PGx in DTCG? Doesn’t stand up to Useful testing.


HT Don Rule today as well as the ENTIRE Pharmacogenomics Advisory Group that I am a proud member of.


Don wrote this comment a few days ago

I was curious about what SNPs the DTC companies offer so I wrote a little applet (http://snpweb.cloudapp.net/#/PharmGKBSNPs) to compare them to the SNPs in PharmGKB. It turns out the the Cytochromes are particularly sparse.”

Well Don, you are correct. Even more so, as we began to review SNP data it became crystal clear on Monday.

The reason I was pissed about 23andMe doing the CF testing is because they missed hundreds of potential carrier alleles. What was even more so angering when I realized, you could be “tested” by one of these DTCG companies for “Plavix Metabolism” and come up with the absolute wrong answer.

Imagine that. Most people turn to DNA for an “absolute call” but when you don’t look for the right SNPs or all of the needed SNPs, you miss a whole bunch.

Quick story. I had this pulmonologist physician, an elder statesman, super smart, Ivy league trained come up to me and say “Hey Steve, can you help me out?”

He is a sleep doctor too. He said “I have been trying to test for this narcolepsy gene and I can’t get the right answer”

I said “Sure Dr. X, what do you mean ‘keep getting the wrong answer’?”

He Said

“Well I am looking for HLA DQB1 and they keep telling me about this HLA DR, I have sent this test 3 times now and still gotten no information about HLA DQB1.”

I did a big ‘ol face palm.



Instead it searched for an imperfect haplotype……

That’s the problem. If you don’t test for exactly what you are looking for, you will never find it. Nor will you have the correct clinical answer.

If you only test 2 SNPs for CYP 2C19, you will never be able to accurately predict what someone’s metabolizer status is.

What people should be using to assess metabolizer status of medications is something like the DMET Plus with additional PCR or another platform. AmpliChip does a nice job, but we have to be serious when it comes to medical care.

You Cannot, I repeat Cannot take the advice from 23andMe when it comes to metabolizer status for Plavix.

Please, please, please listen to me. Even 23andMe states it on their post about Plavix

This DTCG test is not ready to be used in the clinic or even trusted to tell your metabolizer status. Right now, they are not testing enough SNPs for me to be happy with it and use it in the office.

Don’t stop your Plavix! Instead go get a clinical pharmacogenomic test done by someone who understands the limitations of the labs.

That drunk who lost their keys is still looking under the lamposts because that is where the light is……….

That is a stupid way to do clinical pharmacogenomics.

The Sherpa Says: Pretending to be clinical without standing up to clinical rigor is a recipe for disaster. I await the lawsuit from in stent thrombosis for the poor sap that trusts 23andMe enough to stop their Plavix.
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Why did P&G invest in Navigenics?

I kept beating myself up, trying to figure out why the largest food/products company in the world put money in Navigenics. Was it for nutrigenomics? Was it for the captive audience to market products to?


Until today, when I read in American Medical news that Proctor and Gamble BOUGHT MDVIP in December of last year! Man how did I miss that one?

Terms of P&G’s acquisition were not disclosed. It was made by P&G’s FutureWorks unit, a new-business generator that’s intended to connect the company with external partners and expand P&G’s scope beyond its core businesses into new channels.”

So, P&G is looking for the whole enchilada in personalized medicine here.

Too bad, Navigenics‘ tests are currently not useful. But maybe someday they will be……

The Sherpa Says: Navigenics is not the target. MDVIP was, so don’t believe anyone who tells you otherwise…

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A moment of Clarity. Some DTCG is not bad.


Ok,

Here is the G-d’s honest truth. Not all SNP/DTCG companies are bad. What do I mean by bad?

Not all SNP/DTCG companies misrepresented that which is not medically useful as medically useful.

I look at Pathway and Counsyl for example. Fast followers looking to say what they do and mean what they say.

Some of these DTCG tests could be clinically relevant and useful. The problem I have, is that there is no point at which I can say, “Hey I just want the clinically relevant stuff!” No ear wax please.

I need that as a clinician. If I want a huge panel of say CYP450 tests, where do I go? there are some labs that do this and charge and arm and a leg. One company, who I used charged the patient thousands of dollars because insurance wouldn’t pick it up.

That cannot ever happen again.

With the addition of these tests with some clinical value, there must be a value add of inexpensive and RAPID TAT (Turn Around time)

A classic example is my last post. Provided these tests become validated clinically, in a patient who can’t give me her Gail risk information (tough not to, but it could be a real case) I would use that other panel

The same is true for BRCA founder mutations. Provided you won’t drop it in some google database that they get served up mastectomy ads, some patients are afraid of needles and that is a barrier.

There are some very good things here. These good things are getting drowned out by some very bad things.

We can work together if you are willing to bend.


The lack of really effective clinical utility and the existence of commercial interests increases the confusion though. It’s hard to sell something that is interesting, “fun”(?), quite expensive, but not actually that useful to the majority right now. Hard to sell means sometimes over the top marketing.”

What medicine cannot tolerate is Over the Top Marketing. It leads to inaccurate statements. This is something extremely forbidden in certain states. In fact, some states don’t allow advertising to patients at all, or there laws are so strict you couldn’t say anything than

“Dr Murphy, accepting new patients, take insurance”

Why is this? It is to prevent false claims and promises. Doctors can’t make money back guarantees. They can’t make statements which are not based on fact in advertising. A lot of companies in a rush to get out young science and feed the hype cycle for grants and whatever have been all too guilty of this hype.

So when I get a comment from one of my readers who says (paraphrased)

“Hey all this bashing you do on DTCG is making us in the science end of the SNP reseach look bad”

It prompted me to say, hey, I wouldn’t have to throw so much cold water on it if it weren’t being hyped so much by DTCG…….

So I guess my point is simple.

Hey DTCG, your opportunity is to leverage your amazing platforms to launch medical services, TO and WITH physicians.

Keep the nonmedical exactly that, NONMEDICAL

Keep the Medical EXACTLY that, MEDICAL

People can benefit by knowing their 2D6/2C19/2C9/VKORC1.

But there are some hurdles to be overcome

1. How can I trust your results?
You have started by enlisting or creating CLIA certified labs, that is a good start. Maybe FDA cert would be nice. Not needed, but nice. There currently is only AmpliChip that is FDA approved….Would like others.

2. How can I know your interpretation is correct?
By using board certified molecular pathologists, I can get a comfortable feel for the fact that the results have been vetted by your specialist. This is muy importante!

3. How can I integrate the results into my EMR/PHR/etc.?
This is going to be super important. How can I save these results linked to patient care? Sure, some would pull paper and put it in the chart, others would prefer a pull in and link. You have to think how to do this.

4. What if the interpretation changes?
Will you take responsibility to contact Either the ordering physician or patient when a result changed? This will be important as we learn more about the nature of these genetic changes.

Doctor’s rely on these 4 things from most labs that they use. The depend on these services to be provided professionally and accurately.

These 4 things are EXTREMELY hard to do. But NEED to be done if you really want to be a part of the medical community. But even if you don’t, I think your customers deserve this sort of validation and service. Don’t you?
Take the jump, create a medical arm. Work with us.

The Sherpa Says: This is what is needed. Medicinally used DTCG that is “Allowed” to be of clinical use. A new Terms of Service, just for doctors, with a validation process that is transparent. And a Marketing process which is truthful.
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SNPs for breast cancer risk? It Depends.

I hold in my hot little hands a copy of the NEJM, March 18th edition. In it there is an article which isn’t even released yet.


Entitled
“Performance of Common Genetic Variants in Breast-Cancer Risk Models”

Remember when we did this for heart disease risk? FAIL WHALE…..

Do you think it will happen again?

The Study

10 common genetic variants


I had to create a couple of pages on SNPedia for this list FYI…..

The Methods:
Cases and controls-WHI, ACS CPSII Nutrition Cohort, Nurses Health Study, Prostate/Lung/Colorectal/Ovarian Cancer Screening Trial, and Polish Breast Cancer Study.

Cases-Woman who had received diagnosis of invasive breast cancer.

Risk Models Used-A hybrid of the Gail model…..I.E. Not exactly the Gail Model.
1. First degree relatives with breast cancer
2. Age at Menarche
3. Age at first live birth
4. Number of Breast Biopsies

They acknowledge that they were unable to get atypical hyperplasia and Mammographic density. Both of which have improved Gail.

So, This Gail is a little hobbled and not the best predictive model…….

The studied models- 5 logistic regression models
I don’t have the supplementary tables and methods yet.

The nongenetic model-Gail Model
The Demographic/Genetic Variant Count Model-included number of alleles.
The Demographic/Genetic Individual Variant-Accounted for individual effects of each SNP
The Inclusive Model-Gail, Genetics Demographics
The Demographic Model
And Random….

When we do these sorts of statistical analyses we look for a couple of things.

A. Number of people reclassified and how?
B. The Area Under the ROC Curve


Results-

1. The Inclusive Model Yielded and AUC of 61.8%
2. The Nongenetic Model yielded an AUC of 58%
3. The Genetic Individual Variant Yielded an AUC of 59.7%
4. The Genetic Variant Count Yielded an AUC of 58.8%
5. Breast Biopsy BY ITSELF Yielded an AUC of 56.2%

That is a 3.8% difference in Yield from Genes and without Genes integrated into the weaker Gail Model.

Lastly, they asked. Well, does this Inclusive Model do a good job of discrimination of High risk vs. low risk.

The Answer- It determines lower risk better than Gail. It does not determine higher risk better.

The authors of this study have stated that

“As in Diabetes and cardiovascular disease, the addition of the common SNPs added little to the predictive value of the clinical models. On the basis of theoretical models, Gail has shown that increases in the AUC similar to those observed here and not sufficiently large to improve meaningfully the identification of women who might benefit from tamoxifen prophylaxis or screening mammography”

Take Home

The addition of these factors only creates a minimal statistical increase that is of no useful clinical benefit.

The Sherpa Says: If the press says “gene tests fail to improve risk assessment” You can be assured that the DTCG industry is no longer the darlings. If instead they say “Improvement in risk model” well, then you have chance to woo them back! It Depends…….
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How can MDVIP use Navigenics Test for Medicine?

I have been harping on this say what you mean. Say what you do. Theme lately.


I am a board certified doctor who practices personalized medicine. I see patients and apply the principles or pharmacogenomics, risk prediction and prevention tailored to each individual patient. I do this by taking a 3 generation pedigree, using current clinical risk models and pharmacogenomic or other genetic tests when indicated. That’s me.

I have this nagging pain about MDVIP, Ed Goldman and Navigenics.

Some MDVIP members are using Navigenics tests for medical risk prediction. Navigenics is ok with this because hey, they’re doctors.


The contents of our Site, including any risk estimates or other reports generated by the Services (collectively, “Your Report“) and any other information, data, analyses, editorial content, images, audio and video clips, hyperlinks and references (collectively, “Content“), are for informational purposes only and are not intended to substitute for professional medical advice, diagnosis, or treatment.

The part I want to focus on is “Are for informational purposes only and are not intended to substitute for professional medical advice, diagnosis or treatment”

It seems to me that this will be the more popular language in a Terms of Service for DTCG.
Notice that nowhere does it say, “This report is not intended to diagnose or treat”

I think that while it is nice to not say that, when in fact people are using it to diagnose, it is even goofier to say that it is not intended to substitute for a professional’s diagnosis. Ok, so are you saying

1. This is not to be used for diagnosis/medical advice
2. This is to be used for diagnosis, but the professional’s diagnosis trumps ours
3. This test is meant to be used by professionals to aid them in diagnosis and treatment

I am really confused here. Is this a medical test or not. Just come right out and say it!

The Sherpa Says: Say what you do, do what you say you do. Isn’t that what the Common Framework of Principles is About?

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BRCA testing by 23andME is the same as Myriad Genetics.

February 2009 23andMe entered into clinical medical testing of DNA variants which are the exact same variants Myriad Genetics tests for. There is only ONE use for this test. That is a clinical use. When these results are obtained clinical counseling is the standard of care for delivery of these results. Not a flashy webportal……

Minimizing the seriousness of a medical test looked just as awkward by us in the first video as it should be by showing it on a blimp or at a cocktail party or highway billboard sign…..All things that Linda Avey and Anne Woj decided to have their company do….

The Sherpa Says: Misha is correct, Medical Geneticists painted themselves into a corner by harboring in the rare disease port. This allowed people who have no G-dDamn business in medicine, to play doctor at parties and on the internet!

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The FDA, 2c19 and the ACC

Did anyone see the FDA issuance of the better warning that as many as 14% of patients will not benefit from Plavix/Clopidogrel?

Did anyone see the cold shower being poured on by the press and the cardiologists?

Christopher Cannon Assoc. Prof at Harvard says:
The ACC will need to develop protocols, “Thus a real conundrum”

He then says “I expect mass confusion in response to this FDA warning”

Well Chris, It’s not as if we haven’t been shouting from the rooftops about this for over a year now…….

“The test costs about 500 USD according to Courtney Harper PhD, Director of the FDAs division of chemistry and toxicology devices. But cost isn’t the only issue.”

Which BTW is false 23andME is cheaper……But wait, isn’t that medicine?

“The time to get a result varies. It may be a few hours to a day or two, or other labs may take a few weeks”

This is absolutely true. It takes me 3 weeks for a test from Quest. I am certain that there has to be some lab to do it quicker…….

BUT, the FDA has only approved AmpliChip for this testing…..

This sounds to me like the FDA needs to approve some kits and PDQ with the ACC meeting coming up like,

My guess

1. The ACC will address and release its prelim algorithm

2. The ACC conference will have even further data regarding this released.

3. The last step is to FDA in some kits to do this test, quicker and more standardized.

We need a company that can direct us to

So the question, why all the cold water on this killer app? Well, because it is getting lumped in with DTC genomics, which is feeling a backlash from hype and failed promises. Or trying to play medicine.
As well as a flat disregard for medicine. So when the press and the healthcare providers are against you, you can feel it.

But this is what I have been frustrated about all along. I saw this coming. Doctors blowing off PGx thinking it is SNPChip Hype. Journalists pouncing on overpromising and intellectually dishonest DTC Genomics companies…..

This is why I was so mad about the blimp.

When something really awesome comes around, people are burned out from Open Bars……

The Sherpa Says: Let’s really do this. Genomics and PGx IS medicine. Let’s say it proud, Let’s ay it loud. Quit screwing around to avoid regs. Let’s how the world how we can use this to help mankind!

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……..DTC Genomic Medicine?

Back in February of 2009 Myriad decided to do testing for genetic founder mutations………

Yet they claimed it wasn’t medicine and should not be used for medicine.

BRCA Ashkenzi Jewish founder mutations offer information that can confer an elevated risk of Breast, Ovarian, possibly melanoma, Pancreatic and maybe blood cancer.

There really isn’t any other thing that these tests can be used for other than medical decision making and diagnosis. The diagnosis would be Genetic Risk for Cancer. There is a medical code for it in the International Classification of Diseases 9th Edition. In fact there are multiple codes. The v84.0 super family of codes.

Granted this presentation was a bit manic and the iPhone volume control was horrible (turn down your speaker volume). But the point is clear. Either founder mutation testing is a genetic mutation, or it is not.

You cannot have it both ways. Say what it means. If that means your state requires physician consultation or ordering, do it.

If it doesn’t, well, I strongly recommend you receive that healthcare provider service.


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The problem with Comparative Whole Genomics……


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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Just 4 million? What 23andMe is worth.


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!


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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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 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.


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!

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?


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.

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.

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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Enter the "Not" DTC Genomics Rep


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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Congratulations Navigenics. You ARE a clinical lab! Uh-Oh…


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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Lp(a) Maybe there’s something there that wasn’t there before?

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


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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AJHG is in and my Favorite Muin is in it! But He Is NOT the Father!



With breast cancer as an example, we examined the combined effect of uncertainties in population incidence rates, genotype frequency, effect sizes, and models of joint effects among genetic variants on lifetime risk estimates. We performed simulations to estimate lifetime breast cancer risk for carriers and noncarriers of genetic variants. We derived population-based cancer incidence rates from Surveillance, Epidemiology, and End Results (SEER) Program and comparative international data. We used data for non-Hispanic white women from 2003 to 2005. We derived genotype frequencies and effect sizes from published GWAS and meta-analyses. For a single genetic variant in FGFR2 gene (rs2981582), combination of uncertainty in these parameters produced risk estimates where upper and lower 95% simulation intervals differed by more than 3-fold. “


Did you get that?

They took a look at what it really means to give point estimates for lifetime risk of disease comparing with population risk data. In this case they chose breast cancer…….and FGFR2

Their conclusion?

Epidemiologic parameters involved in computation of disease risk have substantial uncertainty, and cumulative uncertainty should be properly recognized. Reliance on point estimates alone could be seriously misleading.

Do you get what they are saying? Let me break it down this way. When I see a patient for BRCA testing they always ask

“How high is my risk?”

I say: “Well…….it is a range.”

Most people don’t like ranges. In our little rat brains we think a range means uncertainty and probably a little guessing. Most patients don’t like to go to doctors who give ranges or guesses.

Nor do people like buying things that don’t give them “exacts” People very often, when left to their own devices would choose black and white over gray. They just don’t like feeling uncertain.

That’s precisely the big problem with how genetic testing has been marketed.

Think about it.



On 23andMe: Find your Norovirus resistance!!

OR


Sounds pretty certain to me…..

Do you get it?

Well, the answer is simple. Nothing in life is certain. Nothing, except death and taxes.

This study shows that if your model relies on too many uncertainties, your risk model fails. This is the biggest problem with the DTC Genomics companies’ models. They are based on too much uncertainty and as such fall in the realm of fortune teller rather than risk prognosticator.

This is precisely why I have said “Data is Data, but Data can be Garbage.”

And Garbage In = Garbage Out.

The Sherpa Says: with any risk model there is uncertainty, no surprise there. But the real surprise is the marketing of it as CERTAINTY to an unsuspecting and primed for certainty public.
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What about the SACGHS registry? Another missed opportunity?

Remember this? From GenomeWeb

“After extensive fact-finding, consultation, and analysis, the committee found significant gaps in the US system of oversight of genetic testing that can lead to harms,” SACGHS states in the report. “The committee also identified novel opportunities that would enhance oversight.”

What are these novel opportunities to enhance oversight?

“As reported by Pharmacogenomics Reporter in February, the establishment of a mandatory, web-based registry for all laboratory-developed tests is one of the main vehicles the committee is proposing in order to improve how the federal government regulates genetic tests [see PGx Reporter 02-20-2008]. “

The 21st Meeting of SACGHS will occur in February of 2010. I wonder if this recommendation has gone on deaf ears. With all the turmoil surrounding health reform, will HHS take genetic test regulation up? One of 3 or 4 things may happen.

1. Health reform happens, billions flow into HHS and they form a committee to set the SACGHS recommended registry up.

2. Health reform happens, they are so busy that this gets queued.

3. Health reform doesn’t happen. Nor does the Registry.

4. Health reform doesn’t happen, thus the HHS has the time and attention to set up this registry.

But what I really want to know is: “Will the HHS including DTC genomic testing give these companies a perceived seal of approval?”

Better yet, will these companies be listed?

PWC has said Personalized Medicine will grow at 11% (How the hell they come up with that figure g-d only knows) Do I think DTC genomics will be included in the growth? Probably not. This type of testing will not grow until it is less than 100 USD.

The Sherpa Says: Like I said before, unless PM can cure cancer or prevent HIV it is likely to be difficult to sell. No matter how many meetings Harvard/Scripps/Etc has. What needs to happen is promotion of physicians (like my group) who are actually implementing PM.

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