October 14, 2004
NHGRI Aims For $100,000 Genome Sequencing Cost In 5 Years

The US government's National Human Genome Research Institute (NHGRI) is allocating $38.4 million dollars over the next few years to development of cheaper DNA sequencing technologies (and FuturePundit thinks this is still too little, too late).

BETHESDA, Md., Thurs., Oct. 14, 2004 The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), today announced it has awarded more than $38 million in grants to spur the development of innovative technologies designed to dramatically reduce the cost of DNA sequencing, a move aimed at broadening the applications of genomic information in medical research and health care.

NHGRI's near-term goal is to lower the cost of sequencing a mammalian-sized genome to $100,000, which would enable researchers to sequence the genomes of hundreds or even thousands of people as part of studies to identify genes that contribute to cancer, diabetes and other common diseases. Ultimately, NHGRI's vision is to cut the cost of whole-genome sequencing to $1,000 or less, which would enable the sequencing of individual genomes as part of medical care. The ability to sequence each person's genome cost-effectively could give rise to more individualized strategies for diagnosing, treating and preventing disease. Such information could enable doctors to tailor therapies to each person's unique genetic profile.

DNA sequencing costs have fallen more than 100-fold over the past decade, fueled in large part by tools, technologies and process improvements developed as part of the successful effort to sequence the human genome. However, it still costs at least $10 million to sequence 3 billion base pairs the amount of DNA found in the genomes of humans and other mammals.

"These grants will open the door to the next generation of sequencing technologies. There are still many opportunities to reduce the cost and increase the throughput of DNA sequencing, as well as to develop smaller, faster sequencing technologies that meet a wider range of needs," said NHGRI Director Francis S. Collins, M.D., Ph.D. "Dramatic reductions in sequencing costs will lead to very different approaches to biomedical research and, eventually, will revolutionize the practice of medicine."

In the first set of grants, 11 teams will work to develop "near term" technologies that, within five years, are expected to provide the power to sequence a mammalian-sized genome for about $100,000. In the second set, seven groups will take on the longer-term challenge of developing revolutionary technologies to realize the vision of sequencing a human genome for $1,000 or less. The approaches pursued by both sets of grants have many complementary elements that integrate biochemistry, chemistry and physics with engineering to enhance the whole effort to develop the next generation of DNA sequencing and analysis technologies.

"These projects span an impressive spectrum of novel technologies from sequencing by synthesis to nanopore technology. Many of these new approaches have shown significant promise, yet far more exploration and development are needed if these sequencing technologies are to be useful to the average researcher or physician," said Jeffery Schloss, Ph.D., NHGRI's program director for technology development. "We look forward to seeing which of these technologies fulfill their promise and achieve the quantum leaps that are needed to take DNA sequencing to the next level."

Note that to get from $10 million to $100,000 per genome in 5 years would be a 2 order of magnitude drop that would be almost as much of a drop in scale as happened in the previous 10 years. But maybe the various research teams can pull it off.

To get to the $1000 genome requires a further 2 orders of magnitude drop in costs. Note that the press release provide any indication of when that goal might be reached. You click through and read the full press release and you will notice that the bulk of the funding ($31.5 million by my calculations) is for achieving the short-term $100,000 genome goal. Much smaller amounts of money are allocated toward the development of technologies that will enable much more radical advances. This seems like a mistake to me.

In my opinion too much money has been spent on using sequencing technologies and not enough on developing new sequencing technologies. Even this $38 million is not much for development of new sequencing technologies since on a per year basis it amounts to well less than $20 million per year (it is hard to calculate an exact amount since some of the grants are 2 years and some are 3 years). When the federal government is spending many hundreds of millions per year (I'm too lazy to look up NHGRI's total yearly budget but this is a very small fraction of it) using sequencing technologies that are orders of magnitude more expensive than what we could have in a few years then it seems obvious to me that the money spent over the last few years on sequencing should mostly have gone to develop cheaper technologies. The focus on short-term results by using current technologies is very unoptimal.

Update: To put the spending for faster DNA sequencing techniques in perspective the National Human Genome Research Institute has a total budget of almost a half billion dollars.

Mr. Chairman, I am pleased to present the President's budget request for the National Human Genome Research Institute for fiscal year 2005, a sum of $492,670,000, which reflects an increase of $13,842,000 over the FY 2004 Final Conference appropriation.

The National Institutes of Health are spending over $28 billion per year.

President Bush yesterday (February 2) sent to Congress a $28.6 billion budget request for the National Institutes of Health (NIH) in fiscal year 2005, a 2.6% increase of $729 million over the current year's funding. The National Science Foundation (NSF) would receive a 2.5% increase of around $140 million to $5.7 billion, but the Centers for Disease Control and Prevention (CDC) would be cut by 8.9% to $4.3 billion, a reduction of $408 million.

Aside: As the baby boomers begin to retire and an enormous fiscal crisis erupts I expect total NIH spending will go down, not up. More money will go toward treating the already sick with existing technologies rather than doing the scientific research and technological research that could so revolutionize medicine that people will rarely get sick.

One reason that biomedical scientists ought to get on the aging-reversal rejuvenation SENS (Strategies for Engineered Negligible Senescence) bandwagon is that when the fiscal crisis erupts medical and biological researchers need to have a rosier future achievable by research to sell to the public. Nothing less than an incredibly rosy scenario of rejuvenation and the end of most diseases will be enough of an enticement to keep the research bucks flowing and growing when the strains on the US federal budget become enormous.

Share |      Randall Parker, 2004 October 14 02:06 PM  Biotech Advance Rates

Toby Sargeant said at October 14, 2004 5:24 PM:

Incremental improvements shouldn't be sneezed at, especially when they deliver order-of-magnitude scale improvements. As an example, it's doubtful that we would have access to quantum computing now if Intel et al. had decided to invest all their efforts in that direction, instead of slavishly shrinking feature sizes.

Until there is a new sequencing technology on the horizon (and yes, looking for such technology should be funded) then working on the 'easy' problems of improving chemistries and robotics to increase the speed and quality and decrease the cost of sequencing are very important; we simply don't know how long it will take to come up with something fundamentally better. Some time ago I heard of a quantum optical technique which was supposed to be going to allow one to read bases off a strand of DNA directly ~100kb at a time. Since then, I've heard nothing. Given that I work close to the area, there's a reasonable chance I would have heard about anything that was getting close to being commercially applicable.

Also worth pointing out is the fact that sequencing the genome of a new species is not the same problem as sequencing the genome of a new instance of a pre-sequenced species. From my reading, one of your primary reasons for wanting cheap sequencing is so that it becomes practical to sequence an individual's genome for medical purposes. Affymetrix have already started to produce resequencing kits that rely on the fact that amongst humans, differences are small enough that the saquencing can be done using hybridization to permutations of the already known sequence. At the moment this is restricted to small portions of a genome, but they predict that one or two iterations of the technology will result in a single chip that will resequence an entire human genome. Given that Affy chips tend to cost about $1k each, your goal should be achieved soon. This is another example of optimization of an existing technology paying off much much faster than looking for an entirely new paradigm.

Randall Parker said at October 14, 2004 5:38 PM:


I get that the technologies for testing SNPs are not an exact overlap with the technologies for doing sequencing of "virgin" genomes. However, SNP testing does not provide a complete picture of sequence differences. There are the large-scale copy variations, or LCVs, and probably other sequence differences such as deletion mutations that are not going to get caught by SNP testing.

Now, maybe some of the SNP testing technologies can be adapted to work for LCV, deletion, and other genetic variation testing. I don't know. Or perhaps what is needed are more grants from NHGRI for the development of tests for these other types of genetic variations.

Yes, I get that there is a lot of bang for the buck in going for improvements on existing processes with robotics and other approaches. I just think there ought to be far larger pushes for more revolutionary advances in instrumentation that can enable much greater leaps in our understanding.

Michael Seaman said at October 28, 2004 11:32 AM:

Interesting article. I disagree with the prediction that NIH spending will do down, so we can spend more money on existing treatments. Despite the tone of your article, most of the NIH spending is directed towards developing better drugs and treatments that will affect patients in the near future. NHGRI spending is less than 2% of total NIH budget, according to your figures.

To take one example from the present, the federal government spends about $15 billion annually, through Medicare, for kidney dialysis (most recent figures I could find were 2001). This number will skyrocket in the next twenty years as the population gets older, more obese, and more diabetic. We can either keep throwing money at this existing treatment, or spend a tiny fraction of that on research to cure or prevent the disease, or at least on better treatments. It would be a mistake to cut the research money in favor of just more of the same.

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