Coriell and OSU integrate GWAS into an EMR!

Ok, so enough with the acronyms.....

I am back and will be blogging more often again. So for those who still lurked around, tell the others that the Howard Stern of Genomics is back. I took a social networking holiday for a solid 2 months, plus the addition of having my practice change quite a bit after my USA Today and follow ups in the local papers.....

Today I want to announce that Coriell Personalized Medicine Collaborative and Ohio State University will be using data from an arm of the CPMC and OSU to integrate genetic risk data into the medical record.

Correct me if I am wrong, but I don't know of anyone else doing this exact same thing.

Ideally they will also continue to roll things in like PGx data. (I know this data will be coming soon)

By integrating things like Plavix response, you can make more gametime decisions easily.

I.E. Patient presents to the ED with a heart attack. Armed with prior knowledge about plavix nonresponder, you pick Effient.

What is so awesome about this arm is that Primary Care Physicians, Cardiologists AND patients will be participating and receiving results.....

They will be studying the behavior and knowledge of participants in the study, we have seen other data on this sort of thing, I wonder if we will see the same thing here.

For risk data? Probably. For PGx Data? Probably not.

Why? A plavix response in the medical record is a game changer.

3 Reasons

1. The clinician will be hit in the face with a "Plavix doesn't work here"

2. The physician may even find they are a nonresponder

3. There has got to be some hustling attorney out there, who will be lurking once they see the CPMC/OSU release. I am certain at least the physicians will be thinking so.....

You can read the Presser Here

The Sherpa Says: Study of clinical use and behaviors will be key to know how vital this data is and thus how tightly we should regulate its use in medical records i.e. 23andMe clinical BRCA testing! P.S. Like our new crest?

For Personalized Medicine CPMC is the Gold Standard Study

Ok,

So I just wrapped up a meeting with some, well, nearly all of the most brilliant minds in Pharmacogenomics. Where was I? Yes, on the cover of USA Today's life section.....But where was I really?

Conference? No.

VC event? No.

I was at the Coriell Personalized Medicine Collaborative (CPMC) Pharmacogenomics Advisory Group meeting.

Yes, that sleepy 'Ol Cell Line joint in Camden New Jersey.

I am certain you all know about the CPMC now. But in case you have been sleeping.

Coriell is climbing the mountain, gaining collaborators, building camps. They are essentially doing all the hard work of study analysis so that you don't have to.

Brilliant if you ask me.

Who in the world has the time or money to cull data, looking for important findings?

Google funded "projects", Academic Programs and Not For Profits.

Who do you trust to give you unbiased reports?

NFPs.

Who is the NFP here? Coriell.

Are you curious what the CPMC does?

Why will CPMC win this battle? Even 23andSerge agree that CPMC is the gold standard

1. They have independent advisors and scientists

2. They have nearly all the best independent advisors and scientists

3. They have the support of the government, the community and oh yeah, the FDA isn't investigating them......

4. They have Mike Christman.

5. They have a team who believe in this moral imperative, not a pay check or stock options.

I vowed never to post what transpires at these meetings, but rest assured, it was truly academic heated debate with egos left at the door. This is precisely what you want when someone is going to tell you what your genetic material means for you.

The Sherpa Says: Coriell is on to something here. Something so valuable when the 1000 genomes and the rest of the genomes go public. Someone has to make sense of it all and study what it means......I am proud to be a part of it.

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.

Quest, where he had sent the blood, did not test for HLA DQB1

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.

Hooray! Invited to GAPPNet!!!!

In what turns out to be a brilliant decision on part of the CDC, they have created this network of collaborators called GAPPNet.

Which stands for Genomics Applications in Practice and Prevention Network..... I think I had mentioned the great work of the CDC on this for quite some time.

I first noticed their work while trolling through webcasts of the SACGHS meetings. The first which caught my eye was when Dr. Muin Khoury breifed the committee on the public health initiatives in this space.

This was back in 2005 when we were trying to think about how best to expand access to genetic testing. My partner and I at the time were wet behind the ears in this space, in fact our initial feelings were very similar to Anne Wojcicki and Linda Avey......until we began to ask for advice and watch these meetings......

That's when I became convinced that the best way to bring this to the masses was not through some disruptive Web App selling genetic tests without any care for regulation.......it was through tested and proven methods which were not being used, as well as through deliberation on which genomic applications needed further study and which were ready from prime time..... Which is why I am so excited to let you know that I have been invited to the GAPPNet meeting in October!!!

You can read a little bit more about GAPPNet in this article, or you can browse the website.

GAPPNet will be comprised of stakeholders, which include researchers, practitioners, policy makers, educators, and representatives from academia, government, health care, public health, industry, and community and consumer groups. Over the next 2 years, CDC and NIH will convene GAPPNet stakeholders to provide greater support for the following functions:

• knowledge synthesis and dissemination
• evidence-based recommendation development and dissemination
• translation research, and
• translation programs.

So you can imagine my excitement regarding this group.

We have developed an educational curriculum for residents in Internal Medicine. I have been serving the on ICOB of Coriell's Personalized Medicine Collaborative, evaluating the science of each GWAS study. Helix Health of Connecticut is also involved in the CPMC.

We also are actively looking for great research to involve our patients.......research that is ethically conducted and involves institutional review boards.....

So a lot has changed since 2005 when we wanted to "Democratize Genetics"......... I am certainly glad we will have GAPPNet to help guide the way on these things........

Lastly, I want to point out an article in the ACP Internist. On the front cover was an article about, you guessed it.......DTC genomics scans......Titled "A Brave New World of consumer gene tests" The article misses the point and lets Dr. Topol, an adviser for one of the DTC companies issue talking points........ It does point out Navi's early gaffes, but it then downplays 23andSergey

"23andMe is the cheapest test at $399, and includes more of what Dr. Topol calls “recreational information,” such as whether one is disposed to have hard or soft ear wax. All told, it gives feedback on a whopping 114 traits and diseases.

“23andMe is a little more for fun. It does include some serious medical conditions, but the proof or evidence doesn’t appear to be quite as rigorous,” Dr. Topol said. “It makes for good cocktail party chatter.”

23andSergey is for fun????? WTF? Did you forget that they are testing pharmacogenomics and BRCA variants Dr. Topol? Hardly Party Chatter.....

"Yeah, so I have this deleterious mutation which increases my risk of ovarian cancer 16 fold......could you pass those little cocktail weenies please???"

Jessica Berthold's editor should have picked that one up? Even in the clinical medicine media we get this parroting of 23andSergey's talking points. What in the hell is going on here?

Thank God they asked Greg Feero a question or 2 on this.....Otherwise, this could have been a love fest!

I repeat, 23andMx AKA 23andSergey are testing for variants in the BRCA genes and also pharmacogenomics......2 things which aren't EVER "Just for Fun"!!!!

Hopefully, EGAPP and GAPPNet can clear up that little confusion.......

The Sherpa Says: "The greatest thing the devil did was convince the world he didn't exist!"

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......

Why 23andME? Why Now?

A few people have been asking me these questions after my recent blog post. Andrew and Daniel (Two prolific bloggers in the personalized genomics space) are both asking these questions and rightly so.

1) Why did 23andMe take such a risk? They had a nice Novelty genetic testing game working (albeit flawed). Why risk by going into truly defined medical practice?

I think this move rests on 3 assumptions

A) Most people won't buy a dunkin' donut's coffee today as they cut back costs. Why spend 399 on a vanity bobble?

Thus B

B) People pay for medical necessities still. So to sell tests, they can make it look like a medical need.

C) Most investors are looking to shorten their ROI time frame especially in this economy.

2) Why now? Why take the risk now? Aren't they risking their already set income stream by rocking the boat?

A) Have you seen the economy? The FDA isn't exactly priority number one in Washington now.

B) California is about to go bankrupt, I don't think CDPH will be focusing on these tests at this moment, leaving 23andME to force their way into medicine without being regulated.

C) If they don't make this move now, they may never have the chance again. Take a look, in 6 months the economy will be better. The FDA/CDC will have their joint Genomics department set up to police these measures AND WILL HAVE STIMULUS monies behind them to bring down the hammer...

So now is the perfect time to move...........The attention is on the Economy Stupid!!!!

The Sherpa Says: If the organized specialties such as ACMG, NSGC, ACP, CAP etc. move on this, they will be left with scratching their heads as to where their lab monies have gone? Let's face it, the clinical department is only kept around at these centers because of the profits which are brought in by the labs.....

Recessionary Discretion......HotCoupons4U!!

Yes,


I am a big fan of the race to the bottom. At least in the case of SNP scanning. We have seen Navigenics drop their price, deCode drops off the earth and 23andMe???? Well, in a discretionary move they show use the true value of SNP scans.....




I give you HotCoupons4U.....The 23andMe special, pay close attention...


From the website.....




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Now correct me if I am wrong, but aren't they charging 399 USD for their test......so at most 23andMe thinks that their test is worth........199 USD AT MOST!!! Oh wait, this is off their family pack.....Oh, you know the one, where Anne Wojicki says you can drug your kid with benadryl for fun....and the same one where they say collecting your child's DNA is tough with the spit kits.......

Why would they lower prices even further? Because its your genome they want....not your money!!!!!



How it works:
1. Order a kit ($399 USD) from our online store.
2. Claim your kit by the claim code, spit into the tube, and send it to the lab. (The claim code is the 12-character code on the front cover of your green Spit Kit box. )
3. CLIA-certified lab analyzes your DNA in 4-6 weeks.
4. Log in and start exploring your genome.Learn more from https://www.23andme.com/howitworks/Available discount codes for 23andme: “spit party” or "SPIT"

I would like to add:

5) Release your genome into the wild and allow 23andME to profit off your folly without HIPAA protection or a certificate of confidentiality, like the one awarded the CPMC......

The Sherpa Says: Ahh Yes, it is coming in clearer now. The cost of a SNP scan is Zero US dollars.....until we prove it has value. Add on top of that the 1000 USD Genome and we will soon see that the real commodity is the interpretation and ongoing services revolving around your genome that will matter........Just like Thomas Friedman said about the Internet.......

HT-BC at EG

Coriell Goes Live!!!

Today the Coriell Personalized Medicine Collaborative website goes live. After many months of really hard work they are ready to show everyone what a Personalized Medicine Collaborative Study looks like. I maintain, without the information to be generated by Coriell, we have absolutely no clue what the heck these DTC SNP scans are clinically worth.

I can tell you what 23andMe thinks they are worth-$399 even for study participants.....

Navigenics- 2500 USD unless being a study participant, then it's $375.......or if you only want access for a year it's $495

Coriell says-They are FREE to participants $0, unlimited genetic counseling included!!!

This is a powerful statement and I am proud to be a member of the Informed Cohort Oversight Board of this "First of Its Kind" Cohort Study!

Why is this important:

1) We don't know if people actually do anything helpful with the tests that they buy from DTC.

2) We don't know whether they have any useful additional information to add towards our risk predicition capabilities. In fact 9p21.3 when added to standard clinical factors including family history, was absolutely useless in helping us risk prognosticate for heart disease. So 23andMe is useless in this aspect.

3) These tests should never have been sold as even "pseudo-medicine" without something other than basic science to back them up. As I said in Number 2, even excellent basic science can fail clinically.

4) No One, and I mean NO ONE, should be able to sell your data to another company without your permission!!!!!

The website is fantastic and lists some significant information. Including important Privacy Information.

Certificate of Confidentiality
The Coriell Institute has been granted a Certificate of Confidentiality under a federal law (Section 301(d) of the Public Health Service Act). This means that records from the CPMC study may not be disclosed, under federal, state or local court order, without your written approval. Data that are protected by a Certificate of Confidentiality may be disclosed to the Department of Health and Human Services if required for audits of research records.

This is stronger than HIPAA and nothing like this is offered by 23andMe or Navigenics!!!

Heck, those companies aren't even considered HIPAA protected agencies. IMHO, that is a risky thing!

Even better, Coriell Collaborates with several healthcare institutions who have enrollment events.

Who is Coriell?

Here they are!

Get ready world! The team is world class and the research is the first of its kind in the world!!!

The Sherpa Says: Today marks a revolution in personal genomics, the day that the world sees this research and that it needs to be funded and carried out......AT ZERO COST to all participants!!! This is ethical research, plain and simple.