The Infer Game

What really gets me upset is that marketing people infer something but don't outright make a claim.

They do this because to make a claim which isn't true is grounds for the FTC to investigate you, but if you "infer" something, you don't make the claim.... Why do I jump on this?

Because I don't play "infer" for my patients.

In fact, health information and healthcare is too important to "infer" anything. You cannot manipulate peoples' trust in you....

Either we can justify via science and current medical practice or we cannot. Why let people dangle in the wind with false information.....

But this little game is nothing new. Vitamin hucksters and weight loss supplements play this "infer" game too.....so I guess the DTC genomics companies want to be seen as Hucksters....otherwise, why infer something which isn't true......

This went on with Navi's most recent blog post

It is possible that the Factor V mutation also confers a selective advantage to people who carry one copy, but scientists just aren’t sure yet.

If you carry the mutation, you can take steps to prevent becoming ill as a result. And, if you meet someone else who carries the mutation too, it’ll be a little like finding a long-lost brother or sister! Somewhere back in the human genetic family tree, the two of you have a “Factor V” ancestor in common.

The inferring that goes on is that there is some treatment that can prevent clots in these patients with Factor V Leiden. The truth is, there is no treatment to prevent these clots whose benefits outweigh the risks........

I already made this point with 23andMx's goofy CEO Anne Wojicki who made claims in a similar fashion on Charlie Rose the other night....

Pay attention closely, if the FTC doesn't jump in and investigate these companies' suspicious practices.........I will be surprised......very surprised....

Are you pissed at the inferring game too? Well, you too can voice a complaint to the FTC....

The Sherpa Says: DTC genomics companies are lucky that their product doesn't cause arrythmias, sudden death, liver failure or loss of smell.......But even if they don't their marketing claims certainly still do stink......

Great Job Mike! 2C19 meets the grade!

I was flipping through the internal medicine news yesterday when I saw a colleague. Mike Murray, Clinical Chief up at the Brigham who had given me some good advice re: being a fellow and academia......

He and a couple other internal medicine geneticists write a column called "Genetics in Your Practice"

Which is a welcome addition to what my wife and I (Both Internists) believe is one of the best print publications out there for keeping ahead of the curve with IM and subspecialties....

Well,
Mike wrote about Plavix, which, as you know, I have been all over since the studies came out in January showing significant differences in outcomes clinically with patients who cannot activate Plavix. Why was I all over it? Because it had met some criteria which I think will define what a good PGx test is......

I have as of yet failed to detail precisely what these criteria are.....It just so happens, Mike did a brilliant job of it.....So without further ado. Dr. Mike Murray, Internists, ID specialist AND geneticist defining the criteria....

From Internal Medicine News

So, what will bring a breakthrough application in pharmacogenetics? I believe that a true breakthrough into the mainstream will occur when the gene-drug pair has many or all of these characteristics:

▸ A widely used drug. There are currently some excellent examples of gene-drug pairs as models for the clinical application of pharmacogenetics; however, they happen to be with drugs used by only a small number of subspecialists. A true breakthrough application will need to be a widely used medication.

▸ An “essential” drug. Although we may eventually get to pharmacogenetics testing for almost all medications, a true breakthrough application will not be for a drug for which the application is usually elective (e.g., onychomycosis therapy) or for a drug that has equivalent substitutes inside or outside of the class (e.g., a diuretic for hypertension).

▸ Potentially severe consequences from use of the drug without pharmacogenetics guidance. The motivation for using a pharmacogenetics approach is mainly safety or efficacy. The breakthrough application will need to help the prescriber avoid morbidity or mortality associated with side effects or ineffective treatment.

▸ A narrow therapeutic window. Aminoglycoside antibiotics are classic examples of drugs with a narrow therapeutic window, where underdosing can lead to disease progression and overdosing can cause adverse effects.

▸ Pharmacoeconomic advantage. The application of new technology to guide gene-drug decision making will be more attractive for clinical uptake in instances where it offers cost savings.

▸ Straightforward genetic interpretation. Much of current genetic testing deals with complex interpretations of sequence data where variants unique to the individual patient have to be judged as causative, noncausative, or of unknown significance. In 2009 the most straightforward diagnostic genetic testing is based on screening for common variants that confer increased relative risk.

▸ Validated significance of gene-drug pair. There will always be varied levels of confidence in any data set; however, replication of significant correlation in more than one large, well-designed study will be the most likely to be associated with rapid clinical uptake.

This is precisely what Plavix is......And it is precisely why it will lead personalized medicine this year.......Not genome scans, not whole genomes, Plavix pharmacogenomics...... Mike, yet again, you have crystallized criteria which I often find nebulous......

The Sherpa Says: If we judge all tests by this criteria we would be better off.......Imagine how many less tests would be ordered. Bad for business, great for medicine......

23andMx looking to cook the books in CA with SB 482

Daniel MacArthur and I have been noticing something and he decided to cover it today, which is why I have decided to provide a counterpoint here....Also GenomeWeb published on this. SB 482 is a bill I glossed over in a post in the past and was recently interviewed for in the San Jose Mercury News.......

Daniel leads this as 23andMx leading the regulatory push.....but this is more insidious than that. This is 23andMx trying to cook the books and create laws which exempt them from the stringent regulation which they should receive......

I told this to the newsies over at San Jose on Sunday, so I am going to post this today......

It turns out that this bill SB 482 essentially exempts DTC companies from facing the harshest regulations that medical providers/labs have to face

From Daniel
"In other words, 23andMe is pushing to have companies purely providing analysis of genetic data regulated separately from those doing the actual laboratory testing. Since 23andMe out-sources its testing to an external laboratory, this would exempt the company from some regulatory requirements. The move follows some fairly serious regulatory controversy over direct-to-consumer testing in California a year ago."

Which I predicted BTW....... But in all seriousness, these portals to lab services view themselves as NON MEDICAL entities, that is the crux of this argument, and by passing this bill it would set legal precedent as being non-medical and not facing medical regulations......

But that bill should fall flat. Why? Because it is written with a false logic. I am about to explain the correct logic............

The assumption is, that by only running an algorithm on biodata and giving a risk number, you are not practicing medicine.....nor is it running a laboratory....

Thus they don't need healthcare regulation or medical lab regulations.....but they are dead wrong.....

The first myth: Running an algorithm on biodata and giving a risk estimate is not medicine.......

Answer: IN FACT it IS medicine, the AMA guide book for Current Procedural Terminology acknowledges that this IS medicine and it should be coded with the number 99420 of the evaluation and management code..... I run something called a reynolds risk calculation on patients. It is a computer algorithm found at www.reynoldsriskscore.com. Give it a shot, you will see it is very similar to a DTC genomic test. I bill and get paid for providing this medical service......

The Second Myth: Because we don't run the test, we shouldn't be responsible for CLIA regulations. We are not a laboratory.....

Answer: This company actually accepts ownership for the sample and provides specimen handling which is delivered to an analytical facility.....By merely handling the specimen they need to be considered as part of the healthcare unit, or apply for CLIA exemption. Any handling of any specimen can be billed for and should be regulated as such..... Not the shipper, the company/person/lab who takes ownership of the specimen.....

Lastly,

I was on twitter last night when I saw this ugly retweet come from the account at 23andMx RT @dane: @23andMe BTW, you saved me $25 for a CF test - used my and spouse's 23 results instead. Thx! (via @23andMe)

Which raised eyebrows from myself and Daniel

"@23andMe For once I agree with (Steve) - implicitly promoting your chip as replacement for a validated CF test is a risky move.about 19 hours ago from TweetDeck"

I basically said that this is the type of shennanigans coming from a company who isn't being regulated.

If they were, this insinuation that using a 23andMx test for a clinical use, would never bubble up.....but it did.

And I am willing to bet the twitterer for 23andMx isn't medical at all....... Which is once again why, oh why SB 482 needs to be shot down immediately....

I am glad the ACLU is on this, but the AMA, The ACMG and the NSGC need to be all over this bill too........

As you can see from the edits, this bill was initially proposed as a healing arts bill, which is what it is....... But even with that, 23andMx has no use for YOUR laws.......

The Sherpa Says: 23andMx deleted that tweet, so at least they understand that what they are doing WAS and still is wrong......

Anne Wojicki, First Benadryl doping, now Factor V

I was actually watching the Charlie Rose interview with the 23andMx ladies....When Charlie Asks what the advantage of 23andMx is.

Anne and Linda both say "The problem with the GWAS is that you aren't followed over time. You get one shot and people can't give you further information"

What Anne and Linda are saying is: The Coriell Personalized Medicine Collaborative is the gold standard, we are merely trying to monetize something they are doing for FREE.


In addition, we are not IRB approved and are unethically doing this business, which is ultimately research. Which IS being done by a Not For Profit Medical Institution, Who is charging nothing I.E. FREE, and we would like to do what they are, but charge you 399 and have the right to sell your data......

Oh and did we mention that Google just put another 2.6 million into our bank accounts?????

But probably the funniest thing Anne had to say was at minute 18 of the clip on the PGP site..... Anne says "It's early, but there is a lot of interesting and valuable data in there (the genome scan)"

She then goes on to say "For Instance, there is a genetic marker for Blood Clots called Factor Five Leiden. Charlie, I am certain you must travel a lot. Wouldn't you like to know if you were at risk for these clots?"

That is when it hit me, for the 3000th time.

A.Neither of these ladies is in medicine
B. Neither of these ladies are PhD scientists
C. Neither of these ladies understand what it really means to be carrying out this type of study.

Hence

1. NO IRB
2. Promoting Factor V Leiden testing despite evidence to the contrary and a HUGE AHRQ report
3. Doping up their kid for transcontinental flights with benadryl!
4. She even said you might want to take medications for Factor V Leiden! OMG!

Why is the world listening to these silly ladies????
Why aren't they listening to themselves?

They both plainly stated, Coriell is the best study and that they want to be Coriell, without ever mentioning the name Coriell.

But the best line in the ENTIRE interview came when she said "With budgets these days, you may or may not end up flying economy class these days........." Charlie quips "WHEN WAS THE LAST TIME YOU FLEW BUSINESS CLASS?"

The Sherpa Says: There you have it, 23andMx's leadership endorsing Coriell's study. For FREE, not 399 USD. Oh and with an IRB and without Google.......

Watch Out Corporate Bloggers, FTC is on to you!

Now not only am I bashing corporate bloggers (Some may even call me corporate) Now the Federal Trade Commission has gotten into the game. It turns out that the FTC is on to the game of freebies for good blogging.

So to all of you who took free Navi or 23andMx or DeCodeme scans in hopes of them getting good press on your blog, you may have some issues. At least if you are in the US.....

From the Yahoo News

What some fail to realize, though, is that such reviews can be tainted: Many bloggers have accepted perks such as free laptops, trips to Europe, $500 gift cards or even thousands of dollars for a 200-word post. Bloggers vary in how they disclose such freebies, if they do so at all.

The practice has grown to the degree that the Federal Trade Commission is paying attention. New guidelines, expected to be approved late this summer with possible modifications, would clarify that the agency can go after bloggers — as well as the companies that compensate them — for any false claims or failure to disclose conflicts of interest.

So what does this mean for the genomics blogging world? A ton. I remember many, I mean many bloggers getting free kits. I also remember many people writing glowing reviews. I also know that the corporate blogs have been "inferring" things about what a genome scan can and cannot do........

The Sherpa Says: Just another case of government coming in and regulating for the protection of its citizens. Because of their commoners inability to sift through bull$h!t and hype. Time will tell what these new powers will do to the blogging community. I wonder what it will do for Twitter??? Wouldn't the government save a lot of money if they just made marketing illegal?

Crazy Friday, Awesome Call, Tru Blocks the Sherpa

I was amazed the first time I met Francis Collins, longtime a hero of mine, Francis was gracious and kind when I met him. I also share a common bond with him. Francis' Intern at UNC was a guy by the name of Jim Sabetta, one of my instructors....


That being said, before I started HH, I watched webcast after webcast of the SACGHS. This was 2005 and 2006 I'm talking about. I did it because it was research. But I saw a guy on there who inspired me, who had such a sense of reason that the whole group respected. His name is Muin Khoury.....and I just met him Friday!

It turns out we also have people in common. But more importantly, we have a healthy respect for family history in common...... This guy and his team at the CDC have been researching Family History tools and the state of the science of family history pretty aggressively. This team is a heavyweight in the field and I am blown away by what they are doing.

Why?

It is the cheapest whole genome, phenome, metabolome scan we have today. The best part is that it covers multiple people with just one take!


They are actually researching the role effect of family history on behaviors and diseases! Something which NEEDS to be done, just like it does for SNP sandcans. Except of course, Family History costs nothing.....and has some good data already! Their FamilyHealthware methods have just been released! I will cover this further in depth in another post....

I am a little ad that I didn't get invited to GAPPnet, but am very excited to see what this conference in August on the state of the science in family history will bring.....More on this later


"Update" of TruGenetics.

While I WAS optimistic that a physician was at the helm of this company, I was reminded once again that we can be shady as well. It turns out, Dan Vorhaus AKA Genomicslawyer, read the fine print of the consent form. HT Daniel MacArthur too! It turns out Free is not so Free. Its now out that if you consent, you give the green light to TruGenetics sharing your results with companies and that your data goes into a database for "research" OK, that's strike one and strike 2......


The high heater came when I was following the COO of TruGenetics on Twitter......I challenged some of thet things he had said, like I do @Lindaavey @23andMx @Navi......But unlike those companies that stand up and defend themselves and agree to spirited debate with me.......@Achamedian the COO of TruGenetics "blocked" me!

Strike three TruGenetics.

You are out! I am deeply disappointed that you wouldn't debate me. It shows your TRU-Colors, to run and hide and also hide the fact that you are taking people's DNA for compensation of about 299 USD...... Not impressive. Nor is your call rate and error rate of 5%...... I guess you get what you pay for, when of course that product isn't hyped by large PR firms...


The Sherpa Says: Don't sign up for TruGenetics and if you do, at least you now know that they have a shady COO who runs from the questions and from the Sherpa!

Free Scans, Free Scams? Maybe Not! The race is on!

Misha just posted on what I believe is the true value of all of these genome scans, currently.....

Free, until value is demonstrated in a way that doesn't include a "testimonial"

There is a new company called "TruGenetics" which is Enhancing Life Through Genomics

As I prep for my 11 AM conference call with the CDC, I have to get this post out there.....

They are giving away 10,000 scans for free. That's 500,000 SNPs from your genome, for free!

There are some big questions I have.

1. Who the hell is running this?
CEO-Jason Chien, MD, MS, Chief Executive Officer
Dr. Chien is currently a faculty member at the Fred Hutchinson Cancer Research Center and in the Department of Medicine at the University of Washington.

COO-A.Edward Mohebi, MBA, PhC, Chief Operating Officer
Ed is a serial entrepreneur with wide breadth in the healthcare and technology sectors. Namely, Digital Systems, Siemens, and Microsoft Corporation

2. Why?
To offer services!

3. What are they offering?

Sample of Over 200 Traits & Diseases

• Abdominal Aneurysm • Alzheimer's Disease • Atrial Fibrillation • Brain Aneurysm • Breast Cancer • Celiac Disease • Colon Cancer • Crohn's Disease

• Diabetes, Type 2 • Glaucoma • Graves' Disease • Heart Attack • Lupus • Lung Cancer • Macular Degeneration • Multiple Sclerosis

• Obesity • Osteoarthritis • Prostate Cancer • Psoriasis • Restless Legs Syndrome • Rheumatoid Arthritis • Stomach Cancer

Ok, so this looks like they are headed to rival 23andMc with a social network and some physicians involved, at least as the CEO here......But not the Google Power.....

More to Come on this one! The challenge is on to make a business off of people's DNA. Good Luck.

The Sherpa Says: HT to Misha for this....and likely HT to George Church.....What in the world will 23andMc do? Take another 3 million from Google, that's what.......

Factor V Leiden testing not useful?

I was at morning report about 6 months ago after hearing a talk from the Leiden people. It turns out they had never intended the testing to be used the way it has in the US.

In fact, it seems for the last few years, everywhere you turned, every doctor was doing genetic testing......this time not for Hemochromatosis, which, again is not particularly useful as a screening test for disease state. This given the low penetrence and of the disease in those who have the mutations (Which is once again why DTC HFE testing is silly)

This time it was for Prothrombotic state with Factor V Leiden and GP20210A mutations/polymorphisms.

Why did we do this? Well, we ere taught that having these mutations put these patients at risk of having Deep Vein Thrombosis. Even perhaps that we give aspirin or blood thinners to these patients to PREVENT DVT etc......

In fact companies sprang up offering DTC thrombosis testing. It was actually one of DNA Direct's first offerings, before they wisened up and got into the clinical genetics business. But after this my guess is healthcare plans may balk at their advice to do Thrombophilia testing....So much for letting genetic counselors guide test management.....

But back to my story....

At morning report, I posed a question to the residents........
"What piece of evidence exists that indicates that we should be doing genetic testing for patients who have had DVT or Pulmonary Embolism?"

They were shocked at my answer........

"There are really no good studies which make me want to do genetic testing!"

"What?" they said. They even argued that I was wrong! Vehemently.......finally it is nice to see what I said have some teeth. Imagine that, a gene guy arguing against genetic testing.

Did you see? AHRQ, the research organization that is part of the Department of Health and Human Services.....(to be read as the comparative effectiveness organization)

Well, they find, upon reviewing 7777 titles and including 124 studies, they find..........

No direct evidence that testing for these mutations leads to improved clinical outcomes in adults with a history of VTE or their adult family members. The literature supports the conclusion that while these assays have high analytic validity, the test results have variable clinical validity for predicting VTE in these populations and have only weak clinical utility.

And we are talking Odds Ratios of 10 here guys and gals

Heterozygosity [odds ratio (OR) =1.56 (95 percent confidence interval (CI) 1.14 to 2.12)] and homozygosity [OR=2.65 (95 percent C.I. 1.2 to 6.0)] for FVL in probands are predictive of recurrent VTE. Heterozygosity for FVL predicts VTE in family members [OR=3.5 (95 percent C.I. 2.5 to 5.0)] as does homozygosity for FVL [OR=18 (95 percent C.I. 7.8 to 40)].......

So I really think we need to be very serious in analyzing our clinical utility of genetic tests......

Whether SNP scan or Genome or Single Molecular test.....The Government is on to this molecular game now......they will not rest until all waste is removed from their system. When insurers see what the government is doing they are likely to follow.

Which means we will begin to see even bigger claims of BU11$H!T out of marketing folks to overcome the overwhelming "MEH" coming out of the US Government and the physicians......

It is just good medicine to look at clinical utility of a test before ordering it. Which is why I predict only bad doctors will not heed the call of AHRQ here and why I still maintain MDVIP is practicing bad medicine by integrating a test with no current clinical utility into the care of their patients....

Stop the partnership Ed, I beg you.......

The Sherpa Says: I am completely unsurprised about this as I have been avoiding the hypercoag genetic work up lately. After the scientist from Leiden said that this was a ruse.....I began to wonder how many millions insurers had paid for this testing.......Thousands get PEs every year, even more get DVTs.......Maybe resource management would be better through Generation Health than DNA DIRECT

Love my readers!

The other day I was flooded with emails from my readers about my post about the whole genome scan dirty little secret. Some agreed with me others vociferously defended the need for "further study" But the best was an email from someone who worked for one of the big scan companies, can't say which one, can't say who.

I Quote

"The speculative questions that you ask about interpreting whole genome sequencing indirectly relates to exactly what the cyclical problem is with an industry of genomic researchers who don’t practice science. Instead, they practice following the recommendations and protocols developed by instrumentation vendors, as if Mike Hunkapillar, Sue Siegel, and Jay Flatley had once parted the Red Sea"

I tend to agree that this comes down to a question of thought leaders in the field. This reminds me to the initial flack received by David Goldstein and even the Ire by Kari Stefansson expressed towards David. But then others soon stepped up and voiced their concerns here. The same thing happened when I expressed concern and reminded everyone about the laws that exist for DTC testing...

Why as a field, does genetic have this lack of willingness to challenge? I think it is for a fear that the spotlight which now shines so brightly will be dimmed because of controversy.

I disagree. Controversy is what will make this field the most robust, the best press worthy and most exciting field of "everything" for the next century.

Let's face it, there is no way that the lights will dim on Genomics. The real question is what will be the representative face of the field. Right now, it is all hype and iPhones and California Silicon Valley.........

I await to see its next face.

Maybe it will be Moses?

The Sherpa Says: It all comes down to the fact that there are so many more data points to look at than just the genome.......

The Genome Scan Dirty Little Secret

You know what I love, you take a company who is inferring that science IS clinical utility and then you hire them to perform interpretation on something that in it's current for is often uninterpretable......and then you sell that for something on the lines of 90-48, 000 USD.

My business is healthcare, my business is also risk prediction, but what my business is most is disease prevention......

My profession is physician, my oath is to do no harm and if I must harm, do so healing or palliating suffering....A noble profession to be sure.

But no one, I repeat no physician is leading the charge to do whole genome scans for risk prognostication.

Maybe for certain disease detection, but not for true risk prediction.

But, guess what? The business people are...... The business side of Genomics is all about getting "these little babies" into the hands of everyone......

Billions of people at 99 dollars a piece is a lot of money.....but the one thing that may hobble this model is what I like to call the dirty little secret of whole genome scanning.

You can read about it at my other posts
1. We have no clue what it really means.....Merry Christmas
2. Nature is So Wrong
3. Ok Guys, Seriously.
4. Rading the Medical Commons, A Pirate's Life for Me

Or you can let me recap. Currently DTC genomic companies are testing 1 million single nucleotide polymorphisms. We have in our body combined, 6 billion of these little nucleotides....

Sure the SNPs were safe, heck a SMALL minority had some science behind them.....but most were razzle dazzle and hyped by researchers to the press.....

Oversold and Overhyped.......If you thought that was something, wait to see the hype from the "Whole Genome" crowd.....

You see, even the most skilled, erudite, knowledgeable geneticist can be hobbled by the explanation of certain genomic changes......

A. If they changes often aren't in genes, then the biology needs to be elucidated, that takes years.
B. If the changes are in genes but that no one has seen before, how do you know what to predict will happen?
C. If we see a change which has been seen but has a wide variety of phenotypes, how do we explain the risk?
D. Most importantly, how do we modify disease risk based on genomic information for most of these things?????

My point is, you have disparate DTC companies calculating risks in different ways and even worse, recommending or "inferring" recommendations for lifestyle changes. Unfortunately, the quit smoking and lose weight isn't exactly "Science" or medicine, which is why they can get away with it.....

What about when a whole genome comes along at 30x coverage? Well, Illumina plans to do that and "outsource" the interpretation to these companies who are "interpreting" based on some very, very soft science already.

What in the hell do they plan to do with this whole genome interpretation?

In my mind these are the keys to get whole genome scan to utility.
1. Formalize some sort of standard interpretive algorithm AND THEN TEST IT CLINICALLY
2. Research the phenotypes which emerge from each and every genomic change out there.....Some like George Church plan to do this in the wide open....which may not attract the millions of people and dozens of years needed for this one....
3. Study the actions which will be proposed for each of the genomic changes to reduce disease risk or to treat disease.....

IFF you can get 5 common diseases captured with this, then you will have a successful system. But then the problem with this is what Illumina already knows...."you will be diagnosing disease and thus enter the realm of clinical test"

Which they have already prepared for by mandating physician ordering of their whole genome scan....

A long post I know......And a long way to go before this is useful at 99 USD per person.

The Sherpa Says: The incidentalome is just the beginning of the nightmare about to be unleashed with whole genomes.....

OK Guys, Seriously.......

What I loved about the second day of CGS coverage was that Dan now had some partners covering some of the space, heck I even saw twitter messages straight from Illumina.....

I want you all to listen to some very important statements. Francis Collins had his genome sequenced under an alias by 23andMe, deCode Me, and Navigenics - tells them here at Consumer Genetics Show - He says

1. Substantial differences exist in info revealed (carrier, non-medical, ancestry); not clear which markers are tested
2. Interpretations sometimes vary, even with the same data; exhorts DTC companies to collaborate on this.

3. Parents willing to pay nearly $2K for cord blood banking are unlikely to be daunted by cost of genome sequencing as it falls.


So here's the take home. When you get a cholesterol test, don't you want to have a uniform explanation and values? The same is true for genomes. This is why it is so damn hard to run a bread and butter lab.

You have to compete on different things......Insurance preference (Which often involves undercutting your costs), Turn Around Time, Integration into MDs work flow......

By exhorting DTC to have "Uniform" explanations he ultimately spells what will likely be the case for this business.....one big conglomeration of a company doing genome sequencing OR 5 mega companies, all competing on turn around time, Insurance preference, and MD preference........

This is fairly evident by the move made by Illumina.....where
1. ONE Company does Sequencing
2. 5 companies do interpretation
3. 1 company does the medical care

Do you see where I am headed? DTC genomic companies in the current form are doomed, unless it finds a way to adapt.

I told Dietrich Stephan that a way back and his investors rebuffed......Well, I am doing it anyways, without them......

You didn't hear about the Illumina move? Well, in spotlight stealing moment, they showed an iPhone app for your whole genome a whole genome at 30x coverage for 48 Thousand USD. ORDERED BY PHYSICIAN, counseled and then tested, a consumer can then get on their iPhone (maybe) or at least their new Mac and surf their results...

This could be a fantastic thing, if it were not for the Incidentalome that this will unleash!

Incidentalome?

Well, in radiology their is a term for finding something on a radiology scan which you weren't looking for. Most often this "Thing" is a benign cyst that regresses or is just an artifact...... But as physicians we end up doing a full court press work up and costing even more money than we thought possible......

Zak Kohane wrote an article about precisely this in 2006 in JAMA...........

He estimates "false positive" rates could be higher than 60%

So my point is this......50k or 5k or 500 bucks, the genome is going to cost about 500 bucks in less than 5 years.

During that time....WE STILL WILL HAVE NO F*CK*N& CLUE what most of the information in it means......And we will be trying to explains things which may mean nothing......... I remember the blog post I did about the geneticists sitting at a table with Comparative Genomic Hybridization Results.....They all said "I Dunno"

We may not know for a very, very, very long time......Francis Collins tells a joke

"A geneticist's wife was talking with her friends........She says "We've been married 20 years now and He keeps telling me how 'We are GOING to have a great sex life' "

The Sherpa Says: Give me a freaking break, Guys, Seriously. What the hell do you think is so great about this $H!T? Seriously? This will cause more confusion and likely more cost. What revolution does this bring? I can see PGx, but that is really about it. OK, maybe NBS too....

Consumer Genomics Spin

Thank God for Dan Vorhaus AKA @GenomicsLawyer on Twitter and a nice wrap up by Emily Singer

But like a groupie believing everything one reads, I want to caution those who attend that conference.

I heard major exaggerations and one might even say misstatements from the people presenting.......

The biggest one upset me. I am a fan of Jeff Gulcher's. I think he is a great guy. And his 1 in 100,000 story about finding aggressive prostate ca because of his SNP risk is very real. But, he claimed something which had been proven incorrect.

It had been proven incorrect months ago...... Maybe he did what DTC does best.....they imply things...... Jeff implied that their SNPs for CVD actually reclassify women's risk......

In order to prove that he would need a cohort and he would have to control for all other things AND he would have to have been studying this cohort for about 20 years.....which to my recollection has not happened with deCode.....

More importantly, the SNP they discovered was not found to add ANYTHING useful to the current classification system for risk of heart attack....

However, there is something which reclassifies approximately 40% of women and 17-20 percent of men......the Reynolds Risk Score, studied by Paul Ridker et.al. up at Harvard....

In this great example, clinical risk factors are combined with genetic factors, in this case Family History and it outperforms Framingham Risk Stratification........

But to state that their tests perform the same or even to insinuate this, well, that's just intellectually dishonest and I wouldn't expect that from Jeff......which means he "must have been mistaken"


So today I look forward for more exaggeration at CGS as I call in to the ICOB meeting for the Coriell Personalized Medicine Collaborative......I implore others to follow Dan @genomicslawyer and look for the same.

The Sherpa Says: We must always listen with a critical ear to what is said by people with money or power or both......

Consumer Genomics Show

Is off and running. If you have a twitter account Dan Vorhaus @genomicslawyer, pound for pound the best twitterer around in this conference twittering space is covering the conference at #CGS

I won't make any further mention of the conference except to regret not being able to sit across the table from Linda, Jeff, Dietrich et.al.

Prior Authorization for a Medically Necessary Test?

As if this couldn't get any worse for genetic counselors, who BTW get paid next to nothing by insurers........ United Healthcare is now requiring Prior Authorization for BRCA testing. In their policy bulletin from May, Volume 31.......

The coverage determination made regarding BRCA testing for your patient will be based on the UnitedHealthcare medical policy for BRCA testing, which is based on the clinical evidence and is closely aligned with the criteria developed by the organizations listed above. This coverage determination will be conveyed to you promptly by either phone, or letter or both. Of course, adverse determinations are subject to all applicable appeal rights.

Add that to the list of scut work which the counselor will get stuck doing.... So much for same day testing in a timely fashion! At least you get an appeal!

My guess is that this set of patients will get the services they need, in a very, very delayed fashion. I sure hope we don't see a cancer develop in one of this patients while their testing is "awaiting approval"

A huge loss for cancer genetics, but also a stopgap from the misuse of testing which has been going on for a couple of years now, while Myriad has profited handsomely......MYGN...

Buttressed next to this claim is the fact that United will proved you with access to an "independent" genetic counselor..... How's that for lipstick on that pig.......which has me wondering, will that counselor be from DNADirect or Informed Medical Decisions.......DNADirect, BTW went from online test supplier to care provider........a sound business decision which I hope Navi will come to shortly.....

The Sherpa Says: Increasing barriers to prevent abuse is likely what will happen with healthcare reform....which is what shouldn't happen. What should is in the NYT Sunday....Hey, we do that!

rs2200733 ok, now what?

I am busy pouring through all sorts of association studies which I had let sort of slip through my fingers. I have been cue'ing a lot of these and only in the last few days have been able to get to them. Most of the SNP that the press put out there now seems to be dying off pretty nicely.

Although there are bits of useful data out there, most is just noise......but one of the SNPs which caught my eye was rs2200733 studied in Icelandic, Italian and other Caucasian populations with a small replication in an Asian population as well......What does rs2200733 predispose to?

Atrial Fibrillation. A condition that can lead to unannounced strokes, syncope, and heart failure (at times) Atrial fibrillation is the most common arrhythmia in the United States.

About 2.3 million Americans have atrial fibrillation (Go, 2002). Men have a 50% higher incidence than women at any age (Benjamin, 1994). Among individuals 50 years of age and older, the prevalence is higher for Caucasian individuals than African Americans.

The prevalence of atrial fibrillation is 0.1% for individuals under age 55 and 9.0% for individuals over the age of 80 (Go, 2002). HT CPMC.....

Here's why I am revisiting it? It popped up on my screen as a SNP with a study which purported an Odds Ratio greater than 2...... In my mind, no SNP should be even looked at without having this.....why?

Well, most clinical scenarios have
1. Good risk prediction tools already, as with the 9p21.3 issue
2. No true benefit of presymptomatic detection, i.e. no effective prevention (Parkinson's)
3. No ability to guide therapeutic decision making..... This is true in 99% of cases, aside from pharmacogenomics that is.......


So why am I looking again at rs2200733? Because this may actually be a case where I think it may augment my other clinical tools of prediction......Maybe.

Why only maybe?
A. Most of my patients get annual physicals with annual EKGs.....and often AFIB manifests with symptoms....
B. Most of the patients with AFIB are elderly and in the studies some indicate earlier AFIB pops, some don't which may be confounding in the study
C. Most of the people with AFIB that I see report a family history of some sort of arrythmia, most often AFIB.....

That being said, there is a population <10% who end up with No family history, Present Early and present with a stroke....It is rare, but does happen.....so I naturally would want to watch that population more than not......But does that mean I should do "More" for them?

In the age of Comparative Effectiveness, I may not be allowed to..........There is no ICD9 code for genetic predisposition to Atrial Fibrillation......

But maybe people would pay more than the 20 dollar copay for care???? Probably not that often, but maybe.....And for what? A home monitor to be hooked up on them 24/7?

It turns out

DeCode sells a test with this SNP, Is on the Affy and Illumina Chips, I.E avail for 23andM- and Navi.............
None of these are actually valid clinical tests yet though.....Similar to other "clinical" detection tools we have today.

So what I am going through is in essence mental acrobatics while I await a company to do a study which proves that there is some benefit and some action to be taken here.......

The Sherpa Says: While a promising SNP is out there, it is just that a promising SNP. Most of these things won't affect me clinically for another 5 years. I wonder what the public will do with this data? Will they go see a doctor? Who ultimately would be asking the same question I am.....and waiting for the same data

GAPPNet, Hacked Records and ICOB

Happy Donut Day Everyone!

"Wha?"

That's what I said as I walked into my Dunkin Donuts across the street from our new HQ. The guy saw me coming in, prepped my coffee, Large Blueberry, Milk and Sugar......

As I went to pay, he said, "Happy Donut Day" I barely understood what he said when the manager said "Pick your donut, FREE"

OMG, as if I wasn't fat enough. How many other of my readers took the free Donut today. I looked around in my DD and it seemed everyone took the donut.

People certainly are game for free......... Speaking of FREE, the Coriell Personalized Medicine Collaborative is in essence a Navi/23andM- scan for FREE. I just got some more results this week. I don't have Hemochromatosis HFE type, Hooray! This can be yours as well.....

That is if you are willing to participate in the study. Which BTW, will be covering some markers which are NOT covered by any DTC company.........And these markers ARE CLINICALLY RELEVANT!

So what I am getting at is that the early adopters should not be paying anything for these services........

While the donut fills my sense of hunger for food, the SNP scan fills your hunger for knowledge. Either way, it should be free. Yes, only on Donut Day, but on non-Donut day it is only priced at 99 cents.....which is where the SNP scan will be soon enough....

Speaking about the SNP scans, I am sitting here pouring through literature for the CPMC's next ICOB meeting, which I will be attending via satellite from my outpost on the Gold Coast......

We have some interesting SNPs to debate about........It seems as if we aren't the only ones doing this......EGAPP does it as well and it sure is nice to have an EGAPP member on the ICOB......

But now the CDC has created GAPPNet. Huh? GAPPNet? "Mind the GAPP." Get it? What is it?
From the Site:

"GAPPNet aims to accelerate and streamline effective and responsible use of validated and useful genomic knowledge and applications, such as genetic tests, technologies, and family history, into clinical and public health practice."

I wonder why they didn't call us.
At Helix Health of Connecticut we do this everyday.....Never mind the website, we are rebuilding it, just like the offices....... I really hope they do, as the inaugural meeting is on my birthday........I won't hold my breath though......

Come on Muin, just email me.......PUHLEEEEEZZZZ!!!!! There, enough begging for the day.

So you can read about GAPPNet in the ACMG journal Genetics in Medicine, provided you have a subscription, at 1k per year, sorry blogosphere......

As I close on this Donut Day, I want to say, not everything that is "Free" is ok. Remember that when it comes to storing your medical records........From Forbes on the 3rd, UC Berkley medical records hacked...... To protect your records, we are investigating NSA level encryption tools......You can never be TOO PARANOID......(Devilishly Crazy Laugh)

The Sherpa Says: To charge a price, you must prove value, to demonstrate value you can't go on Oprah and say it has value, you have to PROVE it has value.......You do that by "Just Doing It".......

The power of Twitter and why blogging matters.

I am certain there must be a million stories like this out there. Devoted Twitterer attends conference that others cannot, recaps the talks via twitter as physician/new papa/blogger/entrepreneur virtually attends the conference via twitter and can give color commentary......

Or this one: Conference presenters hamstring regular news, while blogger gets strategic advantage by not registering as a journalist. Thus scooping the press...... Well, I have now seen and appreciated both in real time.

This weekend while I was recovering and taking care of our newborn I was able to attend a conference the AAAS hosted a conference entitled "Personalized Medicine, Planning for the Future" it was a scientific freedom, responsibility and the law program......... The microblogger was Dan Vorhaus Esquire and the venue was Twitter.....I know I would have loved to watch the streaming webcast, but alas I had dirty diaper and feeding duty, so I could not get to my laptop.......which led me to the next best thing......my iPhone.

What an amazing invention that IS actually worthy of Time's invention of the Year.......

The next story is a slap down of Daniel MacArthur (Pound for pound the best genomic blogger out there) Welcome back from 2 weeks away Daniel, take your beating! Credit Science Insider

June 2, 2009

Cold Spring Harbor Wants Scientist Bloggers to Follow Media Rules

At a recent meeting at the Cold Spring Harbor Laboratory (CSHL) in New York state, Daniel MacArthur from the Wellcome Trust Sanger Institute in Cambridge, United Kingdom, brought into focus how fuzzy the line between journalist and scientist is becoming. In addition to reporting on genetic variation in a gene that is active in fast muscle fibers at The Biology of Genomes meeting, MacArthur wrote several on the spot blog posts covering advances discussed by the participants. Francis Collins also mentioned results on his new Web site.

A specialized Web-based news service, Genomeweb, complained. Apparently there is some rule regarding when journalists can release information. Usually they are allowed to do so AFTER the meeting.......but Daniel did it before the journalists could, thus scooping them.......

As a blogger who has been sued in the past due to blogging, let me tell you.....this could be scary business..... More importantly, it raises the question about Twitter.....Is twitter a microblog? Or is it a super fast SMS txt?

You see where I am headed with this.

In order for personalized medicine to progress, we all need to be in constant contact to let the flow of new ideas move........Could we actually be legally held to restrict its flow? Personally I think blogging and twittering is not exactly journalism, but it could be......even FoxNews has a twitter feed.

So who is and who isn't a journalist.....this could get almost as tricky as internet startup companies pretending to play doctor by running tests on your DNA and reporting results as if they were actually predictive of something.........

The Sherpa Says: Have to run, patients all morning. But as you drink your coffee and look at your DTC test results and analyze your CYP1A2....think about how much more that ability to microblog at a conference will affect your life than some 1 million SNPs will.........

Wonderful Weekend! The Consumer Genomics Show Surprise!

First, a little personal info. I am the proud father of yet another Murphy Daughter! This weekend has been amazing for me. Even better, as we went into the hospital I received an email. Normally the only people emailing at this time are my patients or I am getting results from lab tests I ordered.

So, I felt obligated to look when the iPhone buzzed.

It was an email from John Boyce....... Who is John Boyce? From his website: John recently served as Head of Business Development for Helicos BioSciences, where he was responsible for identifying new market opportunities in which the company was able to develop new applications that gave it a substantial competitive advantage.

John founded Delphi Bio a strategic consulting group for genomic start ups.......

So about a week after I got done trashing the Bubble Con known as the Consumer Genomics Show I received this email from him and Bob Green over at Harvard.

Why did I bash the conference? Well, from the line up of speakers, it looked like a wonk fest attempting to hype Consumer Genomics even more than Oprah could possibly do, BTW did you see the Newsweek article stating that Oprah should stick to talk shows and stay away from Medicine?
Further adding fuel to my cynicism......

But when I read the request it blew me away. They were trying to make Bob's panel, Fair and Balanced.

You see, I think the big problem here, no offense Francis, is that the scientists we have on the cautious optimism side are actually pretty quiet and can get pushed around by the larger than life scientists and business people (GMC? Linda, et.al.) Which on a round table makes for a one sided conversation........

Thus, Enter the Sherpa or as Jeff Gulcher calls me "The Howard Stern of Genomics" But, alas, I had to respectfully decline. Why? Why would the Sherpa shun this opportunity?

Well, I just told you in my first line. Number 2 has just arrived and I am calling in for an ICOB meeting while feeding the baby...... So, I take back a lot of what I said about the Bubble-Con, it appears that there are some people striving to give the show a balanced feel. But my guess is, the pragmatic optimists like myself, will be in small number. Which is exactly what happened with mortgages, financial derivatives, .coms, I could go on and on here.......... So when the VC enter the halls, just remember, I would have if I could have........

The Sherpa Says: A consultancy group in Boston is now offering tickets for the show at 6 USD, and even deeper discount than DNA123........I would have loved to see this show play out.....I guess I will just have to send my crew......

HT-Genomicron for the b-day cake