Thursday, May 29, 2008

Mind your P's and Q's

In another Hairbrained "We're not doing medicine" scheme I point your attention towards

From the site

Who shops for genetic tests?

Genetic tests are not just for people with concern about disease or fighting crime on TV.
These are people who have used QTrait:

Families with history of allergies.
Women who learned about their future pregnancies.
Grandparents wishing to buy DNA tests for grandchildren

QTrait offers over 40 genetic tests. Mix and match tests to suit your needs.

(Great....... just like pick and mix candy!!!!)

All 4 tests: $249

All 7 tests: $399
Health & Longevity

All 9 tests: $499
Sleep and the Senses

These types of shennanigans are precisely why the FDA, CDC, IOM, and ACMG are demanding federal legislation outlawing or at least regulating DTC genetic testing. Some of these genes have only been studied in cohorts of less than 1000 people. Not nearly enough to be ready for the medicinal market!

The Sherpa Says:

I left the links in for the shear joy of having you go to this company. Q-Traits, it is only a matter of time before you are sued or break the law. Good luck to you. If I was Navigenics or 23andME, I would lead the push getting rid of these shady customers. It is only making the big 3 look even worse. Trust me, these DTCs are not making it any better for you. And they are practicing medicine too.

Wednesday, May 28, 2008

Genetic Susceptibility to Cancer

I love the pen. It has the ability to befuddle, convince, coerce, and give false or true hope. This is the case with journal articles. I am always amazed by what is reported and what is real. You see, the Buddhists will tell you that all reality is merely false. Why? Because perception is what we view to be reality. Since reality needs to be constant, yet perception not only changes but is viewer is not constant. Hence, there is no spoon.

This is the case with a recent article published in JAMA's clinician's corner. The article entitled "Genetic Susceptibility to Cancer" did something wonderful. It took 161 meta and pooled analyses encompassing 18 cancer sites and 99 genes/344 variants (Trust me, this took some heavy lifting) and evaluated for Odds Ratios and evaluated statistical significance. They then evaluated the false positive report probability (this is very important when trying to decide which genes are noteworthy/FPRP) Most evaluated polymorphisms were from either metabolizing genes or DNA repair genes. Big surprise, especially given Knudson's 2 hit hypothesis. (2 mutations to cause a cancer, thus if you can process the toxin quicker than it can cause damage or if you can fix the damager quicker than it causing cancer, You Win. Or Vice Versa)

So what did they find and what did they list in their abstract?

Findings: 13 of the 344 variants had OR >1.5, Only 4 IMHO were noteworthy (OR 2.0 or FPRP<0.2)>

Reported in abstract: "....nearly one-third of gene variant cancer associations were statistically significant, with variants in genes encoding for metabolizing enzymes among the most consistent and highly significant"

See how my bolding made it seem more important? That is the problem here. All this study let me know is that most gene studies involving linkage and cancer are not significant. But the busy clinician reads this as the bold. Not that there are only 3 Linkages worth a hoot with OR of at least 1.5

Those associations ARE: NAT2 slow acetylator and bladder cancer, MTHFR C677T and gastric cancer, lastly GSTM1 null allele and bladder cancer. This makes sense, especially given the fact that these cancers have been linked to environmental exposures....

The Sherpa Says:

Abstracts are misleading. To fully report on these articles one must really read the article. How does the busy clinician or journalist have time for that? The Sherpa is even finding it hard! As for Senator Kennedy, that cancer is likely genetic. IMHO

Tuesday, May 27, 2008

Senator Kennedy's Cancer Family History

Dr Lubin, my partner at Helix Health of Connecticut asked me this question.

"Am I the only one to think about this? Ted Kennedy Junior had Osteosarcoma. His other son Patrick had a Spinal Tumor (I'd love to see the path on that). Ted Senior has a Glioma.....Likely GBM. In addition, his daughter had lung cancer at 43 (Was she a smoker?) and breast. So what this tells me is that the Kennedy family may have Li-Fraumeni or Li Fraumeni Like."

Well, perhaps we should call Dana Farber. Why? Because, Dr Rosenthal over there does not seem to be impressed. from the Globe:

Dr. David S. Rosenthal, former president of the American Cancer Society and the medical director of the Leonard P. Zakim Center for Integrated Therapies at the Dana-Farber Cancer Institute, said that while he is not familiar with the details of the Kennedys' medical history, he considers it "unlikely that the cancers are related." Given the young age at which some of the Kennedys' cancers occurred, and the fact that they were found in different organs, it is unlikely, but not impossible, that there is a common genetic thread linking them.

Hmm, let's see what a little GeneTests search can do. BTW the article was written by a Dana Farber genetic counselor.

Disease characteristics. Li-Fraumeni syndrome (LFS) is a cancer predisposition syndrome associated with soft-tissue sarcoma, breast cancer, leukemia, osteosarcoma, melanoma, and cancer of the colon, pancreas, adrenal cortex, and brain. Individuals with LFS are at increased risk for developing multiple primary cancers.


Genetic counseling. LFS is inherited in an autosomal dominant manner. Offspring of an affected individual have a 50% chance of inheriting the disease-causing mutation. Predisposition testing for at-risk family members is available in families in which the disease-causing mutation has been identified.

Two forms of Li-Fraumeni syndrome are recognized: classic Li-Fraumeni syndrome (LFS) and Li-Fraumeni-like syndrome (LFL).
Classic LFS is defined by the following criteria:

A proband with a sarcoma diagnosed before 45 years of age AND

A first-degree relative with any cancer under 45 years of age AND

A first- or second-degree relative with any cancer under 45 years of age or a sarcoma at any age [Li & Fraumeni 1969].

LFL shares some, but not all of the features listed for LFS.


Birch's definition of LFL [Birch et al 1994]:

A proband with any childhood cancer or sarcoma, brain tumor, or adrenal cortical tumor diagnosed before 45 years of age (Ted Junior) AND

A first- or second-degree relative with a typical LFS cancer (sarcoma, breast cancer, brain tumor, adrenal cortical tumor, or leukemia) at any age (Ted Sr) AND

A first- or second-degree relative with any cancer under the age of 60 years (Daughter age 43)

Well Harvard. Looks like you were scooped by Helix Health of Connecticut.......

To the Kennedys, feel free to call for a full evaluation with Dr Murray up there, if someone at Harvard hasn't had the sense to send you already!

Carrier State IS Disease State. Pre-Disease IS Disease.

In my ever-lasting challenge to Mendel, I submit my thesis. "There is no such thing as a carrier, nor is there such a thing as a single gene disorder."

Why? I have a treatise on the subject. But suffice it to say one thing. "No Gene Is An Island"

In the most recent argument I offer a study recently published in the Archives of Internal Medicine. Did you see the issue? It is a freakin' Gene Fest I tell ya. Too often we tell people you need 2 bad copies of Gene X to be affected by disease Y. But what if Gene X also caused Disease Z? Do the same rules apply? No wait a second, I thought Gene X only caused Disease Y? Well, we now know that many genes are invloved in diseases other than the traditional "Monogenic Disease" Which was reported ages ago, when we were limited to what we could taste, touch, smell, hear, see or feel.

This is the case with Marfan's disease. It is also the case in Cystic Fibrosis. Now a study from the Archives.

Researchers found that the genetic disorder, alpha-1 antitrypsin deficiency (α1ATD), could explain up to about 12 percent of lung cancer patients in this study and likely represents the same widespread risk in the general population. "This is a seriously underdiagnosed disorder and suggests that people who have lung cancer and chronic obstructive pulmonary diseases (COPD) in their families should be screened for these gene carriers," says Ping Yang, M.D., Ph.D., a Mayo Clinic epidemiologist and lead investigator on the study.

Don't you just love widespread, sweeping statements like the one from Dr Yang?

While true, yes the Sherpa did diagnose a 74 year old non-smoking white woman "COPD'er" with A delta 508 Cystic Fibrosis. It is not true that we should screen every 74 year old white woman with COPD for CF or α1ATD. But a careful detailed family history, should be sought out. Including environmental exposures...

In the case of Alpha 1 Antitrypsin Deficiency (α1ATD) much like CF, you need 2 defective genes to have "the Disease"....for now....

So what does this study say? From Medical News Today.

The α1ATD carrier rate among 1,443 genotyped patients with lung cancer was 13.4 percent, compared to 7.8 percent among unrelated control participants.All α1ATD gene carriers were at a similarly greater risk of developing lung cancer, regardless of smoking status. Those who had never smoked were at a 2.2-fold higher risk; light smokers had a twofold greater risk; and moderate to heavy smokers had a 2.3-fold increased risk.

Did they control for other environment or other genes? Yes.
This study actually paired cancer-free siblings with their α1ATD carrier brethern. Guess what? 2 fold increased risk of lung cancer. In CARRIERS!!!!
This serves as a modest control for environment and some modicum of epigenetic regulations.

So what we are saying is, that a previously "benign" carrier state...Is not so Benign! This is the same with CF carriers, Sickle Cell carriers, I could go on and on.

Ladies and Gentleman, I submit to you Exhibit C. Further proof that Mendel has been screwing up genetics and medicine for over a century. We must be careful in how we consult and counsel patients.

The Sherpa Says:
I have been called a blasphemer. But I do maintain, teaching Mendelian Genetics is a disservice to the medical community and to our undergraduate communities. It leads to be rigid in interpretation of things that are very much not black and white.

Friday, May 23, 2008

Sorry to Coriell, Stay of the New Jersey Turnpike

Sorry to the attendees at Coriell Yesterday. They were ready to start participating in the Delaware Personalized Medicine Project. I was scheduled to speak on the topic of "Patient Centered Genomic Medicine" Unfortunately, I was stuck on the Turnpike

Don't get in a car wreck in New Jersey. Trust me!

I don't know if anyone reads Medical News Today but it is filled with great information and studies. Today, it is reporting something which is of no surprise to me. From the article

A new report on genetic testing from HHS' Agency for Healthcare Research and Quality calls for the creation of improved public health surveillance databases and health information technologies to monitor the use of gene-based tests and their impact on patient outcomes.

For the government to spend on this testing, they want to it worth it? The problem with incorporating genomics into medicine is many fold. But the problem paying for these tests include a deep seated need for the government to know if what they are doing is cost effective. More importantly, is it leading to better outcomes. This type of study requires years and years of follow up. In addition, this type of study could be very, very expensive.

The report entitled:

Infrastructure to Monitor Utilization and Outcomes of Gene-based Applications: An Assessment, found current public health monitoring systems lack the capability to monitor the use or outcomes of gene-based tests and treatments. Report authors identified several limitations of existing databases and potential solutions to overcome these limitations.

So what makes a good test? What makes a worthwhile test? Time and study will tell. Until then we must rely on the professionals who have access to the current data. Ideally we would have a BBB of genetic testing. Or maybe just some continuing education.

Whichever Candidate you support it is likely that the government will support legislation, funding AND regulation.....Even If Al Gore is heavily invested in DTC genetic testing. Simply because the corporations may have ethics does not mean they are not exactly hippocratic.

The Sherpa Says: Yes it is true. Physicians not knowing about genetics could get them into malpractice. But running a DTC company could get you in trouble with the Fed....I guess an investor just has to pick their poison.....or their car crash

Wednesday, May 21, 2008

Timing, GINA is Law and the Future of Genomic Medicine

So some very important things came to pass today. All of these things will have a major impact on the future of Genomic Medicine. First and foremost....I have a delivery system for Personalized Medicine. Physician based care is the only way for this future. It may not be sexy enough for Kleiner Perkins, but we have some very strong allies now.

After the best meeting I have had in my career so far I headed to a very quiet space for the webinar.

The webinar is a demonstration of how powerful the webcast can be to convey and cover complex material. This is exactly what Helix Health of Connecticut will do, at a minimum monthly, convey complex topics and bring the thought leaders together to debate and educate. Interested in helping out? Call Helix Health of Connecticut.

How good was the webinar? REAL GOOD. The take home messages

1. It is the legal responsibility of all physicians to learn and provide genomic medical care in one form or another. And informed concerned parties regarding genetic risk

2. There are many things evolving in the care of breast and ovarian cancer, including pharmacogenotyping tumors and patients for chemo dosing and response.

3. BRCA testing is standard of care for at risk groups

4. Education is the rate limiting step to integration, Helix Health of Connecticut will provide alot of that education

5. Envirogenomics is the real key in most diseases

Then as if synchronicity weren't enough at 2:05 pm, when Helix Health of Connecticut began the Q&A session for the webinar, President Bush signed into law, The Genetics Information and Nondiscrimination Act.

President Bush:

I want to thank the members of Congress who've joined us as I sign the Genetic Information Nondiscrimination Act, a piece of legislation which prohibits health insurers and employers from discriminating on the basis of genetic information. In other words, it protects our citizens from having genetic information misused, and this bill does so without undermining the basic premise of the insurance industry.

I also want to pay homage today to -- and not only to members of the Congress who are behind me, but also to Senator Ted Kennedy, who has worked for over a decade to get this piece of legislation to a President's desk. All of us are so pleased that Senator Kennedy has gone home, and our thoughts and prayers are with him and his family.

Now it's my honor to sign the Genetic Information Nondiscrimination Act.

Now with Senator Kennedy's health issues, it is almost certain that his regulation bill will also find a very welcoming administration. Thus ensuring that the bricks and mortar delivery system for Genomic Medicine is the only legal method.

There it is ladies and gentlemen, the blueprint for the future. Helix will help shape this and many others will too. Unfortunately, if you are a DTC company, it is not likely to involve your "scale-able" model. And I ask...."Should It?" Why try to fit a square peg in a round hole?

The Sherpa Says:

May 21st 2008 will mark a historic day for all human beings. It is the day that the model for genomic medicine delivery came to existence, the model for genomic education launched, and the day that the United States Government outlawed discrimination from this information. Lastly, the shot was fired across the physicians' bow, by a very seasoned and venerated attorney and professor...."Genomic Medicine is your legal responsibility" I don't think it can get more clear than that.

Tuesday, May 20, 2008

Thanks To All

Once again, I would like to thank everyone who has surrounded me and helped me launch this new webcast service. Including the wonderful DNA Network! We are committed to doing monthly series for both public and physicians. I really am excited to have this fantastic list of speakers on board. I am absolutely convinced of the educational potential these webcasts can bring to everyone.

In fact, as I actively work on building the next big thing in medical care and genomic medicine, I am creating a novel delivery system for genomic education. Sir William Osler always said to let the patient do the teaching...This is precisely the case with Jessica Queller. No one knows the difficulty of the decisions faced by BRCA carriers better than her.

That being said, even with such powerful genetic risk as BRCA genes, there is another environmental component too. At the webinar I will talk a little bit about those things as well.

Lest, this be confused with Corporate SNP scan companies, I have asked David Ewing Duncan to dispel some of the hype regarding genomicization. He will brief us on the relative role of genomics and why it is important to view risk in the right light.

To really mix things up we have Gary E. Marchant - Ph.D. J.D., Lincoln Professor of Emerging Technologies, Law & Ethics, Sandra Day O'Connor College of Law; Executive Director, Center for Law, Science & Technology, Professor, School of Life Sciences Arizona State University. This is right where TGen is people! We are on the pulse of the legal aspects of these fields too.

Well, enough self promotion. Please sign up. Even if you don't attend, signing up will ensure you a podcast presentation and may just help you our a loved one.

You can sign up at Helix Health of Connecticut and you can see all about it here.
p.s. iGoogleHealth just opened......see opinions here....they amount to 3 day old vistors.

Monday, May 19, 2008

BRCA Webcast Sherpas Repost

I vowed I would never post when family took precedence. I have to break that vow again today. I wish I didn't but there is something so vitally important that I must share with you. Why is this important? Because it might save more lives than have been previously lost.

The scourge of Ovarian and Breast cancer has ravaged several populations. With very few cases of early detection in Ovarian cancer, many women present with spread of the cancer and very poor prognosis. Even more importantly, women who have ovarian cancer and BRCA mutations still are at risk for other cancers including breast cancer. Despite this I have heard comments from Oncologists like "Why do we need testing?" This is why I have pulled myself away from my grief stricken family.

To fight this lack of knowledge I have dedicated and arm of Helix Health of Connecticut to educate and promote genomic medicine. This arm will host at minimum monthly podcasts on very important topics. The first of these is Hereditary Breast and Ovarian Cancers and the BRCA genes. The panel will include a patient with BRCA1. She not only happens to be afflicted, she has written about her experiences. Jessica is gifted with the pen and is a very successful writer. Her book "Pretty is What Changes" raises significant issues and serves as a wake up call to clinicians and patients. It serves to empower us all.

Jessica will join David Ewing Duncan, bestselling author of Masterminds: Genius, DNA and the Quest to Rewrite Life, and a panel of distinguished medical and legal professionals to discuss how the doctor-patient relationship is changing and what the potential liability is for physicians in this new era of breast & ovarian cancer and genomic medicine.

The Sherpa Says: The Helix Health of Connecticut webcast series is dedicated to my grandmother who died at 35 years of age from metastatic breast cancer. Too young for me to ever know. Please sign up for this conference. The information may just save a life......If Helix Health of Connecticut can save just one life then all the hard work is worth it. Please sign up now. Seats are limited, but you can also sign up for the podcast.

Friday, May 16, 2008

Heavy Heart

I vowed I would never post when family took precedence. I have to break that vow today. I wish I didn't but there is something so vitally important that I must share with you. Why is this important? Because it might save more lives than have been previously lost.

The scourge of Ovarian and Breast cancer has ravaged several populations. With very few cases of early detection in Ovarian cancer, many women present with spread of the cancer and very poor prognosis. Even more importantly, women who have ovarian cancer and BRCA mutations still are at risk for other cancers including breast cancer.

Despite this I have heard comments from Oncologists like "Why do we need testing?" This is why I have pulled myself away from my grief stricken family.

To fight this lack of knowledge I have dedicated and arm of Helix Health of Connecticut to educate and promote genomic medicine. This arm will host at minimum monthly podcasts on very important topics. The first of these is Hereditary Breast and Ovarian Cancers and the BRCA genes.

The panel will include a patient with BRCA1. She not only happens to be afflicted, she has written about her experiences. Jessica is gifted with the pen and is a very successful writer. Her book "Pretty is What Changes" raises significant issues and serves as a wake up call to clinicians and patients. It serves to empower us all.

Jessica will join David Ewing Duncan, bestselling author of Masterminds: Genius, DNA and the Quest to Rewrite Life, and a panel of distinguished medical and legal professionals to discuss how the doctor-patient relationship is changing and what the potential liability is for physicians in this new era of breast & ovarian cancer and genomic medicine.

The Sherpa Says:
The Helix Health of Connecticut webcast series is dedicated to my grandmother who died at 35 years of age from metastatic breast cancer. Too young for me to ever know. Please sign up for this conference. The information may just save a life......If Helix Health of Connecticut can save just one life then all the hard work is worth it. Please sign up now. Seats are limited, but you can also sign up for the podcast.

Tuesday, May 13, 2008

The Epi-Genomic Canary

So many people talk about guniea pigs as the research subject. I think this is a disservice for the pigs. Personally I think the Shaft Canary is a much better analogy. You see, the subtle changes from the human guinea pigs may not make big headlines or get the public to listen....But, the canary in the shaft always makes big press.

If you don't know what I am talking about, let me explain. One of coal miners earliest and continuous problems was carbon monoxide. It can kill fairly quickly. But way back when, there were no gas detectors.....we had a vey limited ability to identify the dangerous gas. So what did they do? They carried a surrogate into the mine...The canary was a pretty easy to read detector. If the bird died, then you should leave the mine shaft.

With our ever expanding set of genetic risk profiling we need an easy way to read and interpret it. The problem is not that there exists a risk profile. The problem lies in what we can avoid to decrease that risk. Thus the new canary......
I spent the afternoon speaking with David Duncan, if you don't know about David, let me fill you in. David is a writer/editor and I covered him and KK of Quantified Self briefly the other day.

David is the bestselling author of Calendar (published in 19 languages) – Chief Correspondent of National Public Radio’s “Biotech Nation”; Contributing Editor and Columnist, Portfolio; Director, Center for Life Sciences Policy, UC Berkeley. He is author to articles and short stories, and a television, radio and film producer and correspondent. He is the co-host of NPR’s Biotech Nation.

David has been working on himself for the last few years. He has done things like expose himself to environmental toxins like mercury to see if he can detoxify the load, 321 toxins to be precise. He also has been getting genomic screening and recently joined our project at The Delaware Valley Personalized Medicine Project.

David is poised to really bring attention to the utility and limitations of modern Genomic Medicine. He also is going to show us how Enviro-Genetic interactions affect the Everyman. In addition to this testing, he also examined the Mind and body through things like functional MRI, systems biology analysis. If you ask me David, your genotype OddsRatio of 1.6 for MI is only useful when you mention your family history. I would like to see your 3 generation pedigree.
We talked about many things including the erosion of med students' genetic knowledge, Helix Health of Connecticut (The Early Years), 50 year old white men, Navigenics, 23andMe, Josh Adler, and the future of medicine.
The Sherpa Says:
David is the Canary, not the Guinea Pig. I admire him and look forward to his future experiments. I hope he didn't take offense to my "50 year old white man" comments! Thanks for coming into the mine with us David.....Your work is a necessity that will save countless lives.

Monday, May 12, 2008

Jessica Queller and the Sherpa

So I can finally announce my big news. Helix Health of Connecticut will be hosting a webinar with the Author of Pretty is What Changes: Jessica Queller. I am excited to let everyone in on the big news. I will be letting you all know where to register shortly. With the recent introduction of books like Jessica's in the market it is becoming obvious that there is a significant population of women who are sharing their tales.

The reason I love Jessica's book is because it is written in a such a readable fashion. You can tell that Jessica is a storyteller even without knowing she writes for Gossip Girl!

So before you attend the next Helix Health of Connecticut webinar you can read her book!

More Info to follow!!!

Stuck at the Ritz

I just received my itinerary for the Beyond Genome Conference in San Francisco? What's this conference? Well, in case you missed it.... The conference is the biggest organization of stakeholders and speakers of Genomic Technologies, Genomic Medicine and Policy Wonks. There are 4 themes which the conference is organized around.

1) Applying Sustems Biology
2)RNA Interference
3) Personal Medicine
4) Targeted Gene Therapy.

It is a must attend conference. I will be speaking for approximately 20 minutes on Patient Centered Genomic Care. I will be bookended by Kari Steffanson and 23andMe.... The lead off is Misha Angrist of PGP fame and GenomeBoy distinction.

That's not why I am writing. I am writing to tell you that if you want a room in San Fran from the 9th to the 12th you can forget about it. Unless that is you are willing to be stuck at The Ritz Carlton......If you are, come and chat with the Sherpa.

The Sherpa Says:
Hopefully Kari won't punch me ;) nor will Ryan kick me.....I hope.

Saturday, May 10, 2008

Workman's Compensation, Stereotypes and GATTACA

Have you ever had back pain? Almost everyone has. Who has sciatica?

Sciatica a very common condition accounts for a significant amount of lost work days, medical costs and psychologic stress. Treatment failures are not uncommon, are often related to posttraumatic or work-related injuries, and may result in litigation. Although most people experience back pain during their lifetime, only a fraction experience lumbar radiculopathy or sciatica as a consequence of root compression or irritation. Almost 5% of males and 2.5% of females experience sciatica at some time in their lifetime. It is so costly to society and common that in Sweden they did a cost-benefit analysis and found the surgery to be cost effective. Although studies casting doubt on its effectiveness are now in the mainstream.

Because the majority of the cases are work related....I propose to you.......The following study:

Let's genotype everyone who had disc herniation and see what comes up......

Sounds interesting? It is. Well, it turns out in Japan that they did just that. The study entitled

What did this group find?

"A splicing-affecting SNP in THBS2 and a missense SNP in MMP9 are associated with susceptibility to Lumbar Disc Herniation"

Did it stand the Sherpa test?

Odds Ratio? It was 3.03. You betcha. This is stronger than any of the SNP chip companies SNPs. For just about anything....

Replication? Not Yet....

So why do I even bring this whole thing up? Well.....First off did anyone remember Burlington Northern Santa Fe Railroad Company? It turns out this company was secretly genetic testing their employees. You don't? Let me recap. In 2001 it was reprted that this company was testing employees who developed carpal tunnel syndrome. They tested 18 people who had filed workman's compensation claims. It turns out they had developed carpal tunnel while workin' on the rail' road.....(all the live long day)

They performed genetic testing to see if these workers were predisposed to carpal tunnel syndrome, another horrible but operable condition which costs tremendous money to society.

Guess what? Someone(Equal Employment Opportunity Commission) sued the dickens out of them and the company ended up settling out of court. They argued that company policy requiring genetic testing for all workmen's compensation claims related to carpal tunnel syndrome was genetic discrimination. In fact, this case had been used as a example of the rare times, genetic discrimination came to pass.

Here we have a very similar situation. But now that GINA is coming to pass. I would like to pose an alternative.

Young person goes to 23andME/Navigenics/ETC (They just may add this immediately)....gets predictive testing indicating that he is at a 300 fold increased risk of herniating a disc in his back. Avoids manual labor (plays video games all day) never herniates the disc. Did we do society a service? Some would argue yes....I say no.

Let's say, at birth we test the genome. Let's say we find the variants. Instantly this child is marked "High Risk for Work Related Disc Herniation" Based on the societal calculation, it is not justifiable to allow this person to work manual labor jobs. Now, I ask you. Who can tell someone what to do just because of his genetic predisposition? What if this kid wanted to be a firefighter? Should we not let him save lives? What if he wanted to be a Paramedic? A plumber? A carpenter? How far do we go?

The Sherpa Says:

We have to address this issue soon. Because more studies like this one are coming....and I am very scared with the press and marketing push going on, we may end up believing genetic predisposition is everything. The fat cats at Burlington Northern sure did...

Thursday, May 8, 2008

276 pages of pure reality!

Have you read it? Come on.....You didn't. Well, you are missing out. Back in 2004 I started watching the Secretary's Advisory Committee on Health, Genetics and Society. But even more importantly I began watching back meetings that were webcast, including the SACGT. I studied the players in the field, the advisors, the government. I began to notice trends and agendas.

This is why I saw all of the regulations coming. I began emailing members, speaking with advisors, and learning how and when all of the issues would arise and then be solved. Then in 2005 I began to develop the business plan for Helix Health of Connecticut.

The safest climb to the summit is with trained genetics professionals like the ones we have. The riskiest is D-I-Y. The SACGHS is against D-I-Y...notably this 276 page report goes into this in fine detail.

Highlights include

Are Genetic Tests Special?

When considering whether genetic testing is different from other laboratory tests, it is important to understand the viewpoint known as "genetic exceptionalism," the perspective that genetic information is unique among health-related information and therefore deserves special considerations and protections. Proponents of this perspective usually point to the following features of genetic information as being distinct from other types of health information:

• It can be used to make predictions about an individual’s health future.
• It does not change throughout a person’s lifetime.
• It has the potential to reveal information about family members.
• There are instances in which it has been used to discriminate against individuals or selected populations.


....... a nonexceptionalist approach has been taken with respect to Federal health privacy protections. The Federal Health Information Portability and Accountability Act Privacy Rule, which became effective in 2003, treats genetic information as equally sensitive as other medical information and provides the same level of protection to genetic and other types of personal health information. Recent policy recommendations encourage movement away from genetic exceptionalism.

That Being Said....

The Committee is concerned by the gap in oversight related to clinical validity and believes that it is imperative to close this gap as expeditiously as possible. To this end, the Committee makes the following recommendations:

A. FDA should address all laboratory tests in a manner that takes advantage of its current experience in evaluating laboratory tests.

B. This step by FDA will require the commitment of significance resources to optimize the time and cost of review without compromising the quality of assessment.

C. The Committee recommends that HHS convene a multistakeholder public and private sector group to determine the criteria for risk stratification and a process for systematically applying these criteria. This group should consider new and existing regulatory models and data sources (e.g., New York State Department of Health Clinical Laboratory Evaluation Program). The multistakeholder group should also explicitly address and eliminate duplicative oversight procedures.

D. To expedite and facilitate the review process, the Committee recommends the establishment of a mandatory test registry as noted in the following recommendation.

The Sherpa Says:

I will go into this report in more detail later. But If I was Google......This would be mandatory bed-time reading...Looking at these snippets it is clear. The barrier to entering the testing business is about to get MUCH, MUCH bigger. Playing nice with the government will only get you so far.

Tuesday, May 6, 2008

Lancet and the Sherpa

After reading an editorial from the Lancet...I think that they may be reading the Sherpa. Let me know what you think. From the Lancet "Genome Wide Open"

Interpretations of the effects of human genotypes on disease are today just entering the foothills of a forbidding massif. In particular, a much richer understanding of human genetic variation is needed. However, the relentless ascent of human genomics is coinciding with growing public interest in maintaining health and participating in health-care choices. Doctors will face challenges in guiding their patients through genetic terrain strewn with difficult language and concepts, but should be optimistic that shared enthusiasm will make for surer progress.

My Blog?

To usher in the new paradigm of personalized medicine we will need to travel a perilous path. Much like the route through the Himalayas it has punished the naive and self-reliant. That is why I have dedicated my life to being a Gene Sherpa. What is a gene sherpa? The Sherpa speaks the language of the trail, he/she knows short cuts and dangerous paths to avoid. This blog is for those wishing to take the journey and those wishing to become Gene Sherpas.

Sure sounds to me like someone reads the Sherpa......

Keep Climbing,

Osteoporosis and Gene Tests

Osteoporosis, or porous bone, is a disease characterized by low bone mass and structural deterioration of bone tissue, leading to bone fragility and an increased susceptibility to fractures, especially of the hip, spine and wrist, although any bone can be affected.In simpler terms, osteoporosis is a condition in which the bones become weak and can break from a minor fall or, in serious cases, from a simple action such as a sneeze.

About 85-90% of adult bone mass is acquired by age 18 in girls and 20 in boys. Building strong bones during childhood and adolescence can help to preventosteoporosis later in life.

In the U.S. today, 10 million individuals are estimated to already have the disease and almost 34 million more are estimated to have low bone mass, placing them at increased risk for osteoporosis.

In 2005, osteoporosis-related fractures were responsible for an estimated $19 billion in costs.By 2025, experts predict that these costs will rise to approximately $25.3 billion

So I ask you.....if we could prevent osteoporosis wouldn't we. Early detection and identification of at risk populations is key. Recently there were some great studies that came out of Lancet and the NEJM identifying patients which might be at risk. They are definitely associated in some sort of way, but not ready for prime time. Why? Because there are better predictors


Significant risk has been reported in people of all ethnic backgrounds.
Twenty percent of non-Hispanic Caucasian and Asian women aged 50 and older are estimated to have osteoporosis, and 52 percent are estimated to have low bone mass.

So more often in Asian and Caucasian women. What are other risk factors?

  • Being female

  • Older age

  • Family history of osteoporosis or broken bones

  • Being small and thin

  • Certain race/ethnicities such as Caucasian, Asian, or Hispanic/Latino although African Americans are also at risk

  • History of broken bones

  • Low sex hormones

  • Low estrogen levels in women, including menopause

  • Missing periods (amenorrhea)

  • Low levels of testosterone and estrogen in men

  • Diet
    Low calcium intake
    Low vitamin D intake
    Excessive intake of protein, sodium and caffeine

  • Inactive lifestyle

  • Smoking

  • Alcohol abuse

  • Certain medications such as steroid medications, some anticonvulsants and others

  • Certain diseases and conditions such as anorexia nervosa, asthma and others

  • Loss of height (which may indicate a spinal fracture)

So what does genetic testing add to this? From the clinical side....Absolutely Nothing. The risk prediction from these above factors is much higher than the non-statistical significance genes in the New England Journal of Medicine. Nor the interesting findings in the Journal Lancet.

The Sherpa Says:

Listen, back to the basics before we hype up these SNPs in Lancet. Odds Ratios less than 2.0 are not very useful for clinical practice.....So why do they get all this hype???? Because "New Gene For X" Always makes headlines and sells papers.

Saturday, May 3, 2008

2 Women, One Prize, Oprah and a new Industry

The Albany Medical Center Prize in Medicine and Biomedical Research was recently awarded to 2 scientists for their work on snRNPs and Telomerase. Oh yes, that magical molecule that will allow us to live as long as Methusaleh, or some would claim.

What is telomerase?

The "clock" of cellular life was once a mystery to scientists. But soon they found that telomeres, the tips of chromosomes. Or as Dr Oz loves to say, the wrapping at the end of the shoelace, becomes progressively shorter over the life of a cell and when they become too short, cells die.
Dr. Blackburn one of the 2 scientists showed that telomerase can add DNA back to the ends of telomeres and effectively turn back the clock. enabling cells, and theoretically us, to live longer.

This has allowed Oprah and Dr Oz to give quite a show a few months ago and has spurred an interesting testing industry. The picture above is of a shop right here in Manhattan that helps enhance your telomerase activity through a molecule known as TA-65. From their site:
Noel and Eve currently travel between Hong Kong, California, and New York. In 2007 they opened the T.A. Sciences CenterTM, located on the Upper East Side in Manhattan which will market the first anti-aging products derived from Geron's technology. The T.A. Sciences Center will offer telomerase activating nutraceutical and cosmeceutical products to an exclusive clientele.
I wonder if Oprah knows about them. Do you think Dr Oz does? Well, now you know. Here's the big question? Does it work? Or is it too early to tell. Either way, they are doing it for over 20,000USD! I wonder if Dr Blackburn gets any residual income???? Doubtful......
The other scientist? Oh well she only discovered how snRNPs act on pre-mRNA. From Medical News Today
Dr. Steitz is Sterling Professor of Molecular Biophysics and Biochemistry at Yale. She achieved global recognition when she found out how small ribonucleoproteins (snRNPs) behave in pre-messenger RNA, the earliest product of DNA transcription. She discovered that snRNPs get rid of introns, the useless chunks of DNA and pre-messenger RNA, by "splicing" them out and then joining the severed ends together to make messenger RNA. Messenger RNA then instruct the production of proteins, the essential building blocks of the body's biology.
First off......Introns are not useless chunks! Come on Catharine Paddock, PhD......dumbing it down, doesn't mean making dumb statements that aren't true.
Nonetheless, this is the first time 2 women have been awarded this prestigious distinction. It has only been around since 2000 though. So here's to more women in science!
The Sherpa Says:
Interestingly, I couldn't find TA-65 in pubmed. I wonder where the evidence base is for this nearly 30,000 USD therapy. Who said the public won't pay for "health care"? The less evidence, the better the pay. It is truly amazing what a little hype will do. With that much per patient you would hope they could fund some serious trials. It appears they have yet to do just that. Instead they will charge you for their "trials". Sound familiar? Absolutely. Isn't that what Linda Avey said about 23andME? Consumer Enabled Research? But it looks like in TA Sciences case, the profit is good and the research is sparse. Buyer Beware....

Thursday, May 1, 2008

Ball's in Bush's Court and Why I Love Genome Technology Online!

I hope everyone who reads this will subscribe to Genome Technology Online (This is not a paid advertisement this is my opinion).

Why? If you are asking this, it is likely because you have never received the email newsletter.

I am always impressed by their ability to capture the essence of what is going on in the Genome World Daily. They have excellent reports for purchase as well. But frankly, just getting the email everyday makes my heart twitter (I can't get sued for using that word can I?)

Today they poke fun at Corporate Genomics and make mention of 2 very well written articles. One over at the Wall Street Journal. Yesterday I took Marilyn Chase to task. Marilyn, please don't get mad. Just give me a call next time you are writing about genome studies.

And another story at Portfolio. The WSJ article will be lifted by me or maybe they lifted the Sherpa.

Despite heavy marketing by some genetic-test makers, the wide use of genetic tests has been held back by a variety of factors, including questions about the tests' usefulness and concerns that results could be used by employers and insurers to discriminate against people. Critics argue that many tests can't accurately identify which people are at risk for various illnesses.

Tests are often pricey, costing hundreds of dollars. "In the common diseases, there's more predictive information today in knowing family members had it than knowing" the results of the newly developed genetic tests for such conditions as Type 2 diabetes, says David Altshuler, a professor at Harvard Medical School.

Anna, I loved the article. Well written and balanced. Maybe you could get together with Marilyn?

Even better is the article from Portfolio, where KK at The Quantified Self/Wired contributor and David Ewing Duncan go over corporate genome scans. It is funny, but in KK's blog he finds 23 differences in the genome scans between 23 and Me and DeCodeMe....Get it? "23" David also points out several differences. Gentleman, your risk differences from companies is simple.....Unless viewed in the light of family history, these scans are not relying on much in the way of science. One or two very large studies does not equal good medicine. I am sorry to say that, but it is the G_d's honest truth. You need medical guidance to truly determine these risks.

Hmmm...that's funny. I have only been saying that for the last year.....

To give equal time to these parties...We recently saw a wonderful patient who had one of the Navigenics scans. Here's what we found. The patient had a much higher risk for heart disease based on family history. In addition, may have a familial hypercholesterolemia. I am certainly glad that the patient came to us for a family history. We are seeing more and more of these patients. I think it is because of articles like these.

The message is simple. Don't expect much from these scans and in fact you should have some evaluation by a trained medical professional to make the most out of your results. Not to say these companies can't do great things. They just need a litlle collaboration. In fact Our Values mirror theirs.

As for the WSJ quote by Keri Stefansson. Does he think I am an idiot? You may be able to slip this past the public, but not me.......Obviously all that training in neurology made him forget the 1 year of training he did in internal medicine, Or gave him dementia.

Kari Stefansson, chief executive of deCODE genetics Inc., an Icelandic company that markets an array of genetic tests as well as a broad genetic scanning service, says tests for such conditions as Type 2 diabetes are important, partly because negative results may convince consumers to try healthier behaviors. "All preventative medicine is based on the assumption that you can raise concerns," he says. "Are these guys telling me it hasn't been worth measuring cholesterol all these years because other factors also affect heart disease?"

Well Keri....maybe you forget to tell the paper that an elevated LDL or a Low HDL or a high triglyceride level are like way more predictive of risk for Heart Attack than your TCF7L2 genetic test is predictive of Diabetes. At least by a factor of 10 if not 100. In fact his statement just pisses me off. How dare you, as a medical doctor, compare these things! It is disingenuous. You obviously want to confuse the public and have only one agenda. Selling your test! Shame on you... You are supposed to be a scientific physician. What kind of comparison is that? Do you remember your hippocratic oath? I would expect that hyperbole from non-physicians, but from you???? I am embarrassed.

"In every house where I come I will enter only for the good of my patients, keeping myself far from all intentional ill-doing"

The Sherpa Says:

I hate saying that I have big news when the television journalist drops my interviews in the end. But I have some even bigger news. Stay tuned, I will be able to tell you about it in 2 weeks. It does look like the United States will have big news too, since GINA has now passed in the House. So I say President Bush...."Ball's in your court" As for these articles on corporate genomics. Like Senator Obama, scrutiny is not doing the corporate genomics companies any good.