I can’t believe I’m saying this: Go Cal.

UC Berkeley recently announced that they will offer incoming freshman free genotyping at three genetic loci for folate, alcohol and lactose.  This is part of a tradition at Cal to engage entering students with some shared intellectual activity (the “On the same page” program).  I believe it is absolutely critical that we immediately start educating students about genetics, and the use of genetic tests in making decisions in life.  I think that direct engagement with personal data is one very effective way to make all the issues crystal clear.  This should be optional and there should be adequate safeguards, but this should not stop us from getting started in educating the general population about the promise and pitfalls of genetics.   Thus,  I think that this is great and that Cal (a traditional rival of Stanford, thus the title of this post) deserves credit for bringing genetics to the consciousness of our next generation of leaders.  Some have voiced concerns, and these can be handled with reasonable precautions.  I am particularly amused by the concern that knowledge of genetics might induce poor behavior with respect to alcohol consumption.  While this is certainly a theoretical possibility, it is my impression that students are already making poor decisions about alcohol consumption at such a rate that knowledge of genetics is unlikely to affect this trend appreciably.  In fact, anything that gets the pros/cons of alcohol consumption into the discussion while students are sober is probably a good thing.   We have featured alcohol genetics on a site to help high school biology students can see genetics in action.    So, at least in the NARROW ARENA OF PROVIDING GENETIC INFORMATION SO STUDENTS CAN LEARN…Go Cal!

Year in Review: 2009 Translational Bioinformatics

I presented my review of the year in translational bioinformatics at the AMIA Summit on Translational Bioinformatics.   It is highly biased and subject to all the problems of one person trying to do something like this, but I have made a PDF of the slides available here.  These are papers published since January 2009 to present.   I apologize for important papers that I have missed, and thanks to those who provided advice.   As I have mentioned previously, you can also see the 2008 version and the 2009 version.

Way to go CVS Caremark!

I just learned that CVS Caremark has decided to put some pharmacogenomics testing in place for a variety of clinical areas, including cancer, cardiovascular disease and HIV.   This is an alliance with Generation Health.   I am a CVS Caremark customer (thank you, Stanford), and I am thrilled to learn that they are doing this.   It raises the possibility that PGx penetration will happen not by FDA decree or government reimbursement agencies, but by pharmacy benefits companies that see real value to them and their customers.  It will be very interesting to see how this goes.   CVS Caremark is a big company that serves 60 million people.   If their competitors follow suit, we may see the benefits of pharmacogenomics reaching patients much sooner than might occur if we wait for other routes to materialize.

FDA looking for leads in pharmacogenetics.

I was excited to see the announcement of the relabeling of clopidogrel (a.k.a. Plavix) by the FDA.   The FDA exerts much of its influence on drug companies and medical practitioners by approving the “label” that describes the uses, doses, cautions, and much other information about using a medication.  It is the folded up piece of paper that is always inserted into your medication packaging (thus it is also known as the “package insert”), that then unfolds into a huge poster-sized document with tiny font and lots of information.  It is a legal document which specifies what the drug company can claim about the drug, and how physicians are supposed to use it (give or take some “off label” uses, but that is another topic).   I’m sure it is the star of many lawsuits.

In any case, there has been accumulating evidence that certain genetics variants of CYP2C19 that reduce its activity are associated with differential success of clopidogrel at preventing myocardial infarctions (heart attacks).  Also, drugs that inhibit CYP2C19 also reduce the effectiveness of clopidogrel.  Thus, the FDA modified the label for clopidogrel and warned about concomitant use of medications that interact with CYP2C19 and also mentioned that the genetic variants present in a patient may warrant careful assessment of whether to use the drug, and how much to use.  This is another success for pharmacogenetics!

The pharmacogenetics database we are developing,  PharmGKB, is focused on gathering evidence for the role of genetics in drug response.  PharmGKB staff have  a good working relationship with some FDA scientists, and we are all very interested in finding out about other drugs for which there is mounting emerging evidence that genetics may play an important role.  In some cases, the FDA may even launch a process to determine if the label should be modified in light of new evidence.  If you come across compelling scientific evidence for genetic determinants of drug response, let us know at feedback@pharmgkb.org.  We will gather together responses and assess them on a regular basis–we will even alert our friends at the FDA to those that are reaching a critical point!

You can see a list of drugs with specific FDA language about genetics on PharmGKB.

A magazine for biocomputation = BCR

One of the research projects that I help direct is devoted to improving and disseminating the use of physics-based simulation in biology–at all levels:  molecular, cellular, tissue and organism.   It is called Simbios (National Center for Physics-based Simulation of Biological Structures, http://simbios.stanford.edu/) and I may write about it more in the future.  We have done cool things like release software for simulating human motion, superfast molecular calculations on graphics cards, and other things.   But one of the coolest things about Simbios is that part of our dissemination plan is the distribution of a magazine entitled “Biomedical Computation Review” or BCR.   It was the brainchild of my colleague, David Paik, when we were writing the grant, and it is ably managed by David and Kathy Miller, the managing editor.   We tried to model it on the MIT Technology Review, which has great coverage of “techy” stuff from all over, and creates a sense of community among techies (ostensibly MIT alums, but I have no connection to MIT and enjoy it very much).  BCR is available online, but I really recommend that you contact us for a physical subscription because it is fun to hold and read, and it can be read in many places where internet or computers might not be handy or convenient.  We have some regular columns and most issues have a theme such as curricula in biomedical computation, women in biocomputing, human vs. machines, and other fun topics.  If you have ideas, let us know.  We are contemplating an upgrade in the web presence of the magazine.