The problem with Comparative Whole Genomics……

March 11, 2010 — admin


I have been having this debate with a good friend and mentor.


I think Complete Genome Comparison could be a Killer App.

He thinks it could be a legal and scientific nightmare.

I think he’s right.

Let’s really think about this for a second. If history has anything to say about human behavior we need look no further than the secrecy with which gene sequences were hunted.

Hell, even Science makes mention of it several times. The Article “Data Hoarding Blocks Progress in Genetics” might be a good read if you are interested.

Guys like Daniel MacArthur over at Genetic future point out some good points about the difficulty in making sense of all the noise that exists in genomes. But the problems go even further than that. Hell, CNV can differ in IDENTICAL TWINS!!!! Say Wha?

So what do we have to say about this? Phenotype and comparison are kings. Databases of “normals” and disease afflicted need to be developed. They need to be curated, they need to be “shared”

Ahem, excuse me? Did you say “shared?”

Yes, I did say shared.

Exec/USGOVT/BGI/UK/Etc- “Well, sure we would like to give that idea more credence and study it. And the implications it may bring. Would you be so kind as to forward your attorney’s information so that our attorneys can consult with yours in order to bankrupt you and send you away with you radical thinking?”

He has me convinced (a tough thing to do) that the level of collaboration amongst human geneticists and Venture Capitalists might not be exactly the level of their physician brethren….

What happens when you get access to a database, but not “all of it”

Who pays? Who benefits? Who gets rights of discovery? Who pays the Nosferatu? (sorry Dan)

With Sequencing as a Service, do you have these problems licked? Probably not.

So when Daniel points out every geneticist afflicted with a disease feel good discovery, there are about 100 nightmare scenarios of chasing down rare variants that turn out to be nothing except a good excuse to burn through 10 million dollars……..

I begin to say, well how can we pick that up quicker? Comparative Whole Genomics.

Great, which database do I start with? Do I have to use 20 or 200 databases? How can I afford such work? Which one of the 200 won’t make a play legally to own my discovery?

Ahh, yes. It is a good time to be a genome centric attorney. But a nightmare to launch a business where you depend on someone else’s database………

The Sherpa Says: Yes, sugar plums, ponies and lemon drops for as far as the eye can see for Genomics! I hope Andy will bring this back to earth……..Or maybe Glenn Close can show us where the fruit punch swimming pool is?
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What a difference a year makes

March 10, 2010 — admin


It has been one year since I commented on 23andMe’s foray into clinical medicine. I was frankly blown away that such a move would be so blatant without integration of health care practitioners.


I also was blown away that Myriad wouldn’t sue the ever living bejesus out of 23andMe. A year later, no lawsuit. I am still surprised about this one. Don’t you have to demonstrate protection of your patent to keep it?

Maybe Google/23andMe are paying a VIG to Myriad? I don’t know, but it hasn’t shown up on Myriad’s SEC reports yet……

Why was I so surprised? Well, a few months after 23andMe launched the service AND Myriad did not sue, MYRIAD WAS SUED.

I began to wonder if not suing Google/23andMe was a sign of weakness. I was certain Myriad would then shut down the DTC Genomics BRCA testing.

To date, they have not.

This begs the question, does Myriad think they do not have a case and would lose against Google, thus strengthening the case against them by the ACLU? If that is truly the case and we will begin to see judicial activism in patent removal, well, then we could be in for an EXPLOSION of genetic testing labs out there, each doing their own thing, their own way.

An article in Nature Medicine by Brendan Borrell, does an excellent job of discussion the potential backlash and issues related to DTC Genomics and patent holders. Balaji S. of Counsyl took the tech line. “Should we really be charge to look in the mirror?” Well, Balaji, do you have to buy a mirror to look in it? FAIL

The question is: “Will other patent holders see themselves as vulnerable by allowing DTC Genomics companies to test for THEIR patented genetic markers?”

This could prompt a huge wave of lawsuits against these fledgling DTC Genomics companies. Normally, companies sue to shake down, scare away competition and make money or at least protect patents. What we could see is lawsuits designed to crush these young companies in an attempt to scare off the ACLU et.al.

By Myriad NOT suing 23andMe, we may have opened up a new wave of patent paranoia and fear. When that happens companies often turn to the courts to scare away competitors and people hell bent on their (patent) destruction……(ACLU)

It will be interesting to see what this year holds for the Gene Patent……

The Sherpa Says: I would love to hear Dan Vorhaus or Gary Marchant’s or Barbara Evans’ opinions on these things………
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Just 4 million? What 23andMe is worth.

March 4, 2010 — admin


So by now I am certain everyone in the DTC genomics world has seen this BNET story


From the Story

“Is it really the best time for 23andMe, a leader in recreational genetic testing to be handing $4 million to an executive officer? That’s the news from their SEC filing. The official explanation is the $4 mm was a payback to a company officer for a loan, with the money coming from the company’s series B financing, which included an investment from Google. “

Ahem…….


I have flayed them for playing doctor even begged my associates in the past to as well.

Listen, if anyone has a beef with these guys. I do. They had this thought to replace physicians, which is a foolish way to think. You cannot replace doctors. Just empower them. Which is what should have been done here, but instead they were too playing Doctor on Oprah……

But the question “Are these guys going under?” is a foolish question. Drew was right. They are not going under. They, just like ACORN are changing faces to try anew……..

The Sherpa Says: The question should be, “What is this 4 million dollars for?”

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G2C2, finally a tool for genomic education!

March 1, 2010 — admin


Has anyone visited or registered for G2C2 at UVA? I have been championing for years, the addition of Physicians’ Assistants and Nurses into the field of Medical Genetics.


Why? Well, for one, unlike genetic counselors, PAs and Nurses have rigorous physiology courses. Now with PGx, they also are important players because they actually prescribe medications and have pharmacology knowledge. Unlike Genetic Counselors…..

But most importantly, there are thousands of them. No, not 3000, hundreds of thousands in total.


According to GenomeWeb

The center provides cross-mapped learning activities and assessments, outcome indicators and professional competencies, such as Genomics Nursing: Competencies, Curricula Guidelines, and Outcome Indicators.

These are key things for measuring educational outcomes and this will likely be a source of educational research. Something that is near and dear to my heart!

The Sherpa Says: We must educate to move this field forward en masse.


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I was wrong……AHEM

February 27, 2010 — admin

Ok,

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!

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

February 20, 2010 — admin

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 http://www.getconference.eventbrite.com/.


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…..

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9p21…..ahem. Paynter et.al. Smackdown. Again.

February 18, 2010 — admin


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?

Wrong.

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?
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I love my readers, even Renata M!

February 17, 2010 — admin

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 INDUSTRY…at 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 neophytes…like me…who, though we are not of your august standing…deserve better from you.


Renata,
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.

“…to 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………

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How can insurers use DTC genomics to profile?

February 17, 2010 — admin


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?
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Hype, Hype, Hype from a single study.

February 11, 2010 — admin

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.
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FDA, Warfarin, still not as sexy to me.

February 5, 2010 — admin

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?”

Maybe.

Does this testing keep patients safer?

Maybe.

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.
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Holy Crap! MedCo Follows in CVS footsteps

February 3, 2010 — admin


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 et.al. 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.

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Why Dr. Vanier’s Navigenics appointment is good for PM

January 22, 2010 — admin


Now you may be asking yourself. What does an ER doctor know about genetic testing? Well, usually not a lot. But after being in the biz for quite some time, I am certain Vance knows quite a bit. Despite that training at Hopkins……….LOL

I am very happy and this is a tremendous step in the right direction for the Board at Navigenics. It shows that they acknowledge the best way to enter the healthcare market and have an impact on people’s lives is by working with physicians……Something that they were opposed to in the beginning.

In fact one of their PR wonks who is now gone, talks of a doctor who was advising Navi and said

“Teaching doctors about genetics isn’t tough………..It’s impossible” and with that attitude they approached DTC genomics.

I am here to tell you today, it “appears” they have turned that corner.

Time will tell, but my guess is that they will move towards the market rapidly and aggressively. They will use the lab to market to physicians. They already have a relationship with a handful of MDVIP doctors. One of which who has set up shop in sleepy ‘ol Greenwich CT.

I will be happy to help her……

The next question that this company needs to ask themselves is

“Now that we have the right man at the helm, do we have the right product?”

My answer is pretty simple. No. This not the product.

So now, they need to ask. “Do we have the cash to support our venture, UNTIL we have the right product?”

That is only something MDV will know. But, my guess is yes.

Lastly, they then need to ask themselves “Is genetic testing the product?”

Once again, my answer is no. Which means that Navigenics will likely turn into an unscalable set of medical practices and interpretation software……

The interpretation software will soon be a free commodity, just like genetic testing. Why? Prometheus beat the others and Cariaso wins. Thus no patents……..

Which means that the only way they make money is via a lenscrafters model………Which is precisely what I told Dietrich Stephan, Dr. Rothberg, and a whole slew of VCs about 2 years ago now…….

So if any of you are eavesdropping, give me a call and we can run this………..

That being said, Dr Vanier’s appointment is a good thing for PM because it shows that investors and boards now appreciate the fact that physicians must be involved in this process. Which is a win for consumers, because now they have someone who swore an oath to heal and protect the patient at the helm.

So heads up Vance, I will be watching.

Best of luck.

The Sherpa Says: Do or Do Not, there is No Try.
Posted in Gene Medicine. No Comments »

Enter the "Not" DTC Genomics Rep

January 15, 2010 — admin


An attractive male/female (depending on doctor) walks into the office.


“Hi I would like to talk with Dr X”

Receptionist “Who are you, sweetie?”

Rep “I want to talk with the doctor about the FUTURE OF MEDICINE”

Receptionist “Huh?”

Rep “Just let him know that I am offering DNA testing”

Receptionist “Hold On………”

Doctor comes out.

Rep “Hi doctor I am with….”

Cut off by Doctor “I know, I know, Myriad right? You have been coming around here for a couple of years now” “Ya know, I know nothing about DNA”

Rep “No doctor, I am not with Myriad. I am with naviGENICS”

Doctor “Who? Eugenics?”

Rep “No Navigenics, would you like to come to our open bar where we will talk about the FUTURE OF MEDICINE?”

Doctor “Hmmmmm……”

Rep “Don’t worry doctor, we will have a report you can show your consumers (Law 1 broken) and we will let you customize it for your practice (Law 2 broken)”


Doctor “Ok I will see you there.”

That’s the future of naviGENICS strategy in NYC…….

But what I really want to know is:

1. Do the limitations of Pharma gifts also count for Labs. Can you say trips to the Bahamas?

2. Do the minuscule amount of MDVIP docs matter that much as a market? Prob not.

3. Will Navigenics now pursue the GENE Store idea that I pitched to Dietrich Stephan in 2007?

Listen, if the rep strategy worked for Myriad, why won’t it work for naviGENICS? This is a good path for them. I envision a whole slew of lab reps in the future. Now if they could only have a test that is worth some clinical utility………

In order to gain the state license, Navigenics had to meet several requirements, including hire a doctoral-level scientist with expertise in genetic molecular testing, pay a $1,100 fee, and respond to deficiencies cited by inspectors with a plan of correction.

Most important, however, was Navigenics’ conceding to not market its services directly to consumers, as clinical labs are forbidden from doing under state regulations. “They have acknowledged that DTC will not work for them” in New York, Kusel said. “They can only operate through physicians’ orders.”


The Sherpa Says: Imagine TV ads in NYC that say “If you want to know your future, ask your Doctor…..naviGENICS doctor that is. IMHO, a test with little clinical value doesn’t get tested for unless you spend millions on marketing and advertising the way MYRIAD has. Oh, and they have a very clinically relevant test……..
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CETP, Jewish Centenarians and Alzheimers

January 15, 2010 — admin

2005, I am at a lecture in a small conference room in the Annenberg building at Mount Sinai. You know the building, the huge black imposing tower at 101st and Madison Ave.


The speaker, Nir Barzilai. The topic: Living to 100. The take away, people that live to 100 have better defenses against the toxic exposure we ingest daily.

The biggest molecule I learned about CETP. Yup, CETP. So naturally when I learn about something I do a pretty big deep dive. Which is why I went out and bought huge amounts of Pfizer stock when I found out they were making a CETP inhibitor…..what a flop that was……goes to show, not all pleiomorphic effects or unexpected adverse effects are good…….

So imagine my surprise when @lindaavey @dgmacarthur mention that JAMA has a study on it….I listen.

But what do I find? Well, basically what the alzheimer association finds

This relatively small study suggests that variations in this particular gene – linked with long life and lower risk of heart disease – could also be associated with lower risk of dementia. More research is needed to fully understand this link. The government currently invests eight times less in dementia research than cancer research. This needs to change.’

I think this may be too much attention towards a subject in an attempt to hype a genetic finding. I remain skeptical. Since after all, I was burned by torcetrapib…...

The Sherpa Says: Much ado right now, but certainly would be neat if we had some hard core modifier genes involved in APOE alzheimers….
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Congratulations Navigenics. You ARE a clinical lab! Uh-Oh…

January 12, 2010 — admin


So like I have said multiple times. Navigenics is AT LEAST a clinical laboratory if not a healthcare provider.


It turns out that the NY State Dept of Health thinks they are a laboratory and have now awarded them a license to do their “Health Compass” in NY

So I say “Congratulations, you are a dead man”

Why do I say this? Simply because now Navigenics (any one notice that the only other prominent genetics word that uses genics is EuGENICS? Hmmmmm)

As I was saying, now Navigenics will be allowed to be a lab in NY and are given a license. What will that entail?

Uh, Vance, you did read Subpart 34-2 of 10 NYCRR, Laboratory Business Practices in it’s entirety before you jumped into this right??

I did back in 2005 and that’s what shook us even further away from the “BIZ”

The New York State Regulations on Clinical Laboratories are extremely rigorous. In fact, if they offered the hairbrained scheme of marking up tests for my profit, like M.F. did back in 2007, they would be in violation.


Like

Section 34-2.4 Prohibited business practices by clinical laboratories.

(a) No clinical laboratory, its agent, employee or fiduciary shall make, offer, give,
or agree to make, offer or give, any payment or other consideration to a health services
purveyor for the referral of specimens for the performance of clinical laboratory services.

Like I said, Hair-brained scheme M.F.

These laws may impair their ability to run a for profit lab and KEEP their NYS license to test.

Here are a few more doozies

Section 34-2.4 Prohibited business practices by clinical laboratories.

(b) No clinical laboratory, its agent, employee or fiduciary, shall participate in the
division, transference, assignment, rebate, or splitting of fees with any health services
purveyor, or with another clinical laboratory, in relation to clinical laboratory services.

Looks like no deep discounts for the holidays in NYC….uh oh.

Section 34-2.6 Space.

(a) The rental of space by a clinical laboratory from a referring
health services purveyor, or an immediate family member of such purveyor, for more
than fair market value, or under circumstances where the rental amount is affected by
the volume or value of tests ordered by the health services purveyor shall be deemed
consideration given for referral of specimens for performance of clinical laboratory
services, and is prohibited.

No increased rent shenannigans either!

The rest of 34-2.6 is onerous as well. New York is Dedicated to preventing doctors and health care facilities, including labs from engaging in what other business may call standard operating procedure. Why? It may jeopardize the public health….

Section 34-2.8 Professional courtesy.

The provision of clinical laboratory services by
a clinical laboratory for health services purveyors, their families, or their employees,
agents, or fiduciaries at a charge which is below the lower of the applicable Medicare
fee schedule amount or the national limitation amount as defined by the Medicare
program for such services is consideration given for referral of specimens for
performance of clinical laboratory services, and is prohibited.

Looks like the Beth Israel Deaconess program with naviGENICS is a no no as well………

Perhaps the biggest issue comes in the prepared reports…….

Section 34-2.11 Recall letters and reporting of test results.

(a) A clinical laboratory shall not communicate to a patient of a referring health
services purveyor that a clinical laboratory test, including, but not limited to a Pap
smear, is or will be due to be performed, or that a visit to the health services purveyor
for diagnosis or treatment is or will be due. A clinical laboratory shall not prepare such
communication for the health services purveyor to send, or otherwise facilitate the
preparation or sending of such communication by the health services purveyor. Such
communication or its facilitation shall be deemed consideration given for referral of
specimens for performance of clinical laboratory services, and is prohibited.

What does this mean? Any New York State resident who receives a doctor ordered naviGENICS health compass cannot receive direct communication of these results.

NOR can Navigenics customize a report for an ordering set of physicians in NYS. Which the physician just spits out at time of follow up…….

What this can mean is one thing and one thing only……

Navigenics is about to go into the clinical business. With a different name and a different company. They will work together in synchrony with the Navigenics lab team and provide that they deem to be “personalized medicine” But what will be nothing more than Medicine with a personal genomics boondoggle…

Real personalized medicine includes patient pedigrees. Who knows, maybe they will do this?

The Sherpa Says: Not a bright move coming into NYC without investigating what it entailed. I hope someone did their homework and has found a “loophole” Because otherwise, no doctor in their right mind is going to order your tests…..for now……
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Gotta Love It. Even the daycare…….

January 11, 2010 — admin


So the other day I go to pick up my oldest and the businesswoman who runs the show said to me “I have a question” I quickly see her Time Magazine with the cover which asks “Can we change our genes”


I immediately launch into a diatribe about epigenetics. The current state of epigenetics is even murkier than micro RNAs. I basically go on a rant and at the end she says “So can those cigarettes I smoked as a kid screw up my grandson?”

OMFG!!! This is why I hate TIME magazine. AND the lay press, AND the secondary education system in this country…AND………

Ok, here is the real take on Epigenetics. It is a control system, plain and simple, just like these RNAs and whatever else may control t he rate at which DNA does its dance.

Monogenetic disease importance is pretty clear….

Gene Broken (of important protein/etc) + No Repair = Disease Phenotype

But when you can compensate with other genes, or even multiple copies of the same gene or EVEN by upregulating similar genes to carry the load, you have a different story. Which is the story that you will soon hear being told.

The reason our organism exists here is because:

1. We repair our DNA damage pretty well, when we don’t we die, usually of cancer
2. We have redundancy mechanisms which, we will find out have epigenetic control
3. We pass these adaptations on to our kin in multiple ways through behavior as well as, ribonucleic acids, as well as methylation and acetylation and……G-d only knows

Do we have any idea how the “F” all of this works. No, which is why I beg all of you hungry reporters working as freelance or as staff reporters for the will known as Time, please stop hyping “the NEXT BIG THING”

God Damn now I am gonna have to deflate the epigenetics balloon too????

Pretty soon everyone will be saying, WE HAVE A RIGHT TO A PROPER EPIGENTICALLY MODIFIED GENOME! I can see it now…….

The Sherpa Says: How about extra methylation causing cancer? How about low methylation ALSO causing cancer? Don’t believe me? Pub Med it…….
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Personal Genomics Flop…..big Belly Flop!

January 8, 2010 — admin


Daniel and Dan get quoted in an article in the Times yesterday and I am happy for them. It just goes to show how bloggers in this space ultimately shape the space.

That being said, everyone is left wondering “Where in the hell do we go from here in Personal Genomics?”

Well, I know where we are going in Personalized Medicine. PGx.

But as for personal genomics, the path is less clear. First we have to be honest about a few things.

1. Your genome is essentially worthless right now
2. We don’t understand what the hell most of the SNPs and CNVs mean in the genome
3. In an economic downturn, very few people will buy this, no matter how cool it looks.
4. Don’t believe me? How does Time’s Invention of the Year ONLY GET 30,000 (if you believe) customers. How many iPhones sold after the listing in 2008?
5. Things we are certain of in the genome add very little to life planning or healthcare.

Now, if we can overcome those things we have to ask ourselves. Is this a software play or a genome database play. If this is a software investment……

1. Is the software being created that valuable?
2. Can you patent or create a moat around the analytical tools that were created by these companies, or are the tools just rehashing of other tools that exist
3. Does Prometheus ruin the ability to patent these tools?
4. Are these tools accurate and valuable? Ask J Craig fellas….
5. Will the lessons learned justify the investment? At least a few hundred million USD people!

Well, let’s say it is NOT a software play, it is a genome database play.

1. How many people does it take to have a valuable database.
2. Is the database a legal liability worth the risk?
3. Will anyone want to buy the database?
4. Can there be a free database which will be more valuable than the “for sale” database
5. Can the database be curated and annotated easily?

So, after the million dollar open bars and zeppelins and celebs we are left with some real hard questions. Which is why I am very unclear as to the future of this “industry”

Is this really an industry all of its own? Or is this just a rehash of facebook?

Do you remember that fat kid? You know the one who said “Hey look at me! I am gonna make a HUGE SPLASH!”

Well, guess what porky, huge splash made……….

Now how in the hell does that SORE RED BELLY FEEL?

The Sherpa Says: A lot of pain and suffering may ultimately in the end prove worthless and the ripples may die…….Only to have some other fatso cause waves later on……..

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Hackers, HITECH and HIPAA in DTC Genomics, Oh My!

January 7, 2010 — admin

At our practice we run a pretty tight ship when it comes to security of patient records. Why do we do this? Well there are 2 big reasons.


1. It’s the right thing to do.
2. The law will put you in the hurt locker if you don’t

I want to talk about reason 2 a little bit.
Why?

With all of this protection of health information and DTC genomics companies going bankrupt, I begin to really wonder who a covered entity is.

Daniel Vorhaus over at Genomics Law Review has a pretty good break down of it, but I think there may be some nuances not covered. As well as a notable lack of coverage of HITECH policies in the ARRA.

Wha?

Yes the recovery act has stuff on Health care privacy in it. In HIPAA DTC Genomics may not be covered, but I think in HITECH they are.

Why have I been reading this stuff? Because it’s my job.

According to HITECH

H.R.1 150 Title XIII (HITECH)

SEC. 13404


For the purposes of compliance with privacy and security regulations, a “covered entity” and its “business associate” are equally liable as if each were itself was a covered entity.


Which means if I send a DTC genomic test off with a doctor’s order, AKA Illumina, a breach in that data due to the lab or interpretive business associate THEY are just as liable as the physician.

This means that DTC Genomic tests ordered by physicians fall into a completely more risky category than those ordered by Joe Blow.

This one risk may be why DTC is dying not to make these tests gatekeeper specific. Once these tests become gatekeeper specific, DTC will

A. No longer be DTC
B. No longer be free of HITECH and HIPAA

Which means a big ‘ol nightmare for these companies as they want to emphasize the social networking part. You see, social networks have always balanced growth versus security and the same is true for any Internet Technology.

But let’s say this is just one rogue hacker who has decided to hack a genome record ordered by a physician…….Via say a hacked email or website……..

What is the penalty?



This is the scary part.

Sec. 1320d-6. Wrongful disclosure of individually identifiable          health information           (a) Offense      A person who knowingly and in violation of this part--         (1) uses or causes to be used a unique health identifier;         (2) obtains individually identifiable health information      relating to an individual; or         (3) discloses individually identifiable health information to      another person,  shall be punished as provided in subsection (b) of this section.  (b) Penalties      A person described in subsection (a) of this section shall--         (1) be fined not more than $50,000, imprisoned not more than 1      year, or both;          (2) if the offense is committed under false pretenses, be fined      not more than $100,000, imprisoned not more than 5 years, or both;      and         (3) if the offense is committed with intent to sell, transfer,      or use individually identifiable health information for commercial      advantage, personal gain, or malicious harm, be fined not more than      $250,000, imprisoned not more than 10 years, or both. 
So let's say someone hacked a record to get the one up on you, maybe you are a political candidate or maybe a business competitor, or maybe they want to sue you.......
If this rogue hacker performs an act of this on genomic information ordered by a doctor or that can be defined as PHI, these are the penalties. If it is not considered PHI, it is a far lesser offense.......
So the question is, do you want these protections if you are a customer/patient? I would say Hell Yeah.
But do you want them as a covered entity? Uhhhhh.....Ahem.......Well........
As a doctor we have to follow these. Why shouldn't anyone else who has been given the responsibility of handling human samples?
The Sherpa Says: As a consumer HITECH is great. But as a start up company it can prove to be a nightmare. But those who have to risk the most are the huge companies making millions of dollars....can you say class action lawsuit for millions? I know a few lawyers who would be interested in that! I wonder if the DTC Genomics investors thought of that


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5 Technologies going bye bye in this decade?

January 7, 2010 — admin

I read with interest a twitter post by @Blaine_5 @Genomicslawyer and a few other of my friends…..


It turns out there is this theory that what we use often isn’t the best or the most elegant, but it works. Sometimes this turns out to be a rube goldberg machine that we just can’t shake. Much like healthcare and insurance billing……..

Sometimes we see the errors in our way quickly and adjust course. Sometimes we don’t. It all depends on who is putting money into things and what the priorities of the society are at the time.

Think about all the archaic things we still use and do. I think about these every day as I see patients and interact with a system that has been doing some of the same things since the dark ages……..

Foxglove anyone????

Seriously. But that will change with blogs and social networks that allow us to cut most things to pieces very quickly. Engineers are very good at this rapid changes, priests not so much, somewhere in between lie most people.

Stephen Friend has decided to put one of these critiques out there. His 5 things that will be gone in 10 years…..

1. GWAS

“Single nucleotide polymorphisms (SNP) analysis isn’t going to last long as a major driver of biologic insight. Within the next one to two years, people will wake up to “ITEGS”—”It’s the entire genome, stupid.” Technologies are poised to allow analysis of variations in thousands to even hundreds of thousands of people. Do not be surprised when all the people with a disease such as Huntington’s are analyzed for DNA alterations across their entire genome. Groups such as Cure Huntington’s Disease Initiative are already preparing for this world.” Courtesy XConomy


I freaking love it! ITEGS or better yet ITGS! I wholeheartedly agree that this is the platform which will work when combined with technologies to assess methylation status RNA function and expression and combined with………

Phenotypic data such as a physical exam, vital signs and PEDIGREE!!!! Which is why in the end, even the most complex interpretation machine will have a problem without someone to give these other data points. Will it be the clinician or machine which hears the heart murmur? We already know machines outperform in this realm.

But I agree, the boondoggle known as DTC Genomics and research based on SNP scans is a novelty, but there will be better options for discovery.

Why would you pump money down the DTC rabbit hole, unless you are in love with their “logic gates” for processing the genotypic data. Which IMHO should actually all be open source to assure the best and most timeliness. Why let this genome interpretation software be a one trick pony, we know open source works well, why mess with it?

2. Proteomics as the end solution.

I think this line puts it best

“The next wave of insights will be in the hands of those that can build network models of what went wrong in the disease states.”

Uh, paging Dr Lee Hood? Can you hear me Lee?

3. Biomarker signatures as commercially viable robust markers akin to cholesterol or estrogen receptor positivity for breast cancer.

Ah yes, there’s a biomarker for that! I have seen this with PSA, CA125, 9p21.3, I could go on and on. The data and patient population required to really, really get something out of this is in the order of hundreds of thousands of participants. Not even a tiny Island nation going into default could save this model!

4. Indications for drugs determined by Pharma trials……

Yes, I agree. The real next step is to determine WHO should get the drug, not WHAT should get the drug……Pharmacogenomics is going to be a real game changer over the next decade. MARK MY WORDS.

But his 5th I disagree with.

He states the large hunter gatherer approach such as Framingham will not exist. I think he is dead wrong here. There is no doubt in my mind, nation states will yearn to harness genetic technology and cures for diseases in a whole new light and fashion.

Genomics will be one of the new arms races once terrorism and hunger and pestilence and civil unrest and malaria and TB and poverty and crime are eliminated. It will start when we can use the genome to profile for medications and only go further………..This hunter gatherer approach is the best way to do such trials and only governments have the capital to perform them.

The Sherpa Says: The decade is upon us. With birth pangs we will see new technologies destroy the old in Genomics and Personalized Medicine.
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Another Year, Another Bankruptcy

December 31, 2009 — admin

OK,

Tally Time. It is time again to see whether my predictions for 2009 were right. Or if I was way off the mark.

The Highly Likelies first
1. Francis Collins will become the Director of the NIH……..You Betcha I pegged that one.
2. We will see a pharmacogenetics lawsuit……Well, still haven’t seen that yet, despite the FDA label changes

Batting 500, next up

Long Shots

1. X Prize winner: PacBio, ok, maybe I was a year early on this one
2. Oprah’s gene scan bougus. Guess what? It Was!

Still at 500, who’s next

Ridiculous

Ok, these are what they say they are. Ridiculous. I don’t think I can be held to the same standards for these swing for the fences…..

1. Mark Cuban Buys the rights to the 23andME database. Ok, I was off. DeCode tried to steal it and Google keeps dumping money into it……Both just as crazy as if Cuban would buy it……
Maybe we call that a fly out?

2. Next-Next-Next gen Sequencing will debut……you have heard of nanopore right? Is this Next-Next Gen? Or Next-Next-Next Gen? Hmmm. Foul Ball!

3. The last one is so silly I don’t think it was meant to be called………..The US fracturing into territories and fighting against the world…….Not quite yet.

So on to this year’s doozies!

Highly Likely

1. Another DTC failure……yes. I won’t say which one.
2. One of the DTC Genomics companies will get into clinical care. They will set up shops. It may be a newcomer or an old dog. But it will happen.
3. We will have data on PGx testing with Plavix. And it will support the use.

Possible

1. Francis and Kari will start the Population Genome Study in the US
2. The XPrize will be won by Complete Genomics.

Ridiculous

1. Again, Mark Cuban will Buy Sergey’s share of 23andMe’s database
2. Myriad will lose the first round of hearings re: their gene patents……

The Sherpa Says: If Kansas went bye bye last year, this year we will have to “Pay no attention to the man behind the curtain!”
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Lp(a) Maybe there’s something there that wasn’t there before?

December 24, 2009 — admin

I unwrapped the NEJM this week and to my surprise it has a Lp(a) stuff in it. One of the things we do to prevent heart disease is take family histories. We also check cholesterol levels and include something called a Cardio-CRP. One thing we haven’t been including is a Lp(a). Why? The only data I see that is good on this is on women.


We use validated risk tools like Reynolds and Framingham Risk. It was with great interest that I read about this recent “candidate gene” model of assessment for Lp(a) genetic link to levels and risk. Clarke et. al.

They also looked at the other GWAS linked regions and what they found was most surprising in my mind.

LPA, which encodes apolipoprotein(a), was the only true “candidate” gene on this custom array that was significantly associated with coronary disease.

Now why would the other regions not be as strongly linked? Or better yet, why was Lp(a) more likely to be linked and associated?

Well, LPA the gene produces a protein called Lp(a) which is hypothesized to carry oxidized proinflammatory phospholipids, thus promoting inflammation in coronary arteries in turn creating niduses for clot and heart attack.

What do the other regions do? Dunno. I think that is the teaching point here.

GWAS great for illuminating possible pathology, which then in turn must be dissected and validated.

Candidate screens are good for risk markers IFF there is some hint of WTF the proteins are doing for the disease.

This is why I am just flummoxed by the fact that people are still pushing tests which have little to no clinical use or even prognostic capabilities.

Listen, you want to discover yourself? Go get a cholesterol, Glycohemoglobin, and complete blood count. Check your blood pressure, check your BMI. If any of these are abnormal, go seek professional help.

But please, please, please don’t use SNPs that have no science behind them as true science or clinical markers. research them, sure. But using them like MDVIP has……..Risky guys.

Which reminds me. I am taking care of a patient who recently left MDVIP…….the patient had the Navigenics SNP scan done………what do I find on family history?

The patient met Bethesda Criteria for HNPCC………

Guess someone was too busy scanning Unproven SNPs.

That being said, this current study by Clarke suggests a few things

1. Two LPA SNPs explain approximately 36% of the overall variance in plasma Lp(a) lipoprotein levels. That could be like the CRP story. Yeah CRP levels but no association with risk. Big Whoop, but….

2. Both SNPs (one coding for the amino acid substitution I4399M and the other non coding) are associated with coronary disease. Ahem, like to see some replication here……But it could be true.

3. After adjustment for the plasma Lp(a) lipoprotein level, the association between LPA genotypes and coronary disease was abolished. Well…..that means to me, phenotypic testing with Lp(a) levels may be more useful than I had thought…..And definitely more useful than genotype testing.

The Sherpa Says: Hmmmm, maybe we will see much more of this trend. Non-genetic molecular testing being more valuable than genetic testing for risk prediction…..Wait a sec’
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Merry Christmas

December 24, 2009 — admin


Ho Ho Ho!

As I begin to enter year 3 of this blog I have refined my thinking and working to effect change. Personalized medicine delivery will change soon, so will personal genomics. I hope to create some of this next year. Until then, Merry Christmas everybody!

The Sherpa Says: And to All a Good Night!

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Navigenics for 23andMe prices?

December 22, 2009 — admin


Yes, That is correct. As if this stuff couldn’t get any cheaper. It does.

“Happy, healthy holidays! Holiday offer: Our #genetic service for $499 (half off). Use code naviholiday2009 at checkout. http://bit.ly/roe95“

That straight from the mouths of the Navigenics Babes, Seriously. Do you know Katie Kihourany?

Everyone including Daniel MacArthur is yelping about the DeCodeMe free analysis offer, but I have yet to hear anyone screming about the 500 USD drop in price of Navigenics service. Ladies and Gentlemen, this is a 50% price cut.

In what world do you cut your service cost in half? This didn’t even happen with the iPhone. Seriously?

This is a bad, bad sign coming from the team at Navigenics. Nearly a year ago they launched Annual Insight for 499…..Now the whole ship is up for 499……..

I have yet to see how this market is the market for Whole Genome Testing. In fact, my assessment is that whole genome sequencing will not be used widely until it costs less than 300 USD.

Why? Can your genome data play crazy videos of Will Smith? What about making a phone call and downloading songs? No?

Well, what can a whole genome do for you? Good question. The iPhone wins because in it’s ads it shows you what it can do……

These tests and the whole genome have not shown that utility. That’s why they are cutting their costs…..because the can’t show that they have use……..

And that is precisely why deCode is offering its analysis service for free. They want to show you what they do……..

The Sherpa Says: Like I said before, climbing Everest with one Crampon a windbreaker and a map is not what most rational people want to do……

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15 Days Away Gives Time for Perspective.

December 22, 2009 — admin

“Although there appears to be a clear relationship between UGT1A1 genotype and severe neutropenia (and some evidence of a relationship with severe diarrhea) there is no evidence to support or refute the hypothesis that a modified initial and/or subsequent dose of irinotecan will change the rate of these severe adverse drug reations.” -EGAPP working group analysis of UGT1A1 testing

That is where most of personalized medicine (PM) is at today.

Why is this important? Because this precise clinical set of questions will be worked out over the next 10 years.

While I have been taking a break from posting some things have become crystallized.

The first thing: In an economic downturn, your genomic/PM product better have intrinsic value.
Chances are, if you have to have big celebrities and open bars to launch, you need to rethink the product.

The second thing: If you think you can take science to market in less than 5 years, then you need to do one of 3 things.
1. Immediately Cure Cancer
2. Prevent HIV infection
3. No, there are just 2 PM things that will work here.

Do I think there are products that don’t involve direct basic science that will help personalize medicine which CAN go to market quicker than the 10 year revolution we are about to undergo?

Yes. But none involve PhD geneticists. They involve computer scientists, automation, email, etc.

This latest bubble of DTC Genomics existed just so the SV could cut their teeth on genetics for the big bite 5 years from now.

Why is the Sherpa such a naysayer?
I am not. I am a realist planning the ascent of the next tier.

That Tier is clinical utility. Yes we still have the missing heredity here. But let’s say that will come in the next 5 years…..maybe We still have 5 to go.

Those 5 will be used for clinical studies, for outcome and guidance of therapies. But that is only the next tier.

Pragmatic physicians and scientists will demand replication, some will fail, ultimately casting doubt on the field as a whole.

This will further driving pragmatism and encourage naysayers.

Don’t believe me. You have heard the new mammographic guidelines from USPSTF, right? Pragmatists have always said we don’t need so many mammos….

Now so does Consumer Reports !!!

Many people place their trust in Consumer Reports. It is clear, they too see a case for overspending.

In an economic environment a savvy entrepreneur will look for targets like Asia.

As a doctor, I know most PM tools are on the horizon, so I pragmatically pick up my pen and pedigree…..

I am at my ICOB meeting today and am posting this from there. We will be going over several genes and variants. I am excited because OSUMC has now partnered with CPMC……there is no doubt this project will continue to grow in strength and importance as we have quite a cohort.

The Sherpa Says: Poor PM, attacks on every front. But don’t worry, in the end, we win.

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