Sherpa Hits San Francisco

Imagine rounding up everyone that is influential in the Genome Sequencing world on the science side, then add a healthy set of journalists, mix in a group of Venture Capitalists and put the leaders in corporate industry at a table to answer their questions. Including, the Sherpa!!!

This was a whirlwind tour, where I managed to meet with some pretty influential people in silicon valley. I introduced them to Helix Health of Connecticut and our plans for the future of Genomic Medicine. They introduced me to some people looking to make that happen.

Also I was involved in discussion and gave a talk to the group at Beyond Genome Conference, hosted by CHI. I also was asked to advise CHI on a novel educational initiative for them. I am honored. In addition I was able to meet with a good friend of mine and begin to prep for the Coriell meeting next Monday....whew!!!! What a crazy day!

Let's start with the Beyond Genome Conference. I must admit, that since my first crazy days of posting, I have grown fond of Ryan Phelan. The early readers often read about how I thought she was screwing up everything. Well, it turns out. Ryan is probably one of the most thoughtful people in this field.

She presented a wonderful topic at the conference. In it she expressed...."Not all genetic tests are made equal" I totally agree with her. Some are bogus and some are real!

Her talk made me feel that for the regulations, which are coming, she wanted them to be tempered accordingly to their usage. I agree....sort of. If the tests are for medical use, they should be medical. If they are for non-medical use i.e. eye color, height....they should not be regulated like medical diagnostics. Here's where I kind of differ. I think all tests that have anything to do with medical conditions, should have some sort of medical service associated. Much like my specialty's party line.

What amazed me about Ryan was how she broke this down, so eloquently, yet so simplistically. It was actually pretty elegant. I am truly impressed by Ryan. She has been at this longer than any other business. Not longer than any genetics program, but longer than any business.

And let's face it, she was the first person to put genetics in the public eye! That is always a great thing!

I also was amazed at how nice the people I have been shouting at accepted me.........I am certain Caesar felt the same way! The nicest of all was Dietrich Stephan. He even thanked me for publicly supporting him. Which I have in some forums. I think that if you are going to do medical....Do Medical. They are....but they need some brick and mortar to keep out of regulatory heat. Dietrich, if you read this, give me a call. I have an idea for you.....

I swear Linda Avey smiled at me. Even when I said that they had forgotten to address some of the key issues. But at first I was worried when she initially saw me......They could kill. even the CSO of DeCode was nice. I do disagree with some of the things he had to say. Including the power of SNPs versus things like LDL. Or the power of SNP testing to identify predisposition to Atrial Fibrillation.

If there were cardiologists in the audience, they would have laughed. You see. Afib is one of the most common diseases in elderly adults. In fact, a single snp doesn't predict for crap compared to risks like; large heart, high blood pressure, family history. In addition, the talk didn't even mention the score most DOCTORS use to predict risk per year of having stroke from atrial fibrillation.

This is called the CHADS2 score. In essence it is the BEST clinical predictor of stroke in atrial fib. It is also a great mortality predictor. My guess, the AFIB test will not be used. There is no cardiologist who will order this. As for a patient, they would be best suited to know their family history and make note of funny heart feelings. If the test were sold at about 50 USD then maybe it would be worth it. Why? Because, the minority of patients who don't feel their afib would be made aware.

But any more than 100 USD would not be cost effective. You would figure a big company worth tons of money would spend the time consulting a cardiologist or reading about other clinical risk predictors. I really am scared about this side of the business. Monetizing tests and marketing them without proving superiority or non-inferiority to the standard clinical tests could pose economic strain on the system. I do agree that it is a nice to have thing. But so is an echocardiogram or a CHADS2 score!

The Sherpa Says: My point, SNPs aren't everything and medicine has existed long before this new technology. So we need to integrate the 2. Not to try and replace the whole system with new and not completely evolved technology! Lastly, If we don't regulate the renegades in our group, we will only have ourselves to blame for the very STIFF governmental regulation. Lastly, thanks to those who gave me such a warm welcome. I just hope I won't be saying Et Tu Brute!

Are you Serious?

While I was lauding Misha ( One of the 10 PGP'ers) and correcting some misconceptions about the PGP informed consent process....something much bigger was happening. I don't know how I missed it...but I did...


Google Buys Into Navigenics!!! That's right...Google now has a stake in 2 of the big 3.......Me? I am the 4th...merely a little guy. Our humble abode is now protected thanks to the NYS and CT Attorney Generals...for Now, well at least until Google can buy New York State.


From Business Week!!


Size of Investment Not Disclosed
Calling 23andMe an example of a company "generating a whole new batch of information of interest to a broad range of people," Pederson says Google wants to extend its capabilities into genetic testing. The precise path and business contours of the emerging gene-testing market remain unclear, but if Navigenics succeeds it "will generate a lot of a very new type of information with potentially far-reaching value," says Pederson. "We felt it was important to get involved now, at the early stage, to better understand the information generated by this fast-moving field."





Did anyone see my post about the Master Plan????? Did anyone watch the Movie??

Read an excerpt from the story



"The Google Story"

Sergey Brin and Larry Page have ambitious long-term plans for Google's expansion into the fields of biology and genetics through the fusion of science, medicine, and technology. . . .One of the most exciting Google projects involves biological and genetic research that could foster important medical and scientific breakthroughs. Through this effort, Google may help accelerate the era of personalized medicine, in which understanding an individual's precise genetic makeup can contribute to the ability of physicians and counselors to tailor health care treatment, rather than dispensing medications or recommending treatments based on statistics or averages.


"We need to use the largest computers in the world," Venter said. "Larry and Sergey have been excited about our work and about giving us access to their computers and their algorithm guys and scientists to improve the process of analyzing data. It shows the broadness of their thinking. Genetic information is going to be the leading edge of information that is going to change the world. Working with Google, we are trying to generate a gene catalogue to characterize all the genes on the planet and understand their evolutionary development.




Geneticists have wanted to do this for generations."Over time, Venter said, Google will build up a genetic database, analyze it, and find meaningful correlations for individuals and populations. . . . Google's data-mining techniques appear well-suited to the formidable challenges posed by analyzing the genetic sequence.It has begun work on this project, but has not been required to disclose any information about it publicly since the work has no impact on its current revenue and profits."




People will be able to log on to a Google site using search capacities and have the ability to understand things about themselves as they change in real time," Venter said. "What does it mean to have this variation in genes? What else is known? And instead of having a few elitist scientists doing this and dictating to the world what it means, with Google it would be creating several million scientists."Google has empowered individuals to do searches and get information and have things in seconds at their fingertips," he went on. "Where is that more important than understanding our own biology and its connection to disease and behavior? With Google, you will be able to get an understanding of your own genes. Google has the capacity to do all of this, and it is one of the discussions I have had with Larry and Sergey."


My business colleauges say "A rising tide raises all ships" But I have to tell you, I am a little worried that they want to end around healthcare not just end arounding IRBs.


My guess. Google will acquire every single bit of DNA database they can get their hands on. Why? Knowledge is power. And they want both.


The Sherpa Says:


Since this is an industry...couldn't we liken this to the XM/Sirius merger? In all seriousness. These corporate genomics companies see medical genetics as a non-scalable model....so they want to get rid of it all together. Flying to the top of the mountain does not get you back down it. I plead with Google, please get some medical guidance. Please!!!!

First Take by Mailund

The first blog response comes From Dr Mailund of Denmark. Thomas is an Associate Professor at the Bioinformatics Research Center (BiRC), University of Aarhus, Denmark.

His response is telling and it essentially says what is true....we would initially be "Lost" but not for too long

My goal is to figure out ways to analyse full sequence data for disease mapping. With full sequences, a few things change compared to SNP chip data.

First, of course, there is the matter of scale. Now you get 6 billion nucleotides per individual instead of 2×500K or 2×1M as with SNP chips. (This is a huge Point!!! This doesn't include methylation and other epigenetic phenomena either)

Second, you are no longer looking for indirect signals, so there are no tagging and multi-marker methods will not be needed to boost the power of indirect signals. You have all the variation observed (but the types of variation is much more complicated).

Third (and perhaps most interesting), the kind of signals we are looking for will change. With SNP chips and tagging SNPs, we are looking for high-frequent variants with modest effect. High frequent variants is all we are tagging (and these have a modest effect if we are still looking for it, if they didn’t we would have found them ages ago). With full sequencing, we will be able to look for low frequency variants as well.

The Sherpa Says:
We would still need more research.......But I am certain it would come in a hurry! Who's next with their take?

LRP8 and Familial MI....Ho Hum

This month in the American Journal of Human Genetics we have some interesting publications. Including an association study identifying a gene known as LRP8. So what is LRP8? It is a receptor for bad cholesterol. When bad cholesterol binds this receptor, platelets (the bricks in your blood that build a clot) become sticky making it easier to thrombose (form a clot).





I am interested in this study for several reasons. First, it has been shown that platelets get stick even after ingesting a Big Mac. That's correct. Just one fast food hamburger can theoretically precipitate a heart attack. So naturally we would love to know who. Think Personalized Diet/Nutrigenomics. I wonder if Salugen can hear me now? I still haven't received their "Scientific Data" yet. I will publicize it if they do.





Back to the study. So what was studied is a group called the GeneQuest families of familial MI, the control group was some white men who were given cardiac catheterization and found to have no atherosclerosis burden (OOPS). Well, that control does not mean they did not have atherosclerotic burden, because catheterization cannot identify 30% occluded vessel plaques.





In addition their findings were replicated on an Italian cohort of familial heart attack as well. So why do I say Ho Hum?





Let's see: No Odds Ratio was greater than 1.43 This 43% increase in heart attack and coronary artery disease is still less than the family history risk itself. The only good thing was that this risk persisted even when controlling for plasma total cholesterol levels, triglyceride levels, hypertension, and diabetes, in addition to age and sex.





What is your odds ratio for heart attack if your father had one prior to 65?


The Answer: 5.8 according to Maren Scheuner's article on familial risk for MI.





Do you now see why I say HO HUM about this gene? When will we see the gene card panel for MI??????

The Sherpa Says: Listen to all of this hulabaloo about Ventner's Genome. Even Men's Health magazine says you should bank your parents DNA if they die. What good is all of this if we don't have a key to the map? The map will make no sense! LRP8, APOE4, I could go on and on. What good is a genome map, without a guide? What good is the guide without the studies? Why did you buy the iPOD early, only to have late adopters get it cheaper? For the rebate? Doubtful. This is why primary care physicians are late adopters. If you want to get your genome (and I do) then you better be prepared to find someone who will help you understand it...becasue cliff notes, or Navigenics just won't do. Nor will scarfing down Big Macs....

Forbes and Genetics

Way back in 2004 Forbes published an excellent article on inflammation and heart disease. That article introduced me to deCODE. In fact, I was so impressed with their model I began to read about their founder voraciously. More importantly I began to see the wonderful role the media has to play in this new revolution. They can influence the demand just as much as Myriad spending 1 million in Denver to market to consumers. Granted these publications don't have the Oprah Effect (Did I mention that Dr Oz is going to meet the Sherpa?), but they do have some teeth!

But I was also distressed when Forbes published an article that I had a tough time swallowing. In fact it brought me to tears. How can this publication blindly validate and promote these tests without any medical guidance, or suspect guidance at best. I am certain you have all read this article, but you can read it here. The wonderfully hyped name 12 Gene Tests That Could Change Your Life says it all. But before I get into the article, which is misleading and not factual enough to guide decision making, I will investigate the authors via my favorite little spy...uh I mean Search Engine Google ;)

Robert Langreth. He has written many articles some good, some bad. He has been writing about deCODE since 2003 prior to the Big Forbes cover story in 2004. He has been writing about personalized medicine since 1999 as Staff Reporter of THE WALL STREET JOURNAL. He also has written many scathing reports about drug companies, which is why I find it ironic that he endorses deCODE's diabetes test. Which does not tell you as much about your risk as if you had a first degree relative with diabetes. Mr. Langreth was a Staff Reporter at the Wall Street Journal from 1995 to 2000 and an Associate Editor at Popular Science from 1992 to 1994. It was at this time in my search when I figured it out

From a chat in 2002
mherper: What's Kari Stefannson like in person?
LANGRETH: Kari is a charming and very emotional person. He literally had to sell his radical database to an entire country. He did it by a grass-roots campaign, going and speaking to anyone who would listen. He eventually by weight of personal charm won the day over his opponents.
mherper: How can you write about DeCode Genetics when their stock is at $2?
LANGRETH: I wasn't recommending them necessarily as an investment, although I'd argue that it is not a terrible deal right now. I chose them because Kari is doing something that will very likely change the course of science and lead to fundamental discoveries. Whether it leads to a successful business is another question entirely. But since you ask, I figure that unlike many tiny biotechs, DeCode has something unique--the genetic access to an entire country. It doesn't mean they won't go out of business someday. But in the meantime, they are almost certain to have a big impact on science.

Does he have stock in DeCODE??????? It did track up on the day of publication.

We have to be careful to fully investigate our sources. Whom do you trust when giving you information about genetic testing? The company spokesman? The company that sells the tests? What about the middle man? We are entering nebulous waters where the lines of relation can still be hidden. Even from google. When you publish for a peer reviewed journal you have conflict of interest disclosures required. How come we don't have the same for a well read and respected magazine/website?

The Sherpa Says:
Mr Langreth has done some crack reporting on several topics, but to include the DeCODE TCF7L2 test as one that will change your life is a HUGE LIE!!! This test is a party trick at best, a distraction that could lead you to not getting your fasting blood sugar tested (The standard of care for early diagnosis). At best he just boosted deCODE stock. At worst he led you down the wrong trail. Be careful, some who play sherpas actually have stock in the pack the tell you to carry.

Google your genes part deux?

Not since Google partnered with Craig Venter in 2005 to start using the power of the genome have we heard a peep about the secrets that lie ahead for the two, well and possibly Ryan Phelan. CEO of that company which makes money off of testing people rather than a medical(yes genetics is medicine people) model. Stark II laws made it illegal for doctors to make profits from testing people, so why whould pseudo-medicine outfits be able?
Anyways, where was I? Oh Google.....
In this weeks HealthcareITNews there is an article on Google pushing for better health information on the web. Perhaps to harness the power of the two? Google your genes and then learn about the diseases you are predisposed to....All 50 of them :) This whole thing will not fly without doctors? Doctors are trained to build this list of 50 diseases and then whittle it down to 2 or 3. That being said, genetics is a different story. According the recent ACMG statistics the mean age of most geneticists is 52. There are also less than 1000 MD geneticists in the country! 20% plan to retire in the next 5 years. To fill their shoes? Less than half of the 150 training spots are filed. Google is starting to look like they have a chance. Even worse, in medical school the Association of American Medical Colleges ranks genetics as the 3rd most important topic yet none have a prerequisite of genetics in undergrad for entry. Your internist or pediatrician or Ob knows less about genetics than Google. Who will deliver the future and personalized medicine???? Not them. Maybe Google. Maybe cutting edge genetics practices that have specialized training?
What do you think?