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Posts Tagged ‘Pharmacogenetics’

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Warfarin Pharmacogenetics: The Biochemistry

In Uncategorized on November 21, 2008 at 12:19 pm

post to news.thinkgene.com

More in-depth version of the coagulation cascade

Image via Wikipedia

Warfarin (marketed under brand names like Coumadin, Jantoven, Marevan, and Waran) is a drug that inhibits blood clotting – the formation of insoluble fibrin clots which stops bleeding. The drug is used to prevent/treat thrombosis – the formation of blood clots that can cause life threatening damage (through clogging of blood vessels).

Since the natural clotting ability is inhibited with this drug, serum concentrations elevated above the intended level can lead to severe side effects – life-threatening bleeding complications. Consequently, monitoring of patients using Warfarin is critical.

Some patients are at higher risk than others, and pharmacogenetic analysis can identify individuals that are either overly sensitive to the drug or metabolize the drug inefficiently. Both these conditions leaves the patient in risk of complications. Such patients should be monitored carefully and a reduced Warfarin dose is usually strongly recommended.

Metabolism through Cytochrome P450 (Cyp450) enzymes displays individual variation for many classes of drugs, so also for Warfarin. Cyp 450 pharmacogenetics will be covered in a separate post. This post will focus on the biochemistry of oversensitivity to Warfarin which can be described as follows:

Blood clotting is a multistep process involving a number of proteins and co-factors (see image above). Warfarin inhibits the maturation (post translational modification) of some of these proteins, clotting factors II, VII, IX and X. Unmodified, these factors will not function properly and the formation of the insoluble fibrin clot is inhibited.

The post translational modification in question is carboxylation, and it uses Vitamin K as a co-factor

carboxylationimage from: Vita Kbv

Vitamin K is decarboxylated in the process and needs to be recycled. The enzyme Vitamin K-epoxide reductase (VKORC) is essential in this cycle. It is this re-carboxylation by VKORC that is inhibited by Warfarin.

vitamin-k-cycleimage from: Linus Pauling Institute, Oregon State University

Warfarin mode of action summary: more Warfarin leads to less Carboxylated Vit K. Consequently less Factor II, VII, IX and X is carboxylated and inhibition of clotting occurs.

VKORC’s susceptibility for binding Warfarin varies between individuals, and this is the basis for the pharmacogenetic assays. From Wikipedia:

Polymorphisms in the vitamin K epoxide reductase complex 1 (VKORC1) gene explain 30% of the dose variation between patients: particular mutations make VKORC1 less susceptible to suppression by warfarin. There are two main haplotypes that explain 25% of variation: low-dose haplotype group (A) and a high-dose haplotype group (B). For the three combinations of the haplotypes, the mean daily maintenance dose of warfarin was:

  • A/A: 2.7±0.2 mg
  • A/B: 4.9±0.2 mg
  • B/B: 6.2±0.3 mg

VKORC1 polymorphisms also explain why African Americans are relatively resistant to warfarin (higher proportion of group B haplotypes), while Asian Americans are more sensitive (higher proportion of group A haplotypes).VKORC1 polymorphisms lead to a more rapid achievement of a therapeutic INR, but also a shorter time to reach an INR over 4, which is associated with bleeding.

Contributing to haplotype group A is a polymorphism in the regulatory region of the VKORC-gene. The A-allele of this SNP decreases the activity of the VKORC-promoter (less mRNA – less protein – higher proportion of total VKORC protein affected) and subsequently increases Warfarin sensitivity (see OMIM for more). This polymorphism (or ones in linkage with it) is normally among the SNPs that are tested for in the lab.

To conclude, identifying individual genetic variations allow us to predict protein variations that in turn predict sensitivity to certain drugs. In the case of Warfarin such pharmacogenetic analysis can be life saving.

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New post on Sciphu.com, the advantages of blog publishing

In Uncategorized on May 19, 2008 at 8:54 am

There’s a new article on SciPhu.com. It’s about pharmacogenetics…..but what I really want to communicate is how superior this way of publishing is:

Here’s what I have experienced while blog-publishing:

1. It is fast. I decided I would publish some data that I already had presented in a talk, since this data wasn’t really fit for a major article. It took me an hour or so to write up and publish the whole thing.

2. One of the reasons it is fast is that it is less rigid in its form. You yourself decide on formatting, wording, whether to use a reference list and how to format this list, or if you would rather have your references as hyperlinks in the text.

3. Papers published on SciPhu.com get hits from google searches. Since the whole text is searchable the hit-probability for people looking for your subject is higher than that on pubmed or any other site where searches are based on title, abstract and keywords. An example is the gel-drying paper which is hit daily by google searches like “SDS-PAGE cracking” or “vacuum drying PAGE” or similar. Although in this case, you could surely search laboratory method web-sites, the fastest way to find your information is probably a google search. This means that any paper published like this has the potential of high visibility. In addition you can get day by day hit statistics, which is probably interesting to many.

4. Communication with referees is interactive and the paper can remain fluid in its format and content. Since publishing like this is rapid it is also bound to be more error-prone. But, by interacting through the comments section, the paper can be continuously revised to correct errors or unclear phrasings. Also the number of referees can be many and since everyone can see the referee-comments, replying to these referees can be done by anyone, not only the authors. Thus, the papers will be less perfect to start off, but may end up better than those in a traditional peer review journal.

5. It is open access and free to everyone. Anyone’s welcome to publish anything as long as it is scientific. This is true scientific democracy.

7. SciPhu.com lacks the “rigid editor” entry point, and it always will.

This publishing solution is not very high tech (but, it may evolve to be), it does not enjoy the recognition that many of the high ranked science journals do (but with active commenting, it can).

As with so many other things in professional life, the potential lies in the numbers. Only if many of us scientists are willing to use publishing channels like these, will it become a success.

This is the age of the web and no-limit communication accessible to all. My recommendation is: Say goodbye to the stale publishing standards of yesterday and come participate in the interactive self-justice of web-publishing.

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Proving the usefulness of pharmacogenetics

In Pharmacogenetics on March 7, 2008 at 10:37 am

Pharmacogenetics is the analysis of genetic markers that informs you of how efficiently you metabolize a given drug. Three genes are commonly analyzed: Cyp2C9, Cyp2C19 and Cyp2D6. These genes are important for the metabolism of drugs used for treating psychiatric disorders ranging from mild depression to severe psychosis. Of course, there are other things that influence how you respond to a drug, like compliance, diet and smoking, but the genetic differences have profound stand-alone effects. For a patient experiencing adverse events or no response at all when taking his medicine, pharmacogenetics can be a tremendous help in choosing more fitting medications (other brands or another (sub)class of drugs). Pharmacogenetics is thus, a vital part of personalized medicine.

There are a couple of arguments against pharmacogenetics analysis we in the diagnostic lab often meet:

1: It’s too expensive

2: The frequency of mutant alleles in the normal population does not differ from that in a given patient population. Thus, physicians seems to be unable to pick the right patients, and pharmacogenetics ends up as an inefficient (as well as over hyped and expensive) general screening method.

The first objection is easy to respond to: A patient that has to try many different drugs to achieve the desired effect without adverse reactions, costs much more than this once in a life-time test allowing a targeted approach straight towards the medication most likely to be suitable.

The second objection can be countered by saying that the overall frequency in a population is irrelevant to the patient, as finding his individual response to the drug is what matters. This argument however is just an argument favoring screening in any given field of medicine. One can still argue that the overall cost-effectiveness is insufficient. Thus, it seems that one either has to prove that physicians are able to pick the right patients (resulting in targeted diagnostics rather than general screening), or prove that general screening with pharmacogenetics is cost-effective.

Now, it seems that doctors using our lab are able to pick the right patients. This is based on results from a small study we have performed (more details below). The argument saying pharmacogenetics is just expensive general screening, thus, falls.

The study of whether general screening is also justified, we need to leave to others, but indications are that doctors are rapidly learning how to use pharmacogenetics.

Consequently, pharmacogenetics seems to be justified in terms of cost-effectiveness and it is undoubtedly in the best interest of the patient.

Our small study (595 patients) can be summarized like this:

Allele Our frequency (%) Frequency (%) in a normalpopulation with similar ethnicity
2C9*2 11,5 10
2C9*3 6,9 7,4
2C19*2 16,7 9,1
2D6*3 1,3 1,1
2D6*4 20,0 15,6
2D6*6 1,0 1,2
2D6 gene duplication 2,1 2,2
2D6 gene deletion 3,4 2,4

The frequency in all but three (2C9*3, 2D6*6 and 2D6 duplication which had similar frequencies), were higher in our selected population than the normal population. Consequently, it seems that physicians are able to pick the right patients. There seems to be no general screening of patients receiving psychoactive drugs, among physicians using our service.


Pharmacogenetics and Normal Variation

In Uncategorized on December 10, 2007 at 8:29 am

Argument: Doing pharmacogenetics is futile since the frequency of clinically relevant genomic variations does not differ between the patient population and the normal population.

Reply: Since the frequency of most of these genomic variations is high, you would need a large cohort to verify that no over-representation exists in your patient samples. In addition, a negative answer (no variation detected) is not the same as a useless answer, as it can be used to look for other reasons for the condition presented.