How much genome sequence will $10K get you?

Snip from interview at MIT Tech Review (TR) with George Church (GC):

GC: We might never get a
perfect $1,000 diploid genome [the six billion base pairs in a human's
two sets of chromosomes]. The question is, what can we afford and what
do we get for it? Think back to the beginning of the computer industry.
They didn’t say, "Oh, we’re going to get you a $1,000 supercomputer."
No, they said, "What can people afford? And what can we give them for
it?" And what they gave us was the likes of the Apple II computer, and
people started writing software for it. Current personal computers cost
about the same but deliver more. The same thing may happen with
personal genomes.

TR: So what are people likely to spend to know their own genome?

GC:
I think what is affordable — and remember, this is a lifetime expense;
your personal genome will hopefully last you 80 years or more — is
$10,000. If I can save $100 on average a year, it is a no-brainer.
That’s the cost of a couple days of missed work, or one diagnostic test
that can be put off due to low risk, or avoiding bad choices on a
year’s worth of drugs. Then the question is, how much of a person’s
genome can we sequence for $10,000? Seven thousand dollars will buy you
a million base pairs of DNA [using conventional technology], which is
one-6,000th of your diploid genome. Not very much.

Polony
sequencing [a method developed by Church and colleagues] is about a
hundred times less expensive. So you can sequence about 1 percent of
the genome [for $10,000]. That’s not bad. You could focus on likely
places you’re going to have problems.We got a factor-of-ten improvement
in the last six months, so if we could get another 10 percent
improvement in the next year, that would give us 10 percent of the
genome. If we could pick 10 percent of the genome for which we have
lifestyle, nutritional, or synthetic solutions, that would be a good
deliverable for a $10,000 investment. And it will just get better from
there.

Read the whole piece.

David Rotman, Rewriting the Genome. MIT Tech Review, May/June 2006.

David Schwartz: $100 genomes in 3 years?

There are bulls and bears in the world of personal genome sequencing.  Some say affordable genome sequencing is decades away, while others say its just around the corner.  David Schwartz at University of Wiscon is clearly a bull among bulls:

David Schwartz, a professor of genetics at the University of Wisconsin,
Madison, will describe the research at the Human Genome meeting in
Helsinki tomorrow. Within three years, he believes his lab will have a
test capable of reading an entire genome within an hour for less than
$100.

Ian Sample. New test offers speedy reading of genetic makeup. The Guardian. Friday June 2, 2006.

David C. Schwartz profile at University of Wisconsin, Madison

GenomeSweep

Back in 2004, Life Science Insights surveyed a group of genome experts for opinions on the date when cheap human genome sequencing would be available.  Here is a summary of what they said:

Forty percent of the genome experts interviewed by LSI believe that the $1000 genome will not be reached within ten years.  This compares to a mere 17% who believe it will be here in five years. Ten percent of respondents said that scientists would not even reach the $100,000 genome within ten years. Clearly, there is disagreement over how fast these technologies are developing.

Predictions are fun to watch play out over time, particularly when expert opinions vary wildly.  Remember GeneSweep?  The experts in this contest made predictions about the number of genes in the human genome.  They ranged from 25,000 - 300,000.  Here is a snapshot of the distribution of bets, dating from March 2003:

Genesweep

With such wildly different opinions about the future of personal genomics, perhaps a Long Bet is in order.  GenomeSweep anyone?

Zachary Zimmerman, The Promise of the $1000 Human Genome (PDF). Life Science Insights, October 2004.

GeneSweep History from Cold Spring Harbor.

Internet Archive snapshot of GeneSweep page from March 2003.

In case you’re wondering, the winner of GeneSweep was Lee Rowen from the Institute for Systems Biology in Seattle.  Her prediction was 25,947 genes.

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




New URL Digs for the Personal Genome Project

George Church has slowly been piecing together a his Personal Genome Project.  In a significant step, it looks like he has acquired new url digs: http://pgen.us/

454 wins gold in WSJ Tech Innovation Awards

454’s sequencing technology was awarded the gold prize in this years WSJ Innovation Awards.  The money quote:

"Judges saw the [sequencing] technology as ‘potentially’ or ‘clearly’ revolutionary"

Michael Totty. "Innovation Awards: A Better Idea" WSJ October 24, 2005.  (Or listen to a podcast)

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.

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