Interesting Readers

Over the last week I have been working on a little personal genome search project. I was contacted by one of my readers to help her find someone to "donate" her genome to. Initially I was surprised to receive such a request. Especially because I have railed against using the genome for a crystal ball.

But she was vehement that she wanted to donate her genome. Now I Have to tell you that I was then convinced of her altruism. She didn't know where to turn so we began with the usual suspects Dr Church, Dr Collins, Dr Rothberg, Hodosh. But when we were turned away a window opened.

I turns out Dr Venter's Institute is looking to turn out 10k genomes in 10 years. The perfect project.....provided these subjects have appropriate care providers to help out......

Since Helix Health of Connecticut is taking patients now, it seems only natural that we take her on as a patient.

I wouldn't have it any other way.

On another interesting note Dr Robison at OmicsOmics posts on yet another whole genome player who is entering the Archon X Prize.

Base4 (Real Cute) Innovations is pretty young and Keith covers it nicely.

Formed in 2007 with support from the University of Warwick and Warwick Ventures, base4 innovation is a group of highly talented and innovative biologists and physicists from the University of Warwick and Oxford and Cambridge Universities specialising in molecular biology, single photon detection, and nanotechnology.We are developing a new high-speed, low-cost method of DNA sequencing which combines well-known techniques such as photon detection and fluorescent labelling with nanostructures and cutting-edge methods of nanofabrication.

X Prize team leader and base4innovation founder Cameron Alexander Frayling is a researcher at the University of Warwick and the inventor of the innovative method behind this sequencing technology.

The Sherpa Says: This wonderful woman wanted to donate her genome and was turned away. I wonder who would have bit if she was willing to pay. What a shame!

18 Hours to Vote!!!!

Lots of things have transpired since Sunday. I would like to say first, sorry for no posts since Monday. I was preparing for my presentation at the Connecticut conference for the American College of Physicians. Second, I need more submissions for the Genie this weekend. I will be hosting my second and am looking forward to reviewing some great posts. Third, Navigenics is ready to unleash its technology on some unsuspecting consumers in '08. I know at Helix Health of Connecticut we are ready for the wave of "What does this mean?" "What should I do health wise?" etc.etc. etc.

In fact,

We just received a call from a wonderful consumer of the so-called SNP market for nutritional supplements. The big problem here is that there are SOME SNPs which actually predict risk for disease. But what do they get for a report? Eat more broccoli...Thanks.. I am scared that they don't understand about these "genes" really being a part of your medical record. Because some are as strong as a cholesterol panel in their ability to predict risk. The even bigger problem, most are not. And what happens when Navigenics gets out over the skis and says that they are? Who will be left to pick up the mess???? The fewer than 1000 geneticists? The PMDs who don't even have the training to comment on this? This is one of the major reasons why we are reaching out to educate PMDs.

I have a concern with Whole Genome Sequencing.....it really is just a snapshot in time. I emphasize the role of continuing evaluation of expression and epigenetic effects. Luckily, USC just received a bundle of dough to research and evaluate epigenetics. This is a great reason to have a continuity of care with those who have seen and attempted to interpret your genetic data. We can't keep bouncing this reductionist idea of "If we just have your genome, then we can help you live forever and cure all disease" at the market. This is what Francis Collins would call "Overselling the technology" Please answer my poll question "How much would you pay for the oversold genome?" Oops, I mean "The cutting edge achievement know as the Human genome. You should get yours done too."

I was warned by a friend of mine. He said "Shooting from the hip and having no planning of your posts is ONE WAY to blog. Another would be to plan and deliver a message." I say, why not do both. There is more than enough foolishness going on to point out. Let me know what you think.

While giving the talk today I was asked about how we can get physicians up to speed in genomics. I stated "We cannot, we have missed the boat. We were warned in 1993 and again in 2000. Medical schools never picked up the slack. Too few clinical geneticists in the basic sciences. Less than 40 Medical schools have defined courses in genetics. Up until the last few years it wasn't even a prerequisite for medical school. See the Banbury Summit. How can we teach those who never learned the language? Only one way, complete and total immersion. Much like how an adult learns a language. I have used vignettes that have clinical applicability. Unfortunately, this takes at a minimum 2 years to see any effect. If we were to do this today we might be able to make some inroads"

But physicians will not be ready for Navigenics. Boy, it sounds like this is an argument for "Direct to Consumer and Navigenics report based medicine" Well it is not why? What physician delivers care without a physical exam? One who is looking to get sued, that's who. Good luck to all the report makers. I hope you have an army of attorneys because malpractice coverage will not be enough.

The Sherpa Says: Thank you once again to Genome Technology Online I am very happy that they enjoy my musings. I hope my CGC friends did not get the wrong ideas. I am not bashing them, I am bashing the system. A system which I hope you will join me and fix.

Scientists and The Sherpa Urge Caution

According to a recent post at Medical News Today a new article will be published in Science urging caution with the availability of genomic sequencing. I have commented on it several times and now feel like we are beating a dead horse.

Listen, if you want your genome to help you decide what clothes to wear, or perfume, or as a trophy. Then go out and get one. I will never stop you from getting your genome as a novelty. But if you want to use your WHOLE genome to make healthcare decisions.......... Well, you better get a second opinion. The only genetic testing that will work for healthcare has nothing to do with whole genome analysis.......for now. So why get your genome? Because, if you get it once you never have to do it again? Well, you saw how that worked out for the iPHONE right?

On a lighter note, as I sit here in the ICU taking care of really sick people I am left to think....What if we could prevent chronic diseases? These are the diseases which once end-stage put you in the ICU. Where I now sit taking care of end stage heart and kidney disease. That is where the power of the genome lies.....in prevention.

The Sherpa Says: Early adopters are wonderful. The world would not advance if it weren't for those who challenged conventional wisdom. But when it comes to human life........well, I am not ready to "crack a few eggs"

An Attorney General, A Genetic Counselor and Gap Phase

Today my phone blew up. I had five different Venture Capital firms call me to pick my brain about "The New deal with Illumina" as well as "Viability of Microarrays in Pharmaceuticals"

I must say thank you to those who called. I look forward to speaking with each of your esteemed groups.

That being said......I must say that there is a general consensus of the physician side that the time for whole genome analysis for your health is not now. I agree. An excellent scientist Dr Bettinger over at the Genetic Genealogist posed a great question.

"What is your opinion on Gap Phase?....."

"that inevitably long period of time between (1) the availability of inexpensive whole-genome sequencing, and (2) the point when the medical field produces enough specialists in genetics to handle the work load."

Well....I don't think that is what gap phase is. Currently there are less than 1300 geneticists for the WHOLE country. In addition. If we expect personalized medicine to affect things like Coumadin, a drug which is dosed by adult doctors primarily, then shouldn't we have some adult geneticists? There are less than 100 of these doctors in the US. LESS THAN 100!!!!!!! Even scarier, there were less physicians sitting for the genetics boards this year than 5 years ago.

I don't think Gap phase has anything to do with these people. I think GAP phase has to do with literature and evidence based medicine. In medicine, doctors try not to do anything without good data that shows long term outcomes. When they veer from this path you get train wrecks like drug eluting stent mishaps and Vioxx!!!! Soon to be Avandia!!

So what do we do with the gap? We mind it!! We don't jump blindly without looking out for the fall that it may cause. Overselling genomics could destroy personalized medicine's promise! I will not let some overzealous "Let's do it because the technology is there, and so cool" people ruin our future. Even for a quick set of chromosomes!

As for trained professional shortage....When we have fighting between lab companies and the people who traditionally order tests, then we have a problem. Which is the case with Myriad.

There is a great NPR spot coming up. A colleague and teacher of mine Ellen Matloff. She will be on there with Attorney General Richard Blumenthal discussing the controversial Myriad advertisement campaign that is now running in CT, MA and NY. You can listen in online Sunday Evenings at 6:00 PM http://www.wnpr.org/

Ellen is the bane of Myriad's existence and because of this the genetic counselor is notably absent from the Myriad commercials.....hmmmmmm

She has started an online petition to start asking state's attorney generals to investigate misrepresentation in genetic testing. My genetic counselor has a wonderful take on this whole thing. BRCA testing is NOT in Gap Phase, unlike whole genome sequencing for healthcare. It has significant amounts of data and studies. It is clinically useful and can be of benefit when used properly. The problem.....The Fox is watching the Hen house. Lab reps are probably not the best people to be teaching physicians about using these tests, trained counselors and Geneticists are.

I am scared for physicians and this should serve as a warning call.

MYRIAD/23andME/Navigenics/futureunnamedbiotech are saying, "if you aren't with us, then you're against us, AND WE WILL REPLACE YOU WITH COMPUTERS!!"

The Sherpa Says: When my phone blew up today, the question was not, how can we invest in a safe product and service that will benefit people's medical care. It was..."How can we make this scalable?"......The answer does not lie in training genetics professionals....that takes at least 9 years after college. The Answer......All roads lead to Google.......Too bad the data is not there and computer guys haven't been burned as bad as those Vioxx doctors......

Gene Genie and George's Blog

First....Gene Genie is up at Cancer Genetics. Thanks to Ramunas who put up an excellent edition!!

Second and even more importantly......My excellent Chief of Genetic Counseling brought George Church's blog to my attention. My gosh....

His evaluation is right on point. His question is a wonderful one...... Great now we have genomes....so what. How do we get to systems biology? Once we have systems biology on point, we will then have truly personalized medicine. We will be able to manipulate the systems....and physicians will become engineers, systems analysts....

So when will we get there? How will we get there? My gut says there are 25 different signalling systems and perhaps four different common pathways....these will corroborate with the 4 humours........ Welcome back Galen and great to see you again Hippocrates.

The Sherpa Says: Stick around for 2010 it's gonna be huge! I am a firm believer in systems biology. I feel that be understanding cellular signalling pathways, we will see the link between previously unrelated disease. For an example if this take a look at this NYT article.

1000 Genomes???? Coming Soon.

I have been looking at the genome of Craig Ventner. What Surprises me is that we haven't do this sooner. If you haven't heard the diploid genotype of Craig Ventner is up. And several of my buddy bloggers have posted on it. Blaine posted on it here and has a nice wrap up.

From The Canadian site The Globe and Mail

Most experts predict that routinely reading individual genomes will become a reality within five years as the technology to unravel the six billion chemical units that make up DNA gets faster and cheaper.

Kathy Siminovitch, director of genomic medicine at Toronto's Mount Sinai Hospital and the Samuel Lunenfeld Research Institute, noted that the first Human Genome Project rang in at roughly $1-billion (U.S). But with the new generation of "ultra-fast" DNA sequencing machines that have hit the market within the past two years, she said the bill is expected to drop to less than $100,000 by year's end.

The Sherpa Says: Coming soon 1000 USD genomes. Now who will read and interpret them? Even crazier....where is the evidence base behind treatment guidelines adjusted to your genome??? I can here the uneducated physicians now.But don't be scared my brethren internists. Stick with the Sherpa. We will find our way.

Check out my colleague Ogan Gurel MD Mphil

I am sitting on the Phone with the good doctor Ogan Gurel. He is an excellent blogger that always never ceases to amaze me with his posts.

From his site

"Ogan is chairman of the Aesis Group which provides consulting services in the life sciences and healthcare sectors to clients that have included biopharma/medtech companies, hospitals & health systems, private equity firms, venture capital groups and hedge funds. As a healthcare technology expert and futurist, he has been a frequent conference speaker worldwide, addressing the issue of emerging technologies and their impact on the future of healthcare with particular focus on convergent medical technologies"

He was interviewed by INTimeTV. It is an excellent example of how we often forget that there is more than genomics is personalized medicine. Let's face it.......as each day passes, so do the old technologies in how we treat medicine. Unfortunately, your PMD is not keeping up with these changes. How can they? They are too busy fighting insurance companies in order to get paid. But that's a story for a different day.

The Sherpa Says: The future is here, it just isn't evenly distributed......But Ogan has it all

What good is a map?

Imagine being stranded on a raft......An object is floating in the water. You paddle hard to get it. Once you do, you realize its a map. Hooray, you can finally find some land. Or can you?

There are some significant questions to ask yourself prior to having any utility gained from that map.

1. Can you read the map? I used to be in the Navy. We learned how to read nautical maps. But my father, a retired colonel in the Army, would have no clue where to begin. Imagine someone who had no training......


2. Where are you on that map? If you have no orientation, how could you hope to navigate. Where does the sun rise? Simple question. However, when asked almost 15% of Americans do not know the answer.


3. What is on the land you will be paddling to? If you paddle hard to get there only to find out that there are man eating natives, how good was your choice? Did you really want to find that land?

A map of your personal genome is much the same. Jason Bobe over at the Personal Genome comments on some of these topics. Who should be able to read the map? Should everyone have a Tom-Tom or Garmin? Should there be age limits on querying ability. And what if we find out something we didn't want to know? These are serious questions.

The Sherpa Says:

There will soon be a personal genome option. Everyone will be able to have an economically priced copy. We need some guidance on its interpretation. Personally, computers can only do so much. With all apologies to my colleauge Tim Arimond, we cannot program our way out of needing human interpretation. A computer cannot tell when you are scared, confused, upset......yet. I think that personal genome sequencing holds tremendous promise.........But it is only a map.