available for widespread use. Complete Genomics offers its sequencing services for $4,000, which includes computing as well as data processing of six billion bases in a human’s DNA.

“It might be true that the chemistry behind getting a genome sequence is $1,000, or will soon be a $1,000, but we all laugh about the $1,000 genome and the $100,000 analysis that has to go along with it,” said Rex Chisholm, the dean for research and professor of medical genetics at Northwestern University’s Feinberg School of Medicine. “That’s the reality of where we are today.”

But he said that progress was being made, citing NUGene Project’s collaboration with the National Human Genome Research Institute in creating a centralized repository to capture genetic variants that are linked to known diseases.

The implications of affordable genomes entering the clinical realm are still being debated, and the daunting task of interpreting the genetic DNA is an area of concern among geneticists.  

“The use of DNA sequencing as a clinical tool is very much in the research state, and the new instrument will be no exception,” said Mark Guyer, deputy director of the National Human Genome Research Institute. “I would say that so far, no sequencer has generated data that is of the accuracy that’s needed for clinical analysis at least with respect to whole genome sequencing where you might be looking for variants that you’re not expecting.”

“Even rarer than medical geneticists who know how to use the information are people who know how to do the analysis,” Chisholm said.

While cheaper sequencing is on the rise, geneticists now face an onslaught of issues, whether it’s matching the pace of technology in analyzing the genetic information or grappling with the costs of interpreting genomes as well as storing them, which Butte says may take up quite a bit of space.

“There’s no place to put the hard disk,” Butte said. “If we were to save a short-reads per patient, it would be a terabyte of information. It would be cheaper to re-sequence and retrieve a person’s DNA at a trivial zero-genome cost then to store the sequence.”

Yet such issues pale in comparison to what the future holds for genomic medicine, where personalized treatment based on an individual’s genes may one day become reality.

“There are tremendous forces in the community right now to try to figure out how to do this responsibly,” said Bradley Ozenberger, program director of National Human Genome Research Institute. “It’s a fantastic time, really exciting.”