50 million personal genome sequences by 2015?

Just how quickly will the market for personal genome sequences grow? My back-of-the-napkin calculation pegs it at 50 million sequences obtained by 2015, give or take. While this is far from a scientifically derived calculation, my rationale is simply to assume that the trend line for the personal genome sequencing market might look a lot like the one experienced in the personal computer market.

Welcome to 1980
The personal computer industry grew from several thousand units sold in 1975 to 50 million units in 1995. If the personal genome sequencing market follows suit, we might say that 2007 for personal genome sequences was like 1979 for personal computers, and we’ve just turned the corner into 1980 where units sold remains sub 1 million, but growth is noticeable. If growth continues apace, we’ll hit 50 million sequences obtained somewhere around 2015-2020.

PCs 1980-1995: sparkline
pDNA 2007-2015: sparkline

 

Deus ex machina
A difficulty with predicting the future is human agency, or choice. How quickly will people warm to the idea of surfing their personal genome sequence? Although we’re in the early days, personal genome sequencing evangelists are starting to appear in unexpected places. Enter Christopher Hitchens. In a recent interview about his newest book on the Hoover Institute’s show Uncommon Knowledge, he paused and said: “As it happens, I’ve had my DNA sequenced recently. You can get yours done too. And you should, by the way…”. Here is the clip (you can skip the 8 min point):

 

History, on repeat
How else might the personal genome sequencing market resemble the personal computing industry? For some ideas, witness this absolutely brilliant piece of video from Britain in 1969 — a year when computers were not yet “personal” computers, but they were clearly heading that direction:

Part 2, and Part 3

The interviews with people on the street are amazing. When asked, “So what do you think of computers?”, responses range from the aloof “What are computers?” to the utopian “a revolution like we’ve never seen” to the dismissive “yeah, they’re great, but I don’t know what all the fuss is about” to the completely dystopian “the government will use them to control us”.

At the close of the video, renowned professor Donald Michie (University of Edinburgh) had this to say:

“[Computers are] bringing about the greatest revolution the human race has ever known…This revolution could lead to terrible consequences, or it could lead to the greatest advances ever for the human race. Which of these things are to happen, is up to us.”

Fools Game
Attaching a number to a 10 year forecast is a fools game. The timescale may be off-base in either direction. The point of writing this post though is to help set expectations about a near-term future where many millions of people have obtained personal genome sequences (including partial sequences). This point still escapes many people who work in and around the genetics field.

The X-team

The scientists and engineers in the Church lab at Harvard Medical School, who are busy developing the sequencing technology that will be used for the Personal Genome Project, will be competing in the Archon X-Prize for Genomics. The announcement was made this morning in the Boston Globe.

To win the $10M prize all we need to do is to line-up about 200 of our machines and turn them on. Well maybe its not that simple. There are also a few items on the science and engineering “To Do” list, like figure out how to drop the price of whole genome sequencing by 1 or 2 orders of magnitude.

The founding members of the Personal Genome X-team are:

Richard Terry, Greg Porreca, Jay Shendure, and Kevin McCarthy. Go team!

P.S. I wonder what George plans to do with all of those machines after competing in the X-Prize?

Hodosh to lead Archon X-Prize for Genomics

The Archon X Prize for Genomics has appointed Marc Hodosh to lead the $10 million competition. Hodosh is an entrepreneur and tech geek who recently chaired a robotics competition for segway inventor Dean Kamen.The Archon X Prize will be awarded to the first group that can “build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 per genome.” In other words, the winner must be able to sequence 100 human genomes in 10 days for a $1 million.

The X Prize Foundation has published a video describing the competition, check it out:

So far three teams have registered to compete, including VisiGen Biotechnologies, 454 Life Sciences, and the Foundation for Applied Molecular Evolution.Here are the competition guidelines (PDF).Want to compete? Register here (PDF).

Nanopore Sequencing

Harvard Magazine has a write-up on nanopore sequencing, here is a snip:

[Professor of biology emeritus Daniel] Branton reasoned that because the four bases that make up DNA commonly called A, C, G, and T after the first letter of each chemical compound’s multisyllabic name each have different dimensions, he could tell which one was passing through the hole at a given moment by observing to what degree the pore was blocked, based on the number of ions that got through along with the DNA.

The process worked. And because the bases traveled through the pore at a rate approaching one million per second, “You really had something that was orders of magnitude faster than anyone had ever dreamed of,” says [Harvard professor of physics Jene Golovchenko]…

…The Harvard colleagues are competing with many other scientists in a challenge issued by the National Institutes of Health to produce a sequencing method that costs less than $10,000 per genome by 2009, and a method for $1,000 or less by 2014.

Elizabeth Gudrais. A Personal Genome Machine? Harvard Magazine, March-April 2007.

The Harvard Nanopore Group Homepage

George Church: Optimistic about Personal Genomics in 2007

What are you optimistic about? This is the theme of the tenth Edge.org Annual Question, edited by John Brockman. George Church is optimistic about personal genomics. First, he is optmistic about the economics of personal genomics:

We are in free-fall from a stratospheric $3 billion generic genome sequence (which only an expert could love) down to a sea level price for our personal genomic data. Early-adopters are posing and positing how to exploit it, while surrounded by envious and oblivious bystanders. We can now pinpoint the 1% of our genomes which in concert with our environment influences the traits that make us different from one another. Ways to tease out that key 1%, coalesce with “next-generation” DNA reading technology popping up this year, to suddenly bring the street-price down to $3000—about as easy (or hard) to justify as buying some bleeding-edge electronic gadget at an early stage when only minimal software is ready.

While noting that not everyone is ready (or even aware) of this technological leap in-progress, he is optimistic that people are starting to catch-up.

Momentum is thus building for millions of people to volunteer to have their genome data correlated with their physical-traits to benefit the billions who will hang back (due to inertia or uncertainty).

He is optmistic that health information altruism will come to pass in personal genomics:

I am optimistic that millions more will share [their genomic data]. Millions already do share to benefit society (or whatever) in old and new social
phenomena ranging from the Red Cross to Wikipedia, from MySpace/YouTube to SEC compensation disclosures…

And finally:

I am optimistic that we will not be de-humanized (continuing the legacy of feudalism and industrial revolution), but we might be re-humanized, relieved of a few more ailments, to contemplate our place in the universe, and transcend out brutal past.

Read the whole thing.

Several other contributors are optimistic about genes:

Freeman Dyson: "HAR1 ( Human Accelerated Region 1) As a New Tool Leading Us Toward a Deep Understanding of Human Nature"

JILL NEIMARK, The Human Epigenome Project

Samuel Barondes, Finding Mental Illness Genes

Edge.org 2007 Annual Question

PGP Volunteers Needed in Boston

George Church’s IRB has been approved for the first recruitment phase of The Personal Genome Project and he is looking for volunteers:

The Personal Genome Project (a collaborative project with researchers from Harvard Medical School and Partner’s Healthcare) is recruiting seven individuals to participate in a new approach to Human Genome/Phenome comprehensive data integration including ‘identifying information ‘ such as genome sequencing and facial features. The PGP is also championing a new IRB-approved consenting mechanism which frankly discusses the likelihood of disclosure of identifying information in many modern medical research projects and this one in particular. We are seeking a diverse range of volunteers, male and female, from all backgrounds. Our IRB approval restricts us to volunteers with at least a master’s degree in genetics or equivalent. Consent forms will be signed and blood drawn at Partner’s Healthcare Clinical Center in Boston.

If you’ve never heard of The Personal Genome Project (PGP), check out the main page.  I also noticed George has posted a fantastic summary of ways in which anonymity of personal genomic data can be compromised.  This project is designed for individuals who are willing to contribute to the advancement of medical research with their eyes wide open.  For those who see value in making their genomes transparent, George has been careful to make the risks as transparent as possible.  The infovores and health information altruists couldn’t ask for a better leader on this front.
The next task will be to expand the project beyond Boston…Stay tuned.

Nicholas Wade on $1K genome

Nicholas Wade has another piece on the $1000 genome.  Here are a couple snips, starting with an update on what a human genome costs, then and now:

"The first human genome decoding, completed by a public consortium of universities in 2003, cost more than $500 million. With the same technology, dependent on DNA sequencing machines made by Applied Biosystems, a human genome could probably now be decoded for $10 million to $15 million, experts say."

There seems to be a lot of fluctuation in the estimates of the price of the first human genome, typically ranging from $500M or $3B?  Can we nail this one down to within at least one order of magnitude?

David Bentley, Solexa’s chief scientist, takes an oddly conservative stance on personal genomics:

The demand for whole genome sequencing is a long way off, in Dr. Bentley’s view, but not so distant that it is too early to think about the consequences of generating such information. He advocates that two people should control access to a person’s genome sequence — the patient and the physician.

Why not the patient alone? Dr. Bentley said genomes would be so difficult to analyze correctly that interpretation should stay within the medical profession. Otherwise, freelance services will spring up, offering to predict whether a person will get heart disease or their age of death. This potential for misinformation “would have a huge adverse impact on the medical use of genetic information,” Dr. Bentley said.

What does it mean that genomic interpretation services should "stay within the medical profession"?  Does this mean that interpretation should be made by qualified genetics professionals?  In which case I agree.  If staying within the medical profession means making appointments, travel, waiting rooms, and all the rest, then forget it.  Why does the above paragraph pre-suppose that "freelance services" would be inferior?  Couldn’t these services be superior by employing trained genetic experts–of which there is real scarcity in the world, including in the medical profession?

Nicholas Wade. "The Quest for the $1,000 Human Genome" NYTimes, July 18, 2006.

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.

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