Genome X Prize

The X Prize now has named Laurence Kedes of UCLA to lead the Genome X Prize.  Genome sequencing remains far too expensive, but is dropping quickly.  From their webpage:

The cost of DNA sequencing is decreasing by half every two years. Today it
  would cost $20 million and take six months to decode one entire human genome.

Who’s counting?

ANTONIO REGALADO. Prize for DNA Decoding Aims to Fuel Innovation. WSJ Jan 27, 2006.

Genome X Prize

Video Editorial on Personal Genomics

""Personalized genomics" — sequencing an individual’s genome so that
genetic vulnerabilities can be identified early — is a pipe dream
today: It would cost $10-$20 million per person. However, these new
sequencing technologies make it plausible that personalized genomics
will be feasible in the next few decades"

The statement "plausible that…[it] will be feasible in the next few decades" seems a wee bit on the conservative side of technological forecasts I’d say.

Anthony Komaroff. "Personalized Genomics" Gets Closer. Medscape. Feb 24, 2006.

Scientific American: The Personal Genome Project

George Church has the feature story in this month’s Scientific American.  He reviews a variety of sequencing technologies and introduces the Personal Genome Project to the masses.  Snip:

"…we have much work to do in a short amount of time to get ready for the advent of low-cost genome reading.  Software will be needed to process sequence information so that it is manageable by doctors, for example.  They will need a method to derive an individualized priority list for each patient of the top 10 or so genetic variations likely to be important…"

Some new stats on the current cost of sequencing from the article:

Electrophoresis-based sequencing = 150 base pairs per dollar for "finished" sequence
Polony method = 1400 base pairs per dollar

Scientificamerican_january2006

George Church. "Genomes for All" Scientific American, January 2006.

George Church’s page

Church on the Personal Genome Project

George Church of Harvard has an editorial on his Personal Genome Project in the recent issue of Molecular Systems Biology.  Snip:

From my first interaction with Wally Gilbert in 1976, it seemed that a large (but appealing) leap would be to go from his new method for sequencing 30 bp segments to a method to get everyone’s full genome sequenced. Six billion base pairs for six billion people had a nice ring to it. This was still merely a fantasy when we published a paper called ‘Genomic Sequencing’ in 1984 (Church and Gilbert, 1984) and conspired to create a 3 billion dollar HGP later that year (Cook-Deegan, 1989). For the subsequent 16 years, radical technology development (while kept alive in a few ‘back-rooms’) was clearly a minor funding priority relative to ‘production’ sequencing. However, by 2001, the criticisms of the old technology grew and the call for affordable personal genomes became irresistible (Jonietz, 2001). In early 2004, the NIH-NHGRI posted a request for applications, and in October 2004 and August 2005, announced grant awards totaling $70 million for technology leading to human genome sequences for $100 000 in 5 years and $1000 in 10 years (http://www.nih.gov/news/pr/aug2005/nhgri-08.htm). As if the motivation were not already high enough, at the recent Genome Sequencing & Analysis Conference in Hilton Head (October 18), the prospect of a new X-prize arose to encourage this new Personal Genomics field. (The first X-prize, $10 million for re-usable spacecraft, was awarded in October 4, 2005 and is followed by a $50 million prize for orbiting.) Amid all of this positive reinforcement, some key points were left fuzzy—What exactly is meant by sequencing a human genome? What is the utility of personal genomes? What are the ethical, legal, and social implications (ELSI)? The time has come to sharpen these points up. As we begin to purchase personal genomes, we want to know what we are paying for…

The utility of the first personal genome is analogous to the first fax machine, web page, or computer. Until communities of resources build up, these revolutionary new tools serve mainly the ‘early adopters’. These initial participants are heroes and human guinea-pigs paving the way for potentially increasing utility for the general public…

George Church. The Personal Genome Project. Molecular Systems Biology. Published online: 13 December 2005.


Metcalfeslaw3




Metcalfe’s Law




Venter Ups the Ante for the $1000 Genome

In October 2003, the inaugural post of this blog pointed to the announcement by Craig Venter of a $500,000 prize aimed at stimulating the development of sequencing technology that enables the drastic reduction of the costs of sequencing human genomes.  Today Venter announced plans to up the ante to as much as $10 million to speed the "race to the bottom" even more:

Noting that Solexa believes it can deliver a $10,000 genome by 2008, Venter said, “Our goal is really to have a $1,000 genome, but instead of having accountants tell us what it is, we’re going to require people to sequence maybe 100 genomes and really demonstrate the technology. So we’re trying to finalize the rules for this…
We’re thinking of a timeline that this has to be done sometime between 2008 and 2010. We’re trying to raise the prize value to reward the scientists that actually come up with these breakthroughs, not by calculation but by actual demonstration.”

Kevin Davies.  Venter Raises Stakes for “$1,000 Genome” Prize. Bio-IT World, Oct 19, 2005.

Visionaries Need Only Apply

Solexa: On track for $100K human genome

Solexa released a progress report on their genome sequencing platform.  They also claim to have the expectation of being "the first to deliver whole human genome
sequencing at $100,000 per genome."  They have memorialized this expectation in their about us section as follows:

"Solexa expects its first-generation technology to generate over a billion bases of DNA sequence per run and to enable whole genome resequencing below $100,000 per sample, making it the first platform to reach this important milestone. Solexa’s longer-term goal is to reduce the cost of human re-sequencing to a few thousand dollars"

As George Church has remarked, in the realm of genome sequencing technology, its a "race to the bottom."

Update: See also,
Kevin Davies. Solexa Sets Sights on “$100,000 Genome” Threshold. Bio-IT World. October 25, 2005.

Leroy Hood on the Future

Leroy Hood, tireless generator of good quotes (among other things):

My prediction is that within 10 years, we will have a predictive medicine that will have two separate components.

No. 1, it will have the ability to sequence every human’s genome for
less than $1,000. We will be able to make predictive health histories for each individual from the varying genes that come from that
sequencing.

Perhaps a better term than predictive health histories is
health futures.  Is it me, or does having health sandwiched between predictive and history feel claustrophobic?

No. 2, we will have a little hand-held nanotechnology device that
will prick your finger and make a thousand measurements and by
wireless, send that to a server. It will analyze all your past records.

It will say, "Nothing’s changed. You’re fine. Do it again in six
months." Or it will say, "Go see your oncologist or go see your
rheumatologist" or whoever might be appropriate.  Your physician would get an e-mail, too.

There’s more from Leroy:

Take into account that your genome and mine differ by 6 million
nucleotides…

We have to treat you differently than we treat me and everybody
else. How we create an era of highly personalized medicine will depend
entirely on new diagnostic, therapeutic and ultimately, these
preventive techniques.

What we’ll do is feed your genome sequence into a grid network of
computers that will do many different kinds of analyses simultaneously.
You’ll get a summary sheet that says here are the things and here are
the probabilities that you’ll likely have to worry about in the future…

Oh yeah, and this is good too..

It takes five years for people to get anything. The first few times
they hear it, they can think of a thousand reasons why it’s wrong.
Then, after they’ve heard it a few more times, it starts to sound more
logical.

If you’re a missionary, you’ve got to be patient with your
congregation. We are at the very beginning stages of thinking about
this.

Read the whole piece in the SeattlePI.

NHGRI Issues $32 million in grants toward personal genomics

Today the National Human Genome Research Institute (NHGRI) awarded $32 million toward innovative genome sequencing technologies that promise to bring down the cost of a human genome sequence to $1000.  In October of last year, the NHGRI awarded $40 million in grants for sequencing innovations that promise to bring down the cost of a human genome to $100,000 in the near-term. 

Cost Comparison for 1 Human Genome

Nicholas Wade from the NYT chimes in on the cost of genome sequencing…

A price tag of even $20,000 or so, which now seems attainable in the
next few years, would bring whole genome sequencing within the same
range as other medical procedures…

The first human genome to be completed, by the Human Genome Project in
2003, probably cost about $800 million. Doing a second human genome by
the traditional methods would now cost around $20 million. The two new
methods promise to be much cheaper. Dr. Rothberg says a human genome
could be resequenced now by his method for $1 million. Dr. Church
estimates that he can do a human genome for $2 million now and for
$20,000 in the future.

The two methods differ significantly in the price of equipment.

The DNA sequencing machine now being sold by 454 Life Sciences costs
$500,000. Jonathan M. Rothberg, chairman of the board, says a single
machine does the job of a $50 million sequencing center.

The Harvard machine is even cheaper…The most expensive element is a $140,000, computer-controlled digital
microscope…For labs that already possess such a
microscope, as many do, the equipment costs would be small. All they
need do is follow the free recipe provided by Dr. Church.

Nicholas Wade, 2 New Methods to Sequence DNA Promise Vastly Lower Costs, NYTimes, August 9, 2005.

$2 million per human genome

Not to be outdone by the recent article published in Nature by scientists at 454 Life Sciences, the polony folks at Harvard toss the following salvo:

The theoretical price of having one’s personal genome sequenced just
fell from the prohibitive $20 million dollars to about $2.2 million,
and the goal is to reduce the amount further–to about $1,000–to make individualized prevention and treatment realistic.

The sharp drop is due to a new DNA sequencing technology developed
by Harvard Medical School (HMS) researchers Jay Shendure, Gregory
Porreca, George Church, and their colleagues, reported on August 4 in
the online edition of Science. The team sequenced the E. coli
bacterial genome at a fraction of the cost of conventional sequencing
using off-the-shelf instruments and chemical reagents. Their technology
appears to be even more accurate and less costly than a commercial DNA
decoding technology reported earlier this week.

Press Release. "A step toward the $1,000 personal genome using readily available lab equipment." EurekaAlert. Aug 4, 2005.

Shendure et al., Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome,  Science 2005

George Church’s site

FYI: The best discussion of sequencing costs that I am aware is a 2004 paper by Shendure and friends:

Shendure J, Mitra R, Varma C, Church GM (2004) Advanced Sequencing Technologies: Methods and Goals. Nature Reviews of Genetics May;5(5):335-44.

Polonies_2

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