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?

Polony A Go-Go

Since when are undergraduates accomplished in bioinformatics, hacking hardware, wetlab work, and bioethics, and music? These folks do exist. This summer, I have had the pleasure of working with the multi-talented James Kugler, an intern in the Church Lab.

I was just alerted to the fact that he is something of a budding musician trying to break out in the nascent scene of “genome pop“. His debut track will surely capture the hearts of ligase molecules across the globe. And no ballad on polony sequencing would be complete without fluorophores, and this one has got them in spades.

Listen to Polony A Go-Go, by James Kugler.

UPDATE (12:35AM): James does not sound like a 4-inch tall, helium-huffing chipmunk IRL. This is a WP and Flash player bug. Oh boy, I hope James doesn’t find out about this. I have just totally made a mockery of his big debut. Everyone please try to keep this on the DL until further notice. James, if you’re reading, I’ve sent in the calvary. We’re going to get your voice back back to normal soon, real soon…

UPDATE 2 (12:36AM): Oh yeah, it just occurred to me that if you go directly to the song URL, rather than rely on the embedded flash player (that is, do not click on the little blue icon next to song link), you can listen to the song at the normal sampling rate in your browser and avoid the chipmunk effect. So copy/past the URL below and have a listen:


Lyrics below the jump.

Read more

Best Sentence I Read Today

Who knows how long it will take for personal genomes to become useful, but one thing is for certain, someday it will be said that it all started with the genomes of ten volunteers.

From a very thoughtful comment by Willy Lensch on this blog post about last Wednesday’s meeting with the first 8 volunteers and the staff of the Personal Genome Project (including me).

More notes on the meeting to follow soon…

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.

The Incidentalome

A very important paper was published last week in JAMA.  The punch line is this: Once the new high throughput diagnostic testing technologies — like massive SNP panels — are widely deployed there will be a significant spike in both true-positive and false-positive results.  The implications of this fact are deep and wide.

If you’ve got access to JAMA, check it out.  Otherwise, I’ll summarize the important parts the paper later this week. 

Isaac Kohane, Daniel Masys, and Russ Altman. "The Incidentalome: A Threat to Genomic Medicine" JAMA 296(2): 212-215. July 12, 2006. (sorry subscribers only)

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