Friday, February 26, 2010

I was wrong......AHEM


I was wrong. When GC said: “The GET Conference 2010 marks the last opportunity in history to gather a majority of individuals in the world with public personal genome sequences in a single venue,”

I said:

"That is a pretty heady statement by Dr. Church. Does he really think 2010 will be the year that 1000s of people will get whole genomes done?

I say, maybe a little hype. How about hundreds? Maybe...."

I said this with some conviction because I was uncertain that the companies out there would be able to use the genome samples as useful tools, like the exomes Church did or Watson's sequence from the Rothberg team........BTW, Nice release on the Ion Torrents stuff Jonathan. Will you be deploying it with 23andMe?

We will have 1000s of Genomes. Keith Robison took me to task too......but I still maintain that the spirit of what I said remains.

The quality of Genomes will not be such as that of Jimbo and the Boys and XXs up there on stage.......

However, I am paying attention to Ion Torrent and Rothberg's ability to juice this thing up quicker than we can imagine........check here on the 27th for an update.

Seriously, he is going to prove me dead wrong. When I met with him in sleepy 'Ol guilford out by the sound he had some exciting stuff going on. I only wish we could have spent more time together so I could learn about it.......

So my question remains, will George be right or will I? That's the challenge to the scientists in the space........prove me wrong! Crank out 1000 genomes of high quality. Crank out so many quality genomes that we can finally do something with them......I beg you JR.

Prove the Sherpa Wrong!

Friday, February 19, 2010

Hey! It's Pete Hulick! Are you Going to GET?

I want to congratulate Dr Peter Hulick M.D. Medical Geneticist/Internist.

I just read his wonderful article in the Internal Medicine News. For those who don't know Dr. Hulick, he is on heck of a doctor and a really nice guy. I look forward to more articles from him in the future!

Secondly, after all the big splash effort about the GET conference, I would like to encourage readers to attend.

“The GET Conference 2010 marks the last opportunity in history to gather a majority of individuals in the world with public personal genome sequences in a single venue,” says George Church, founder and principal investigator of the Personal Genome Project and professor of genetics at Harvard Medical School. “With rapid advances in technology, the number of individuals with personal genome sequences is expected to rise dramatically, from dozens today to thousands by 2011 and a million or more individuals within the next few years.”

That is a pretty heady statement by Dr. Church. Does he really think 2010 will be the year that 1000s of people will get whole genomes done?

I say, maybe a little hype. How about hundreds? Maybe....

The morning portion of GET Conference 2010 will feature wide-ranging discussions during which personal genome pioneers and globally recognized leaders of genomic science and industry, including the genetic bad-a$$ Misha Angrist, The O'l Man: George Church, Joltin Jay Flatley, "Do You Know Who I Am!" Henry Louis Gates, Jr., Rosalynn Gill, Seong-Jin Kim, Greg Lucier, James Lupski, Stephen Quake, Dan "Where's my refund?" Stoicescu and James "Well, It's True" Watson, will share their experiences and discuss the future of personal genomics. Award-winning science journalists Carl Zimmer and Robert Krulwich will moderate the discussions.

Why is this going to be a great conference? The speakers, that's why.

The afternoon program will additionally showcase:

· Four “prototypes of the future” sessions highlighting the next generation of personalized genomic products, services and activities and moderated by the executive editor of WIRED and author, Thomas "The Death Stare" Goetz.

· The public debut of the BioWeatherMap initiative, a collaboration between scientists and the public using next-generation sequencing platforms to address the fundamental question: “How diverse is the microbial life around us and how can we use that information to our advantage?”

The GET Conference 2010 will take place on Tuesday, April 27, 2010 from 8:00 a.m. – 8:00 p.m. at the Microsoft New England Research and Development Center in Cambridge, Mass. The event will be limited to 200 registrants. To register for the GET Conference 2010, visit

Tommy Goetz hates me, but I still will go because, let's face it, who doesn't love the

"Howard Stern of Genomics"-Jeff Gulcher

The Sherpa Says: An army of geneticists amassing to deploy clinical useful tools in a virtual setting? Nawh.....

Thursday, February 18, 2010

9p21.....ahem. Paynter Smackdown. Again.

Yeah, yeah, yeah........common variants don't work for heart disease.......We got it.

Rare variants matter more........

But the SNP data on 9p21 and others in this recent Nina Paynter paper are correct......

What we have here is a study on 101 SNPs and the association with heart disease followed OVER 12 years. This is precisely what I have been asking for from the dawn of these DTC SNP companies. I remember when all the wonks kept saying, well, we know just ONE snp is not that important as a predictor, but when we have panels of 100 SNPs, we will have the best predictive tools out there.......

In fact, deCode bet their livelihood on it as a diagnostics company.....This has to be the winning strategy, right?


That is the assessment of the current state from this Paynter paper, which IMHO was well written and was a likely outcome after the paper Paynter published in May 2009 which said that when you add 9p21 SNPs to current risk stratification models it added essentially nothing.

We have such robust models for assessing CVD risk, why not focus on things we do not have tools for assessing.

Every day we take family histories of all of our patients. We have hundreds of pedigrees. Non statistically I can tell you, if your parents were fat, had HTN, had AD, etc....there is an increased likelihood of your risk.......REGARDLESS of what some SNP scan says.

If you really want to make this tool useful, then use it for something useful and quit trying to make it fit in every hole!

The Sherpa Says: Face it, to get real personalized medicine we need pedigree studies. Tons and Tons of pedigree studies with candidate rare variants. And a set of "normals"
That costs big money, I get it. Now do you Francis?

Wednesday, February 17, 2010

I love my readers, even Renata M!

This is commentary from my prior blog post and with a great Reader who always gets my thinking about my stances and opinions. Since I couldn't fit it all in the comments page I want to share it with everyone. You can see her comments Why can't google let more than 4096 characters exist on a comments string??? G-d Only Knows.

The Bold is my response

Dr. "Sherpa" - I am confused.

"Are you FOR personalized medicine or not?"

Yes I am for diagnosing and preventing disease, accurately, scientifically and medically. I am for dosing medications as guided by one's genes and environment. I am for identifying genetic risks for disease using accepted standards and even new standards that are medically valid.

"Are you happy NYS licensed Navigenics...and is no doubt on the path of doing so with other companies...or not?"

I am familiar with the lab requirements for NYS. They have met those. I am not so certain applying an algorithm on that data to interpret it is such a good thing here, especially the risk interpretation. Which can be different from other tests like this. Nevertheless, a physician can use this non-medically valid test if they want to in NYS. I am not certain many physicians would use it. The malpractice exposure they would get from these multiple non validated data points are pretty risky.....

"As a pioneer physician you must be aware that one doesn't begin with an optimal end result for an entirely NEW the beginning of the process."

I agree, you have to break a few eggs to make an omelet. But when you are dealing with human life, a different standard begins to emerge......

"Certainly, as a physician, you are."

"So, I am confused by your posts making assertions that cross the line to outright claims of conflicts of interests and...sometimes worse...without a shred of proof."

Renata M, before you accuse me of slander, please tell me which statements you find objection to.

"Why undermine the trust/confidence in this new world in this way? "

Why should we trust before it is proven to us? And why is DTC Genomics equated with Personalized Medicine? It IS NOT PM!

Isn't that what we are seeing in the US now? People who trust inherently often end up hurt. In fact it is the skeptics like Socrates who are venerated. Unfortunately, often after they are long gone or are executed for their beliefs....

"Nor should dated links that no longer apply to the fast evolving and current business/economic climate, technologies and law(s) in differing American States and the international sector be fused - adding to the confusion for me...who, though we are not of your august standing...deserve better from you.

Outdated links? I think that it was an important point you missed there. Jack LORD WAS the CEO of Navigenics. This is obviously not some deal cooked up by Vance. you just can't do that sort of thing in a month's time!

"Is it your belief that ANY executive or Board Member who has a former affiliation is actually acting in the capacity of all former posts/affiliations/occupations"

Renata, you cannot tell me you are that naive? Are you serious? Does Jack Lord have any ties or better yet, stock options? Tell me how much Eric Schmidt enjoyed being on Apple's board? Economically and for his own Company?

"- and - Navigenics Board, the State of New York Department of Health, investment banks and Proctor & Gamble are incapable and/or otherwise conflicted insofar as validating Management and future plans as detailed to the aforementioned?"

Hmmmmm, maybe you can clarify what the hell you mean here? I don't understand how the NYS DOH validates Management and future plans of Navigenics Board and their members?

"Are only physicians capable of avoiding conflicts of interests when they choose to participate in the business sector???"

No, no one is all that capable these days of avoiding conflicts of interests. That is why we declare them on CMEs we give, or in academic positions. It is this transparency that is needed. Do I own a DTC company? No. Do I make money from DTC testing? No. Would I make money off Genetic testing done in my office? No, not off the test.

"For those of us who are not physicians, bankers or biotech experts/lawyers...though your posts are always entertaining and provocative fun...confusing."

I would love to know who you are Renata M. Feel like disclosing? Maybe we could share IP addresses? Hmmmm?

"Fortunately, I try to keep up and have historical context to provide me with not only insights - but a view of where conflicts really lie."

I thought you were a neophyte? What historical context are you talking about?

"I cannot see them with Navigenics, nor with the decisions of P&G, investment banks, NYS Dept. of Health"

You have to stop lumping the NYS DOH in with these companies. The government has a strict protocol for defining conflicts of interest. Which is available to the public.

" validate this fine Company and its efforts to pioneer new, difficult terrain in a challenging economic climate."

I know that some of the people at Navigenics are very fine people. I agree. But Navi is hardly doing the pioneering for personalized medicine. I would say the people doing the family histories, using the PGX testing, seeing patients and applying the science are the pioneers. The people doing the research are the pioneers. The people guiding the governmental policies are pioneers.....

The people trying to make a fast buck here are the profiteers............

I am in this for the long haul Renata M........I am only 33. We have a long way to go. And my interests lie with giving the field Gravitas and a sense of Honor. That is what this field needs......not Sports cars, celebrity endorsement and open bars......

Seriously Renata M, WTF? This is personalized MEDICINE. Not Personalized SHOPPING. Not personalized GOSSIP SHOWS. not Personalized GENOMIC DISCRIMINATION.......

Personalized MEDICINE. Which is altogether separate, intertwined with, but different than personalized GENOMICS.....

"Be well."

You too Renata

End Comment String

The commenter raises a couple of really good points.

1. Just because you have a state approval does not mean what you are doing is medically sound. But people often think that is the case. Ask the chronic Lyme doctors who pump you full of antibiotics here in CT......

2. A Company Board has its own set of operating circumstances.....every one is different and boards of publicly traded companies have different rules and issues from private boards.......

3. Just like Toyota, these companies have a responsibility to get it right. Often, the first time. If they don't they need to recall until it is right.......even though this is not an accelerator issue, it will soon be a doctor using these tests.......(UGH!) issue.

4. I am sick of Personal Genomics jumping on the Personalized Medicine Brand. They are not the same. That is basically like saying a blood type is Medical Care. It could be used for medical care. It could also be used for "fun" Remember that? It could also be used to identify relatedness. It could be used to market a diet fad resulting in millions of dollars of profit...... It could also be used for god only knows.....but it is not always Medical Care......and at least Blood Types are clinically useful.

The Sherpa Says: We have to stay strong of mind here. The marketers are out to trick us into thinking DTC Genomics is NOW, Personalized Medicine! Because that is where the market is.........

Tuesday, February 16, 2010

How can insurers use DTC genomics to profile?

The Answer: They float a trial balloon in the Merry 'Ol Land of Oz......

So when everyone pointed out to me that this NIB in Australia was offering deep discount Navigenics tests, I laughed.......Why?

You did see the story on DeCode in Newsweek and the fate of deCodeMe right? Or Daniel's blog?

You see, these little SNP chips have got to find a market or they will soon die. Even worse, these little SNP tests have got to find a market soon or they will die too.......

And maybe the companies associated (Not the people mind you) with them?

So when I posted about the Humana Executive who was running Navigenics after Mari Hit the Road and the high likelihood of Navigenics trying to find an insurance partner for their little charade.....

That is precisely what I thought when I saw the presser from Navi about Jack Lord, Humana's "Innovation" director running Navi.

I thought, which Insurer would be stupid enough to use the DTC genomic tests to profile patients' risks for disease.....

Well, it turns out that they aren't so stupid over here. Instead, they convince some company in 'Oz to do it as a "trial balloon"

Guess what? It has failed. Thanks to bloggers like Daniel and reporters like Kerry O'Brien

"KERRY O'BRIEN: Are you aware the American Medical Association recommends that a doctor should always be involved in a person's genetic testing and that according to The Washington Post the lack of doctor involvement in precisely these kinds of tests has made the tests technically illegal in some American states.
MARK FITZGIBBON: No, I wasn't aware of those findings, but again using my example I took my test to the doctor. Now, if we need to do more in terms of encouraging people to take these tests to their doctors, we're already offering a counselling service, an advice service as part of the product offering. Maybe that's what we'll do. And this is very much in a pilot stage."

Oops, did KPCB forget to tell NIB that this was Illegal in some states?

So much for Due Diligence.....try Google next time Fellas....

The Sherpa Says: If there is any question how I feel about this test clinically, you can read here. But as to my thoughts on using it to estimate community risk pooling for insurance. Didn't GINA outlaw that?

Wednesday, February 10, 2010

Hype, Hype, Hype from a single study.

You know what pisses me off. The blatant stupidity given to hyping one piece of literature and making it seem as if it is true.

What pisses me off more is insinuating that there is some inherent value in a certain single study without prefacing the factors.

Let me tell you who often does that.

1. Nutriceutical salesmen in a Multi Level Marketing Scheme

2. People looking to sell some fancy medical device

3. Pharma companies creating fake journals

4. DTC Genomics companies trying to prove value from their tests......

Don't believe me? Well, just read the spittoon's blog post about TRALI....which is Transfusion Related Acute Lung Injury......

How does this hype occur? First the study....

It starts with a scare

"TRALI is one of the major causes of transfusion-association deaths in the developed world."-Spitton

Ok. We used to think this was rare and yes, it is more common based on some new agreed standards..... 1 in 300,000 people in some studies.....

Then it continues with baffling science jibberish to make people think you know what you are talking about........

"One reason TRALI happens is that ...... Several triggers for this type of TRALI have been identified. One of these, the HNA-3 antigen, has repeatedly been associated with severe and fatal TRALI reactions. HNA-3 comes in two versions: HNA-3a and HNA-3b........ The likelihood that a woman will have antibodies against HNA-3 increases with each birth.

The new research found that the different versions of HNA-3 are due to SNP rs2288904 in the SLC44A2 gene. Someone who is GG at this SNP will express only HNA-3a. Someone who is AG will express both the HNA-3a and HNA-3b version. Finally, someone who is AA at rs2288904 will express only HNA-3b. " -Spittoon

It finishes with a testimonial and a point of sale

"Confused? Here’s an example from my own family that will hopefully make things more clear:

My mom is AA at rs2288904, meaning that her body expresses only HNA-3b. My brother and I are both AG (we inherited the G at this SNP from my father), so we have both HNA-3a and HNA-3b in our bodies. If my mom was exposed to blood from my brother and/or me while we were being born, her immune system could have recognized our HNA-3a antigens as foreign and made antibodies. So now, if my mom gave blood to my brother or me, we would be at risk for TRALI, even though we all have the same ABO blood type (A+)."-Spitton

What is wrong with this? It asserts that they would absolutely without a shadow of a doubt be at risk of TRALI........based on ONE STUDY!!!

And the point of sale?

"(23andMe Complete Edition customers can check their data for rs2288904 using the Browse Raw Data feature.)"

OMG, Holy Crap, I have to know whether I will be at risk for TRALI. Thank you so very much 23andMe! You have solved my life's problems. Maybe I could get a life alert bracelet with all of the "risks" I have?

Seriously. What would have been nice is a "This is only one study and there is no other replication out there, but, this is interesting EARLY SCIENCE"

We still have not conclusively implicated TRALI to just this.......There is no complete consensus on the absolute pathogenesis of TRALI.

The Sherpa Says: One study a fact does not make. Nor does it make good marketing. Tssk, Tssk. One would figure that they would use proper editing of these things........Oh wait, they fired them.

Friday, February 5, 2010

FDA, Warfarin, still not as sexy to me.

When everyone poo poo'd Warfarin, I became very, very upset. Here was a good clinical case for using PGx tests. Not a great case, but a good case. It was only when I began to think about feasability.

Lets face it, most decisions around starting coumadin happen in the hospital. Why?

Well, most patients receive an anticoagulation injection medication that most people have to be specially trained to administer at home versus a nurse in the hospital. Further, the rat poison known as coumadin is dangerous to take and is tricky to dose. So in the hospital is where a lot of people get titrated to the right dose.

This creates multiple problems

1. Insurers do not like paying for expensive meds like low molecular weight Heparin
2. Insurers do not like paying for extra hopsital days to dose a medication
3. Hospitals do not make any more money keeping people in the hospital to dose coumadin
4. Doctors do like to keep patients safe

This creates a market opportunity with demand.

But the question remains "Will testing get patients out of hospital quicker?"


Does this testing keep patients safer?


Will the FDA change the label?

They already did.

However, how many hospitals can run CYP2C9 and VKORC1?

Not very many.

What is the TAT?

Unless it is 24 hours it will not be that helpful.

Now as a Hospital, what is the ROI?
Now as a Insurer what is the ROI?
Now as a physician what is the cost of interpretation?

From a view point of a clinician who supports Personalized Medicine. We need to get rid of Coumadin and use Dabigatriban.

Is this testing useful? Yes. Is it clinically utilizable. If you are willing to wait a month.

Will this get quicker? Yes.

How much quicker? 2 weeks quicker.....but the fact remains, unless you can get a TAT of 12-24 hours this is not a reality in most worlds.....

The Sherpa Says: Great that the FDA notices the utility, but not great that the test is still too slow.

Tuesday, February 2, 2010

Holy Crap! MedCo Follows in CVS footsteps

By December 21st the writing was on the wall. It was pretty obvious CVS/Caremark had jumped over the number one PBM in the field MedCo.....

How so?

Well, the increased ownership in Generation Health that CVS/Caremark laid down was the way.....

The newest of the benefits management companies.....this time the focus was on genetic testing benefits.

Personally, this type of company should have been formed in 2005 when Insurers were hemorrhaging cash from those BRCA tests........

But, slow and deliberate do Insurers move....

On the 21st it of December it was all but decided for MedCo. Ummm, Ummmmm, who looks like this Generation Health company?????

I knew back then and now everyone knows today.

MedCo buys DNADirect.....

In 2005 when My Partner at the time Leslie Manace went out to "see" Ryan...... In what turned to be a huge probe of Leslie by Ryan, Ryan revealed......"We are interested in PGx" Which was funny because so were we. So much so that we really thought that this was the bees knees and in fact was likely the only useful and scalable testing to come out in the next 5 years.

The DTC Genomics companies were merely a twisted dream at the time.

Well, Ryan. Our hunch paid off.

By Diversifying your DTC genetic testing company into something useful such as a GBM, you have moved shrewdly. And when the PBM leader gets trumped by CVS, you reap the rewards.

I look forward to the first quarter report from MedCo to see exactly how much they acquired you for.

I have been saying on this blog that the answer for these DTC genomics companies is to follow your lead. Now the question is, which big insurer will now but a DTC genomics company?

For MedCo, I am a little disappointed that you decided to choose the exact type of company as Caremark did. There are lots of other solutions out there. I hope you still plan on increasing your footprint in this space. Because it would be bad if CVS/Caremark continues to gobble these companies up and you end up buying the second in class.....

Not that DNADirect is second in class, but Heather Shappell ARE First Class.......

The Sherpa Says: There has got to be a way to make these companies less reliant on people. Even in the genetics testing space, there is a way to automate.