Archon X-Prize Here We Come

This week in the Proceedings of the National Academy of Science an article entitled:
"Single-molecule mass spectrometry in solution using a solitary nanopore" was published.

Why is this mouthful of words important? Well, the future of genetic testing and sequencing is going to change and this is the likely direction. This pore, created by a bacteria (Staph Aureus) is only 1.5 nanometers. For appreciation, the human hair is 10,000 nanometers. What I think is ironic is that the enzyme used to create the pore actually gives staph its ability to really make us humans sick. The technique used is remarkable...I don't know if anyone has seen a tandem mass spec before. But it usually takes up the size of a lab table. This procedure could actually be accomplished on a microchip!!! This study is a proof of concept study done in Ohio and Brazil which demonstrates the fidelity of molecule size prediction. I am sure there will be more to follow.

In addition Harvard has gotten into the game of nanopore sequencing and will likely be the world leader. But this is no surpirse. They have been in this nanopore game since the early 2000s (did I just say that?) The rough estimate for launch in this project has just gone from 7 years to 3.

The biggest problem clinicians have with genetic testing is it often takes too long with some of the quickest results taking longer than 6 hours. Nanopore sequencing could give answers in less than 2 hours. This would allow a physician to dose medicines, change treatments, identify disease in a much more reasonable window of time.

Do I see nanopore sequencing being used in the ED? Not quite yet, but the pharmacogenomic implications for personalized medicine are huge!!!!

Thanks Jason for putting this on the Radar Screen back in March.

Google Innovation? Google Conspiracy? You Decide

In reading through my RSS feeder I stumbled across an interesting video at Testing Hiatus. It comes from the website Master Plan the Movie. Before you watch this YouTube video I first would like you to take a gander at an excerpt from

"The Google Story"

Sergey Brin and Larry Page have ambitious long-term plans for Google's expansion into the fields of biology and genetics through the fusion of science, medicine, and technology. . . .One of the most exciting Google projects involves biological and genetic research that could foster important medical and scientific breakthroughs. Through this effort, Google may help accelerate the era of personalized medicine, in which understanding an individual's precise genetic makeup can contribute to the ability of physicians and counselors to tailor health care treatment, rather than dispensing medications or recommending treatments based on statistics or averages.

"We need to use the largest computers in the world," Venter said. "Larry and Sergey have been excited about our work and about giving us access to their computers and their algorithm guys and scientists to improve the process of analyzing data. It shows the broadness of their thinking. Genetic information is going to be the leading edge of information that is going to change the world. Working with Google, we are trying to generate a gene catalogue to characterize all the genes on the planet and understand their evolutionary development. Geneticists have wanted to do this for generations."Over time, Venter said, Google will build up a genetic database, analyze it, and find meaningful correlations for individuals and populations. . . . Google's data-mining techniques appear well-suited to the formidable challenges posed by analyzing the genetic sequence.

It has begun work on this project, but has not been required to disclose any information about it publicly since the work has no impact on its current revenue and profits."People will be able to log on to a Google site using search capacities and have the ability to understand things about themselves as they change in real time," Venter said. "What does it mean to have this variation in genes? What else is known? And instead of having a few elitist scientists doing this and dictating to the world what it means, with Google it would be creating several million scientists.

"Google has empowered individuals to do searches and get information and have things in seconds at their fingertips," he went on. "Where is that more important than understanding our own biology and its connection to disease and behavior? With Google, you will be able to get an understanding of your own genes. Google has the capacity to do all of this, and it is one of the discussions I have had with Larry and Sergey."

Ok, So now you can watch the movie at Testing Hiatus

Let me know what you think. Does Don't be Evil mean Be Good? Or Does it mean something else?

Vote for Me

What a network we have! Our group at The DNA Network has several bloggers nominated for awards. The groups are

• Best Educational Blog where Hsien Lei at Eye on DNA, myself are up.
• Best Health Blog where Hsien Lei, Myself, Berci at ScienceRoll are in the hunt. BTW Science Roll is doing great with over 200 votes so far!
• Best Blog Design Eye On DNA. Very sharp Hsien.
• Best Blog About Stuff.....what stuff? Personalized Medicine right here.

So get out there and vote. I know we may not look as good as Sanjaya, but we need your vote just as bad :)

Also get out there and nominate. I am going to nominate some more blogs in this awesome DNA Network, because they rock!

-Steve

Chemotherapy Toxicity Genes

Imagine if you could predict who would get the nasty side effects of chemotherapy before giving it. We could then taper the chemotherapy giving less of a dose and achieve the same response. Well, the first part of that dream is here today. At St Jude Children's Research Hospital they have been actively investigating pharmacogenomics and chemotherapy. In a study to be released in the May 15th edition of Blood we have just that.

The major findings include

• During the induction phase Vitamin D Receptor polymorphisms were linked with gastrointesinal symptoms (diarrhea, nausea, vomiting) 6.85 times more likely.
• Polymorphisms in Cytochrome p450-Family 3-subfamily A-number 5, were almost 5 times more likely to have infections and Neurotoxicity
• During consolidation phase the Reduce Folate Carrier polymorphism led to the GI side effects with a 10.4 odds ratio.
• UGT1a1 polymorphisms led to jaundice as well as reduced clearance of an agent called methotrexate (a chemo drug) perhaps leading to increased toxicity as well

This is a major study, that has had some replication in one gene or another. But the compiling of these polymorphisms has not been done. Likely we will need one more round of evaluation. But after that...we could have a pharmacogenomic test for side effects.

The Gene Sherpa says: This is great, but how do we adjust the chemo to avoid these reactions. We will likely need an adjustment scale based on polymorphisms. AKA Personalized Medicine! I am certain St Jude's has this in the works. Let's keep our eyes peeled :)

The Genomic Revolution AKA the birth of Personalized Medicine

An intriguing second post at the "official blog" for direct to consumer testing company DNA Direct brings some excellent points up.

These are points that I often use when trying to tell physicians what will happen if they don't learn genetics.

It often scares the hell outta 'em, or they say "nah no way, medicine is too complicated for the public to practice." Then they go back to practicing medicine the same way we have for the last century, microscopes, gram stains, and paper charts.

The problem has been festering away and the geneticists, internists and specialists have been asleep at the switch. A Summit was held on the subject Bruce Korf, president-elect of the American College of Medical Genetics realizes this. In fact he has been preaching about it for the last 6 years. You can read about it here, here and here.

Some questions

• Who prescribes your blood pressure meds? Your Internists/Family Practitioner


• Who refers you to specialists? Your Internists/Family Practitioner


• Who encourages you to quit smoking? Your Internists/Family Practitioner


• Who argues with insurance to get paid? Your Internists/Family Practitioner


• Who doesn't have the time to see you let alone continue their medical education? Your Internists/Family Practitioner

I am collaborating with Dr Korf as well as leaders in Genetics and Internal Medicine at Yale, Mount Sinai and Harvard to develop a curriculum for residents. The problems

1. Getting the residents to attend conferences on topics the perceive are of no use to them. (why is this? The reason: their instructors can't speak genetics let alone teach it)


2. Finding physicians who speak genetics and can teach genetics. (There are 83 Geneticists who have certification in Internal Medicine)


3. Getting Residents to understand Genetics (Most don't know introns aren't junk)

The solutions? Are tough. I think we need to teach the teachers, we also need to teach the medical students. Physicians have not changed our level of genetics understanding in the last 30 years. That's why they all think Huntington's is the prototypical genetic disease. When I tell them that MI is the new prototypical genetic disease they laugh. How can we fix these attitudes?

Even psychiatrists agree that genetics is important but they realize the lack of knowledge they have.

Whether it is your OB/Gyn missing indications for referrals 9 out of 10 times or 1 in 3 Internists who misinterprets a genetic test for APC. My oncology friends still don't understand mitochondrial inheritance.

Could the lay person do better? Maybe...But could they write a prescription for the Cox-2 Inhibitor they now should be taking? Who will send them to the surgeon? Who will admit you to the hospital? Who will read and review all the articles needed for your care? Who will?

The solution lies in your hands. The solution is to encourage your doctor to learn genetics. Ask him about DNA and your health, ask her about your drugs and your genes. Force the issue, read as much as you can. When your doctor refuses, leave her care. Find a doctor who will learn. But please, please, please don't leave it up to yourself.

The Gene Sherpa says: The solution is up to you. It is up to your doctor. It is up to all of us, together learning and teaching each other. To get the best health care possible. Delivered by a licensed health professional, not by Domino's..........Wake up people or Wal-Mart is where you will get your genomic revolution!!!

African Americans, Family History and Lung Cancer

A pre-publication release of the Journal Chest includes a study assessing family history of lung cancer and likelihood of acquiring a tobacco related malignancy.
From the study:

"In 2006.....estimated that 174,470 new lung cancer diagnoses and 162,460 deaths from lung cancer will occur. Lung cancer remains the leading cause of cancer related death, regardless of gender."

I just saw 2 new cases yesterday myself :(

"Among case relatives, African Americans were 2.44 fold more likely to have head and neck cancers and 1.86 fold more likely to have any tobacco-related cancer compared to white case relatives"

This is where we have to wonder what role detoxifying genes such as GST polymorphisms. It has been show that they do play a role in risk of disease. If only DNA was collected from the participants in this study..........

Most scary for African Americans with a first degree relative diagnosed with Lung Cancer in this study

1. They are 13 times more likely to have head and neck cancer


2. Almost 4 fold more likely to have any tobacco related cancer


3. 4 times more likely to have any tobacco related cancer other than lung

For the Caucasian analysis it appears that African Americans are at 2 fold increased risk compared to their White counterparts when it comes to Lung Cancer.

The Gene Sherpa Says:

We all know smoking causes cancer. But those who continue to play Russian roulette with Marlboros would like to know how hard they should try to quit. This study was limited by only studying early onset lung cancers (less than 60) Kick the Habit Now!

Too Far

So I have been reading another blog linked in my brand new DNA Network a Feedburner network set up by Rick at My Biotech Life. I was invited by the group and I am very excited about participating in the discussion. To have such a network encourages debate and solutions. I love the ability to communicate with other persons about the future of health care. That being said, I think this blog may have gone too far. They are talking about Direct to Consumer Testing

• "Not surprisingly, the genomic revolution has a lot of medical professionals who aren't geneticists* concerned about who's doing what, and how."

Not only Non-geneticists, but GIANTS in the field of genetics (Francis Collins, Margretta Seashore, Kurt Hirschhorn, Ed McCabe, Victor McKusick to name a few) have some serious concerns about how things are going. Including Gene Patents, Enzyme Replacement costs, and yes Direct-To-Consumer Testing. This blog goes on to say.....

• "It shouldn't be a territorial issue, but when money is involved, it inevitably raises this issue."

I would venture to say that these physicians and scientists are less concerned about money than they are the stewardship of their respective fields. Shame on this author for insinuating that they think like her. I know these people and money is the least of their worries. Lastly she finishes with

• What's the difference between a direct-to-consumer company that provides medical services and a for-profit physician group that provides medical services?

The answers are many let me start with the obvious ones first.

1. Medical practices do not get paid for the tests they order for patients. It is ILLEGAL by Stark II laws. Nor do they get paid for the interpretation of these tests.
2. The DTC company does not examine you, they may not even do a family history.
3. The physician group has a referral network to send you to when something is diagnosed.
4. The ideal group will continue to follow you even after the testing.

I could go on but I think you get the picture. Shame on this blog (which is part of my network) for foolishly trying to think they are even in the same category as a group of physicians who have ethical and legal obligations that DTC companies are not even close to being subjected to. Perhaps the physicians who are under their employ are subjected to these regulations, but do they even carry out medical care?

Must we have this argument? Collaboration is what is needed not the "framing of MDs as money hungry" I would say that perhaps there is some self-projection going on with this DTC company.

What do you think?