An Easy Kludge to Examine SNPs

It turns out that there is a large effort to make available all sorts of information about genomics, especially in the medical field, for free including multiple tutorials and results of government financed studies. 
One of the problems for the clinician is that there is too much out there and there are at least three different sets of words for everything studied because for a long time the geneticists, clinicians, and gene researchers didn't talk to one another.  For example, rs1800044, a SNP variant found in a patient with Tourette Syndrome is also known as 657G/T or Arg219Leu and never shall the twain meet, at least in the early research papers.  (Here is a paper that does mention alternative names.)
So if you look up the research sequence number you might not find an important paper under that name and most likely won't know the other nom de genes.
But clinicians don't need to know all the technical aspects of the genome, they need to know how to use the information and what information is both pertinent and valuable for patient care.
Unfortunately most of this information is still hidden in the bowels of research labs and obscure journals.  I suspect that in five years there will be a whole industry whose sole purpose to to sell you software that helps find this information and that the drug companies will be very eager to give you the information that helps sell their products.   The recent brouhaha involving 23andMe and the FDA will most likely be resolved in favor of the money meaning that eventually everyone will have access to the information without oversight of the FDA.
The fact is that anyone with $99 can get this information right now, at least that information found in the exome, that part of the gene set that makes the majority of proteins including enzymes and receptors.  A vast number of SNPs correlated with disease states and medication response are included in these surveys so it is just a matter of getting the information and the individual exomes together is a way that helps the clinician and the patient.
There is a kludgey solution that involves a curious clinician, a computer, Firefox plus an add-on called SNPTips, and a website named SNPedia. 
The solution is a kludge because it involves a Rube Goldberg connecting of the various parts and because it is incomplete.  Not all the information known is on SNPedia - the research is coming fast and furious and is hard to keep up with and this is a wiki effort - and they only have slightly over 50,000 SNPs cataloged at present.  Nonetheless SNPedia is a terrific source for information.
The other reason that the solution is a kludge is that there is no good way to vet a lot of this information.  For the most part the studies are small and focused narrowly on one geographic group.  Hence what is true for a Han population may not be true for a European population in any given instance due to actual differences or the weak power of the studies.  On the other hand, there are some very large studies that are helpful and intriguing results are coming out all the time.
As clinicians we are primarily interested in helping our patients get better.  In psychiatry this usually means making them feel better without causing a lot of other problems such as tremendous weight gain, debilitating side effects or transitioning them into another phase of their illness. Sometimes we have to struggle with the diagnosis or rethink our strategies with patients who fail in treatment.
Genes account for some percentage of the illness we see in individuals.  The days of nature vs. nurture are pretty much over as we have come to the realization that both are involved in the disease process.  The recent upsurge in genomics research that followed advances in gene assays has resulted in a much more sophisticated understanding of how genes work.  For most of us older physicians the language and information is overwhelming but with a little study (and a tolerance for boredom) you can  glean enough information to help use what is available.
I won't go into how to study up on genomics in this column, but I will tell you how you can adapt your existing computer to help you learn more about your patients.
I am an Apple computer guy.  That's because I move my lips when I compute and have found the more expensive alternative easier to use.  But what I am going to say is equally applicable to Microsoft or Linux operating systems.
The secret is to get Firefox from Mozilla and put in an add-on called SNPTips.  SNPTips reads any research sequence number (the "rs" number) and refers it to SNPedia.  The raw data from 23andMe is in text form and easily read.  (I am sure that there will be others offering sequencing with the same data soon.)  When you click on the highlight generated by SNPTips, you are shuttled over to SNPedia which in turn will refer you to the relevant research papers. 
The opposite can also occur.  SNPedia allows you to look up various topics such as medications or diseases and lists the SNPs that are involved with those subjects.  SNPedia is not complete, it is a wiki based entity that relies on the kindness of others, but it is very assiduous about the completeness of the information that it has so it is a good resource.
Here are the steps required to do this:

1) Go to Firefox and download the web browser.
2) After you have started Firefox, go to SNPTips and install the add-on.
3) Have the raw data from 23andMe available on the computer somewhere.  I use a thumb drive in a USB port with an anonymous file name.  Go to preferences in the SNPTips add-on and browse for the thumb drive. 
4) Look up the SNPs you are interested in anywhere on the web and the SNPs will highlight in green if they are on the raw data. By placing the pointer on the highlighted area will tell you which allele is present.  rs6280.  I just put that in there to help you see if you have done everything correctly.
5)  If you click on the highlighted area it will take you to SNPedia for further information. 

What I would like to do with this blog is develop (with the help of others) small disease or medication related pages that can be used as a tool by clinicians.  There are a lot of ethical and medical issues that have to be addressed and resolved but I think that the system I am outlining can be kept private and off of the internet by having the information anonymous and local and always in the possession of the patient until there are laws and software protecting access to this information.
For now it is in a proof of concept stage.  I will provide a few anonymous raw data sets that have been modified from the originals for practice and make them available to others to use as part of this project.
At some point a more sophisticated solution will become available, I am sure.  It will require a combination of clinicians learning more genomics, patient cooperation (23andMe is cheap but it is still $99) , and a thorough evaluation of the value of such information.  We are on the cusp of this technology breaking out and it would be very helpful to be able to use all of the free information that has been made available.

Michael Keyes MD
Fond du Lac, WI