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)

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).

Video: Virtual Genomic Counseling vs. Face-to-Face

The PBS television station KQED in San Francisco recently aired a very thoughtful segment comparing online genomic counseling through DNA Direct to traditional face-to-face counseling via UCSF.  Check it out:


KQED, Genetic Testing through the Web. Feb 20, 2007.
Full discolure: I am employed by DNA Direct.

Video: Craig Venter on Colbert Report

Hat tip, Pedro and to those who forwarded this to me.

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

Genomic Counseling

Tired: Genetic Counseling
Wired: Genomic Counseling

Who came up with the phrase "genomic counseling"?  The earliest data point I can find is from a June 2004 SACGHS Meeting, where Dr. Muin J. Khoury is quoted as saying:

"So how is NSGC [editor: The National Society of Genetic Counselors] going to or has begun to address this range of genomic information, from somatic cell to polymorphisms, and is there a role for something that we might call genomic counseling, and where does genomic counseling end and health education start, and the practice of medicine? So there is that tension between having more specialists versus integrating the genomics knowledge into the practice of daily medicine."

(If anyone knows a different provenance to this phrase, let me know in the comments or drop me a line.)

The question of where the hand-off is from the education (or counseling) of consumers about genomic data to the integration of this information into medical/clinical care is a good one.  In my mind, the answer to that question depends on the type of information genomic data can provide, i.e. whether the information is clinician-centric or consumer-centric. 

Some types of information will be actionable only by the clinician,
e.g. genetic testing to determine warfarin dosing. 

While other types of information will be more
relevant to the actions of the consumer, e.g. CF carrier screening by couples planning a pregnancy. 

There are also types of genomic data that create actionability somewhere in-between, i.e. where a clinicians actions should take into consideration a patient’s preferences.  A good example is genetic testing for irinotecan dosing, where this genomic data should inform the dosing, in light of the patient’s preference for aggressive treatment versus toxicity risk (see the excellent interview with Howard McLeod about this issue). 

Even when genomic information is clinician-centric, there will remain (for the foreseeable future) a role for the patient in creating physician awareness about how this information may influence patient care.  Nobody is more interested a therapeutic outcome than the patient who is at risk.  For this reason patients will continue to be — and increasily will become even more — informed about their care.  In terms of recent genetic testing history, there have been more than one study (or this one) showing that the number one predictor of whether a physician orders a genetic test is patient demand. 

Another question for genomic counseling: What is the likely format?  Face-to-face?  Probably not.

An Interview with Howard Mcleod. To Test or Not Test: An Update on UGTA1T1 Testing.  Oncology Issues, Nov/Dec 2006. (PDF)

Wideroff L et al. Physician use of genetic testing for cancer susceptibility: results of a national survey. Cancer Epidemiol Biomarkers Prev. 2003 Apr;12(4):295-303.

Sifri R. et al. Use of cancer susceptibility testing among primary care physicians. Clin Genet. 2003 Oct; 64(4):355-60.

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.

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.

Entrepreneurial Thought Leaders: Ryan Phelan

The CEO of DNA Direct (full discolure…and my boss/friend/mentor) recently gave a talk at Stanford as part of the Entrepreneurial Thought Leaders (ETL) seminar series. In her presentation, she tells the story of her life as an entrepreneur and her experiences with founding and operating a number of ventures, most of them in the consumer health arena. Among them were Planetree & Direct Medical Knowledge (later acquired by WebMD). Check it out:

Ryanphelan_etl

Video, Audio Podcast MP3, and also available via iTunes (search ETL or Ryan Phelan)

I highly recommend checking out the whole series of speakers and the archive.

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