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…

Video: Rep. Louise Slaughter reflects on 12 year old GINA

Here is Representative Louise Slaughter (D-NY) discussing the importance of GINA on the House floor yesterday:

(If you’re reading via RSS, you might need to go to my site to view the embedded video)

The bill passed in the House 420-3.  If you’re curious, the 3 Nays were Representative Jeff Flake (R-AZ), Representative Ed Royce (R-CA), and Representative Ron Paul (R-TX).


H.R. 493, Genetic Information Nondiscrimination Act  (PDF)

Full proceedings from the Congressional Record, April 25, 2007, ~20 pages (PDF)

# genes in human genome?

18,308 genes according to Carl Zimmer via PANTHER

As Carl Zimmer notes, the presumed number of genes in the human genome has been steadily declining over the years.  Early estimates were in the 100K range.  For historical perspective, Lee Rowen won the GeneSweep competition back in 2003 for betting that the human genome contained 25,947 genes — the lowest estimate in the entire competition.

(hat tip, Hsien)

ORNL, How Many Genes in the Human Genome?

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).

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)

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

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