Gene Genie is Back at The Sherpa!

There are many posts that were submitted. I have to say, we are doing a good job of covering these genes, but probably won't get through them all. I am excited about a ton of this content. But when we move through genetic discovery, talk always falls back to personalized medicine. I have been trying to move away from this term lately. And so has the American College of Medical Genetics. I like the term Genomic Healthcare. It's simple and expresses what is going on today and what will continue for the next decade or two.

So without much ado let's get started!

First the basic science. It is on the shoulders of these giants which Sherpas like me stand when we implement the clinical action. We are all different, every single one of us unique. What makes us this way? Well Yann Klimentidis shares with us some of his thoughts on the SNPs and genes that may make each population special. How can we trak what population you are from? Well, one good way is through mitochondria and now we have a more visual way to look at the mitochondrial genes. Made by a "mitochondrialist" (I would love to see what that conference looked like) the MitoWheel is poised to help those who need just a little more visual model.....May the Force Be With You.

At least if you have blue eyes, then things are looking up. Blaine over at Genetic Genealogist covers that family tree. Now I bet Tom Cruise doesn't feel as special anymore.

Other things make us special. The stuff with which we arrogantly called junk, including introns is proving to make us pretty special. Larry at Sandwalk elegantly covers some of the hot topics in Intronic Junk. This makes him the Tony Soprano of genetic waste management! Nice post.

It's not all about the Homo Sapiens. Even birds get their say at GrrlScientist where the argument for earlier flight is posed. Not really a gene post per se, but it is a Rock vs DNA clock battle. Speaking of evolution, what makes a fish go blind and how do they get that sight back? Greg Laden's blog will show you how. Better blind than dead, but if I have to go, I would like to skip the Black Death. Especially after reading Archeozoology's coverage of the Yersina Pestis Genome. Well maybe I will eat myself to death...or a higher level of evolution. Nature Blogs cover the Big Mac controversy. Nature versus Nurture debate will never end!

So how do we take this to the road? How can we translate these unique findings?
First we have to educate the physicians and get them up to speed. But can we do it? I will be presenting at the Association of Program Directors in Internal Medicine precisely on this topic. The blog PredictER gives some insight as well. Some may say we should just bypass physicians, let's here about our Genetic Future. After that good laugh we can head to Berci Mesko at Scienceroll and find a "23 and Me Hacker" who has created a pretty useful tool to help.

We all know that these technologies will only continue to improve. Unfortunately most MDs don't have the time to keep up. Here's a hint for them....Visit the Gene Genie, which will be at Sciencebase next.

For those who need a quick set of new tests!
deCode first with the PrCA gene, cute fellas, real cute. Hsien and Ramunas both cover this one.
Soon we won't need all of these tests. Especially if the 1000 genomes projects get things scanned quickly. I am certain all sorts of novel technology will be created. This will shake things up.

Until that day we have Family History. I was with a patient and one of our geneticists today. When a patient asked him how many patients he had seen he said "I have been doing this counseling before they even had the test." In heart attack land, family history is still the king predictor of MI risk. But I doubt that the company selling the Kif6 test want you to know that. Well maybe someday I will show up on the WSJ health blog too.....

Thanks to all those who submitted. I hope you enjoyed this. Thanks to Ricardo at MyBiotechLife for the excellent logo!

We need more Samples/Sherpas!!!

Genetic Research is a hard business. You have to fight and IRB to get your I's Dotted and Your T's crossed. You have to write and write and write grants to get funding for your ideas. You have to manage the project and work to keep everything on track. But what will the rate limiting step be in genomic research?

Perhaps it is the lack of samples?

From Medical News Today, an exciting announcement regarding Lupus. Lupus is a terrible disease where the immune system attacks the body's DNA. It can cause horrible things including, stroke, skin disease, kidney disease, brain inflammation. In fact a whole host of persons who have this disease are unable to function in society.

A new finding includes the discovery (Not Validation) of a gene implicated in Lupus' pathogenesis (disease cause) OX40L. These researchers have identified other risks as well. His findings are only mildly interesting as replication will be needed. But what is more telling is his plea to the British people

"Without DNA samples from people with Lupus, we would be unable to study the disease," he says. "Despite the disease being relatively common, DNA samples are in short supply. I would encourage patients to discuss with their GP or consultant about providing a blood sample to help further our understanding."

With all of these companies looking at your SNPs or your Exomes or your Genomes and the vigor with which they launch PR campaigns. One would hope they could donate their datasets to these Scientists in need.

I perosnally have been trying for months to help a friend donate her genome to a sequencing project. Hope fully the Delaware Valley project will take her code. I think that genome sequencing will ultimately win the day over some of this SNP Chip technology. Why? SNPs are not enough. Copy Number Variation will slowly be found to play as large a role...if not more. You can read about some of this here.

The Sherpa Says: Did anyone watch the 60 Minutes special on Sherpas in The City. Turns out that for their health Sherpas are moving to New York. Any Gene Sherpas in the batch? I sure hope so. The Gene Sherpas of the world are coming together for one big collaboration and I can't wait till we all can guide the genomic tourists of the world!!! Stay Tuned for the Sister services soon to show up on the scene. Heads Up L.A., S.F., CHI!!! Are you a Sherpa? Want to join the team? We would love to have you. Can't wait to see you all in NY!

Staying Positive

I was showered with a host of emails from my readers today. The GTO highlight, The Issue feature, Scienceroll's commentary all the readers had to say one thing. Sherpa, take it easy. You beat up on DNADirect and their questionable questionnaires, You picked on Forbes giving hype to deCODE, You pointed out that Navigenics had some sketchy ethics, Slammed Salugen, Attacked Myriad, and Now little 'ol 23 and Me. Did you have to sink this low?

Sink this low?

Wow! Ok, so I have been known to blow my top a time or 2. Can you blame me? Have I stated any incorrect facts? Maybe some, which I have quickly amended. Including the fact that DNADirect does not "mark up" test costs. Even though I am still unsure of how a company who sells tests at cost and charges 75 USD for phone consultation (even less than an academic center that is losing money on counseling pays a genetic counselor) makes any money.

So why did my readership feel this way? The answer. "Why won't you endorse us using suspect science data to give us suspect risk assessments?"

Huh?

Yes, it is true. Even the educated are intrigued by this little black box known as the Gene Journal and Risk calculator. Fine, I like the magic 8 ball too. So here it is. I am putting it on the record. I will not hate you if you use 23 and ME. In fact, I suggest you use it after taking a family history and having the familial risks evaluated. If these SNPs give you more insight than a family history....I applaud you. Here's my last appeal, please realize that this data will not be considered medical records if you use a non-healthcare company to screen your genome.

If you want the BEST coverage, you should use deCODE, 23andME, AND Navigenics services. This is the only way you will get ALL the SNPs your little lemming heart can desire.

Then, when you want to make your genome a medical record and protect it, ask your physician to review the data. If they rebuff, go see a geneticist. Helix Health of Connecticut can interpret the SNPs in concert with your family history. Your Genome In Context........ ;)

The Sherpa Says: Please don't hate me for the aggressive commentary. I am not a hateful guy. I just call it like I see it. Maybe you see it differently and that's the great thing about the Blogosphere. Different viewpoints, Different ideas, The Same Passion.

American Society of Human Genetics speaks out on DTC testing

After a wonderful conference call with some friends regarding the future of personal genomes, I was heartened to see ASHG put out a statement on Direct To Consumer (DTC) testing. Here is what these learned individuals say.

Currently, DTC genetic testing is permitted in about half the
states2 and is subject to little oversight at the federal level. In July
2006, the Government Accountability Office issued a report documenting
troubling marketing practices by some DTC testing
companies,3 and the Federal Trade Commission (FTC) issued a
consumer alert cautioning consumers to be skeptical about claims
made by some DTC companies

While DTC testing also encompasses paternity and ancestry testing,
this policy statement addresses solely those genetic tests that
make health-related claims or that directly affect health care decision
making.

For a test to be of good quality,
the laboratory performing it must be able to obtain the correct
answer reliably, meaning that it detects a particular genetic variant
when it is present and does not detect the variant when it
is absent. A test’s accuracy is referred to as “analytic validity.”
Further, there must be adequate scientific evidence to support the
correlation between the genetic variant and a particular health
condition or risk—the so-called clinical validity.

Currently, the federal government exercises limited oversight
of the analytic validity of genetic tests and virtually no oversight
of their clinical validity.

Several complaints have been filed and
are pending with the FTC about a specific DTC genetic-testing
company, and the FTC recently issued a consumer alert warning
the public that “some of these [DTC] tests lack scientific validity,
and others provide medical results that are meaningful only in
the context of a full medical evaluation.”

So there in lies the problem. They have several solutions.

Recommendations
I. Transparency
To promote transparency and to permit providers and consumers to
make informed decisions about DTC genetic testing, companies must
provide all relevant information about offered tests in a readily accessible
and understandable manner.

a. Companies offering DTC genetic testing should disclose the
sensitivity, specificity, and predictive value of the test, and the
populations for which this information is known, in a readily
understandable and accessible fashion.

b. Companies offering DTC testing should disclose the strength
of scientific evidence on which any claims of benefit are based,
as well as any limitations to the claimed benefits. For example,
if a disease or condition may be caused by many factors, including
the presence of a particular genetic variant, the company
should disclose that other factors may cause the condition
and that absence of the variant does not mean the
patient is not at risk for the disease.

c. Companies offering DTC testing should clearly disclose all risks
associated with testing, including psychological risks and risks
to family members.

d. Companies offering DTC testing should disclose the CLIA
certification status of the laboratory performing the genetic
testing.

e. Companies offering DTC testing should maintain the privacy
of all genetic information and disclose their privacy policies,
including whether they comply with HIPAA.

f. Companies offering DTC testing and making lifestyle, nutritional,
pharmacologic, or other treatment recommendations
on the basis of the results of those tests should disclose the
clinical evidence for and against the efficacy of such interventions,
with respect to those specific recommendations
and indications.

The Sherpa Says:

I am still waiting for the data from Salugen/Luxor...........hmmm I wonder why? Wake up people, this field is filled with snake oil salesmen!!!!

SACGHS and DTC testing

The SACGHS met this month and alloted 15 minutes to the CDC presentation on awareness to DTC tests. The CDC funded three states to study awareness of DTC testing as well as utilization of DTC testing. They also performed a national study. The presentation reviewed this data and of note there were some intersting findings

1. Only 0.6% of the national population has used DTC tests (BTW that's 1.8 milllion people)


2. 14% of the US population is aware of DTC testing


3. 73% of those who were aware, heard through the media


4. Yet over 60% who used the tests were directed by DOCTORS!!!!!!

In addition a survey was administered to physicians. This DocStyles study had 555 physicians who were aware of DTC testing. Of Those

1. Only 4% of MDs report >10% of their patients asking for DTC testing


2. And an amazing 93% of physicians report <1%>
   
3. 96% of physicians report Journal Articles as the most trusted source for Genetic Testing Information. ONLY 6% report that other health professionals are a trusted source for Clinical Testing! (Does this include CGCs or Geneticists?)


4. The majority of info physicians receive on DTC testing is from the media, not Journals.

The Sherpa Says: There are some limitations with the public studies. One thing is for sure.....The media has a powerful lock on distribution of this information. Did you hear that Mr Murdoch? I am truly scared that the physicians do not find other physicians knowledgeable or trustworthy. YIKES!!!!

Sherpa Posts Total 100!!!!

No I am not nearly as prolific as some of my contemporaries, but hey I have only been at this since March ;)

I hit the milestone of my 100th post today. In my championing, flaming, arguing, almost getting sued (Thanks San Fran!), and just plain out bashing quacks I have discovered some amazing people and some amazing sites. The following is a running tally of blogs I love. Some genetic, Some medicine, Some not so much.

• Scienceroll by Bertalan Mesko soon to be MD



• Bad Science by Ben Goldacre MD



• Eye on DNA by Hsien Lei PhD



• Highlight Health by Walter Jessen PhD



• Revolution Health's CMO Jeff Gruen MD



• The DNA Network and its littany of great blogs!



• Mashable the blog for social networks



• Buddhist thought by James Ray



• The Entrepreneurial MD



• Great Pics from around the World at Cosmos



• The latest and greatest at Science Friday



• The Wall Street Journal's Health Blog



• Wired's Science Blog



• NPR's On The Media
  

I know that this only 14 blogs but each is worth its weight in gold. It is Thursday and July so forgive me but I have to deal with some new interns :)

The Sherpa Says: Thanks to all of you. I look forward to the announcement when I hit 500 posts! Let's keep our eyes open and realize that there are a whole lotta people out there trying to oversell genetic tests. Or even worse. Knowledge is just a set of unorganized facts. Wisdom is knowing where to find the answer. I will strive to give you that answer or at least have the wisdom to find it.

WBUR posts on coumadin and Personalized Medicine!

Despite the heavy Boston accent,

On WBUR Carol's worries regarding Coumadin and Personalized Medicine hit home to millions of patients everywhere. This is an excellent example of the press' coverage of my specialty. Dr Sam Goldhaber a physician at Mass General talks about the promise of pharmacogenomic testing in blood thinning and avoidance of its horrible side effects.

Lastly they interview the Pope of Personalized Medicine

Francis says "Is this the scenario we want personalized medicine to enter?"
"The public thinks that this is snake oil (i.e. Direct to consumer testing and nutrigenomics)"

In addition Dr Collins talks again about the 2 Betty's and the potential to miss diagnose and have horrific outcomes.

The Sherpa Says: "Save Betty!!!" We must take the time to educate everyone about the promise and pitfalls of personalized medicine. In My Humble Opinion, the only thing to move physcians will be the slew of lawsuits that happen after we publicize our great outcomes at Helix Health of Connecticut.

Harvard Honoring the Sherpa!

Today I was asked to be on the faculty of Harvard's famous Continuing Medical Education conference in the Genetic Basis of Adult Disease. I am extremely honored to be a part of this distinguished faculty. This year's conference will be held October 12-14th. The last conference topics and website are still up and I am certain the new one will be shortly. I highly recommend it for all physicians looking to become Sherpas or at least to stay up with the breakneck pace of genetic discovery in medicine. Several topics include:

• Genetic Causes of Heart Failure
• Genetics of Lipid Disorders
• Genetics of Cardiovascular Disease
• Genetics of Common Psychiatric Diagnoses
• Genetics, Lung Cancer and Treatment Responses
• Genetics of Gastro-Intestinal Diseases
• Barriers to the collection and use of the Family Health History in Primary Care

So who should attend this great conference?

Internal Medicine Docs
Family Physicians
Genetic Counselors
Registered Nurses
Nurse Practitioners
Physician Assistants

I was at the conference last year and am excited to be behind the podium this year. Please mark your calendars!!!!

Personalized Medicine since 1986???

First I would like to apologize for the lack of postings on interesting topics lately. I am glad that others have picked up my slack. Notably Hsien and Bertalan's interesting posts this week. Or for an in depth post on the politics of health care and the reform movement check out VentureBeat

What I want to pay attention to today is the question I inevitably get asked when I speak to other physicians. "Is what you say feasible in a 7 minute consult world?" The answer is inevitably NO. I do not feel in my heart of hearts that we will ever be able to practice personalized medicine in a 7 minute consult world.

What's needed is a Revolution. We need a place where the patient has access to their records and their physicians 24/7. We need a place where the patient is given the skills to understand and manage their disease. My friend's 12 year old son can quite effectively manage his diabetes, how come a 45 year old venture capitalist cannot? Support is the key and learning is the motion required to open the lock. How do we make these things easier? How can we get doctors to teach their patients? What ever happened to true continuity of care? These are big questions that need answers. I don't have them all. But I am working with some great people who will find those answers.....

So the next question is "How can we have the knowledge to practice these things?" I often tell physicians to go back to college or read a book on genetics. If you don't have the time to do that, then you will fail your patients. This often meets an uproar of disbelief......I am pretty good at pissing people off. Just ask Lisa Lee at DNADirect ;)

In all honesty, we need some clinics who offer personalized medicine consultations. These specialists need to guide care in collaboration with PMDs. I am building this model in NYC! We will be seeing patients in July. Give me a call and we can arrange to start the relationship.

But there has been someone doing this since 1986!!!! Wha??? The HGP was only 3 years in and they were providing these services. Yes that is correct. Greats such as David Rimoin and Maren Scheuner helped form and develop this practice. It goes by the "trademarked" name GenRISK Adult Genetics Program. It has been in practice since 1986 offering several tests that you can see on their site. I have been critical of predisposition tests unless clinically indicated. This is an example of how a personalized medicine practice can be run.

The Sherpa Says: Genomic and Personalized Medicine need to be given in a continuity of care. Family history changes, medical history changes. A one time consultation cannot deliver that kind of service. Oh and what about pharmacogenomics?

Not all drugs benefit all man!

While Bertalan Mesko at ScienceRoll is introducing us to the best medicine 2.0 tools, i am reviewing some results from the American Society of Clinical Oncology meeting last week.

In another example of how we need to examine patients pharmacogenomics prior to instituting therapy the SWOG (South Western Oncology Group) in the U.S. releases results of a collaborative effort with two clinical groups in Japan (Japan Multinational Trial Organization).

The researchers were interested in how these different groups metabolized certain chemotherapeutic agents Paclitaxel and Carboplatin. Now what is interesting about this study presented at the ASCO conference is the fact that they were able to isolate two gene polymorphisms responsible for these effects.

In patients with certain variations in the CYP3A4 gene, it took 2.75 times longer for their lung cancer to progress than in patients without the variations. A variation in another gene, ERCC2, appeared to interfere with how well patients responded to treatment.

The problems with this type of analysis are threefold.

1. The study was too small a size to not need replication


2. The study did not involve the genome of the tumors (Perhaps the DNA repair mechanisms in the Caucasian tumors were better. This would like to decreased cell death i.e. response to chemo. As with the tumors and ERCC1)


3. The dose of chemo was not controlled (although the lower dose worked better in the Japanese)

The Sherpa Says: In order to make useful sense of Personalized Oncology we must look at genomes of both the cancer and the person. I feel that we are introducing erroneous data to confuse us. I hope The Cancer Genome Atlas will show us some better data!

Personalized Medicine. Coming To A Hospital Near You!

The Houston Business Journal today reports on a ground breaking ceremony for Baylor College of Medicine.

"The soon-to-be Baylor Clinic and Hospital will be constructed at Old Spanish Trail and Cambridge Street in the Texas Medical Center area.

The campus will include an adult hospital, outpatient clinics, faculty offices and research space. The fully integrated health care facility, which will focus on personalized, gene-based medicine, will be open for business in 2010.
The Houston-based school also said its "Best Minds, Best Medicine" fundraising campaign is nearly half way to its $1 billion goal for clinical, research and education projects."

Baylor is best known in genetics circle as the place you send your CMA/CGHs. Personally, this is a great accomplishment. They now join the ranks of TGen, Mount Sinai, Duke, Mayo, Michigan State and Harvard in planning and implementing "Personalized Medicine Departments/Hospitals"

The problem I see is: Whom will talk with the primary care physicians in a language they can understand? Surely these patients will get genetic guided therapies and hopefully get some excellent counseling, but will the PMD have the knowledge to understand what was done? What about the patient. Will there be an educational program directed at clinic physicians? Where do non-clinic patients get their care? Will the summary reports be at a level the PMD can digest?

The Gene Sherpa Says: All this planning is great, but can we have something Right NOW?

Personalized Medicine and Prostate Cancer

I had said before how important replication studies are. It does bear some reminding though. replication lets us know that we are on the right track. There can be many false findings in the genome, especially when we are unsure what a certain marker does or does not do(confusing, I know). With that being said I report on a marker that has been linked to aggressive prostate cancer.

Prostate cancer is extremely common and tends to be more aggressive in certain populations. In fact, there are some doctors who opt not to treat the elderly because of the risks outweigh the benefits.

The marker which is being replicated was initially found by the deCode company back in 2006
Northwester reported on the findings at the American Urologic Association meeting this month.
What are they?

1. This marker is twice as common in African Americans (more aggressive prostate cancer is often in AAs)
2. If you carry the marker you are 40% more likely to have a family member with prostate cancer
3. You are more likely to have metastases if you carry this marker

The Gene Sherpa Says: This study shows the heritability of prostate cancer, and more importantly aggressive prostate cancer. Perhaps by identifying those with the marker, then we can go after the tumor more aggressively as there are several ways to treat this Cancer based on "non-molecular" staging.

Great Blog, Great Man

On occasion I like to make note of some person, event or thing that contributes to the future of health care and ultimately personalized medicine. One of these people is Bertalan Meskó.

He is a medical student at the University of Debrecen, Hungary (4th year of the 6). He has set up an amazing blog at Scienceroll whose aim is to make medicine, genetics more readable even for those who are not too interested in these.

If he were just to do that it would be a great thing. However, the soon to be Dr M is planning to help deliver the tools of Web 2.0 directly to physicians as he has to myself. He describes this synergy as Medicine 2.0. I currently am pointing all of my medical students and residents directly to his blog. I highly recommend it.

He has been interviewed several times and presents some great material.

I for one am extremely thankful to have a person willing to translate the technology of today allowing all of us to create the medicine of tomorrow.

Thanks Berci, I look forward to your exciting news.