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Can an old drug be taught new pharmacogenetic tricks?

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The COAG study demonstrates the weakness in understanding variants that affect African Americans, who did worse when the genetic algorithm was used, most likely because the variants that affect their response to warfarin were not included in the genetic test. “It’s still not well understood,” Dr. Weck says, “what all the factors are that are associated with the difference in warfarin response in African Americans. This is another limitation of the studies.”

Says Dr. Gage: “The pharmacogenetic dosing algorithms used in COAG and EU-PACT were very accurate in non-black participants—the R2 was 0.75 by day four or five. In African American participants the R2 was only 0.4. The pharmacogenetic dosing algorithms do not include rare polymorphisms that might have improved the accuracy of pharmacogenetic dosing in African Americans: CYP2C9*5, CYP2C9*6, CYP2C9*8, CALU rs339097, and CYP2C19 rs12777823.” Individually, he says, each of the SNPs plays only a small role in predicting warfarin dose. “But when considered together, they might improve the accuracy of pharmacogenetic dosing algorithms considerably in African Americans.”

Given the diversity of the U.S. population, the inclusion of ethnic-specific variants is an issue likely to recur in future pharmacogenetic and pharmacogenomic studies. It also underscores the difficulty in identifying and studying rare variants in general, race based or not. Though it is the common variants that are the most easily identified and therefore studied, it is the rarer variants that could have the greatest impact on drug safety—another reason the results of the COAG and EU-PACT trials were not surprising. Says Dr. Weck: “I have always felt that we are missing the most important factors, which are the rare genetic variants that have a high impact on warfarin dose response. For example, those would include the rare patients who are CYP2C*3 homozygotes who have extreme warfarin sensitivity and require very low doses of warfarin.” Such patients require only 1–2 mg of warfarin per day and are at most risk of adverse events. (The COAG and EU-PACT warfarin trials had one each of these patients and the UNC trial had none.)

“Current clinical trial designs are not optimal for studying rare variants,” Dr. Weck says. “We could risk throwing the baby out with the bath water for warfarin genetics and pharmacogenetics in general because we have been focusing so much on the common SNPs associated with a comparatively minor effect on response.”
Though the presence of rare variants that cause warfarin sensitivity and raise the risk of bleeding are perhaps of greatest concern, the rare variants associated with warfarin resistance can create a different set of clinical complications. Says Dr. Wu: “If you look at the regression analysis between VKOR and 2C9 and dose, it’s only about 50 to 60 percent in terms of an R2 value, which means there is still great variability between predicted and actual dose needed to maintain a stable INR. And, in my opinion, genotyping is effective for predicting warfarin sensitivity, but the remaining variability is due to the absence of genomic markers that predict warfarin resistance, that is, someone who needs more than the standard 5-mg dose.” This is ongoing, he adds, and identifying additional genes for an R2 value of 70 to 80 percent may be possible. “That could stimulate a whole other round of trials,” he says, “assuming warfarin is still around.”

This was considered when the GIFT trial was designed; it will include a marker of warfarin resistance—the first time this variant has been used in a large, prospective trial. Study subjects are hip and knee replacement patients, who have a higher incidence of thrombotic complications than the general anticoagulant population. Nevertheless, rare variants make demonstrating warfarin pharmacogenetic utility a challenge. “The underlying goal is to protect outliers from complications,” Dr. Eby says. “That guarantees they are diluted by a larger number of patients whose management is not improved by pharmacogenetics. This issue may always be there for pharmacogenetics. We are trying to benefit the rare patients but can’t find the rare patients until we genotype everybody.”

Powerful economics are at work that make continued investment in warfarin genetic research unlikely. Warfarin is an inexpensive generic drug, and pharmacogenetic data would have to be compelling to persuade payers to reimburse for a $200 to $300 genetic test before the drug’s use. This is especially true in light of the latest studies pointing to a clinical algorithm being equally effective. But the reimbursement issue is not solely related to warfarin’s status as a generic. Payers often do pay for a pharmacogenetic test for the generic clopidogrel, Dr. Johnson says. In her center they find that about 28 percent of patients have a genotype that indicates the drug will have reduced efficacy, a percentage that makes testing more cost-effective than the hunt for rare variants. In addition, hospitals facing no Medicare reimbursement for readmissions within 30 days realize they can pay for a lot of clopidogrel genetic testing with the money saved from one readmission they will not be paid for, Dr. Johnson says.


Dr. Laposata

Clopidogrel may have made a better high-profile pharmacogenetics test case than warfarin. Whether genetics are used or not, warfarin dosing is adjusted using INR testing whereas platelet function tests do not carry the same clinical weight. Michael Lapo­sata, MD, PhD, the Edward and Nancy Fody professor of pathology at Vanderbilt University School of Medicine and soon to be chair of pathology, as of July 1, at the University of Texas Medical Branch at Galveston, says a consulting group estimates that the cost of treating a patient who rethrombosed a stent is $25,000, and assuming 60 adverse clopidogrel-related events among a data set of 6,400 interventional cardiology patients, the cost is $1.5 million. As far as clopidogrel is concerned, genetic testing would more or less pay for itself when the price of the serious complication is taken into account. Of warfarin pharmacogenetic testing, Dr. Laposata says everyone was asking the big question: “Is anybody dying because we are not doing it? Does anybody have morbidity or more strokes, or anything like that? So we thought these trials would land on the same side of the street and we could figure this out. They didn’t.”

Despite the difficulty in making a similar cost-effectiveness case for warfarin, Dr. Laposata sees value in the genetic tests. He believes that safety would be greater if patients knew they carried warfarin sensitivity variants, and he cites a hypothetical case of a postsurgical restart in a warfarin-sensitive patient for which a physician might not scrutinize a chart and assume a standard 5-mg dose is safe.
The continued study of warfarin pharmacogenetics and the ability to make a cost-effectiveness argument for testing are hindered also by genetics not being the only factor to have an impact on warfarin safety. Most adverse events occur in the initial dosing period, but warfarin levels long term are influenced also by dietary intake of vitamin K and the addition of other medications.

The introduction of new oral anticoagulants will play a role, too, in how much additional effort will be put into warfarin pharmacogenetics. When COAG was initiated in 2009, none of the new agents had been approved. Unlike warfarin, the genetic influences governing the responses of the newer anticoagulants have not yet been widely investigated. Given the high cost of the newer agents over a patient’s lifetime, it may prove easier to support economic arguments for future pharmacogenetic testing related to their use. Dabigatran was No. 1 on the 2012 FDA drug adverse-event list (warfarin was No. 2), which might bolster the argument for pharmacogenetic studies, and though Boehringer Ingelheim markets the drug as not requiring dose testing, the Feb. 7 New York Times reported an internal company study that supports the role of testing for some patients.

Some physicians, Dr. Laposata among them, believe the newer agents are safer. “The thing that I like best about them,” he says, “is that if you bleed with them, you are less likely to bleed in the head than elsewhere.” Reversal agents are expected to become available in the next couple of years.

Warfarin seems not to be going away any time soon, and its low price is only one of the reasons. Six to nine months ago warfarin was still responsible for 80 percent of anticoagulant prescriptions in the U.S., Dr. Johnson says, and its use has not declined. “We’ve had warfarin for 60 years—it’s a tough drug but there are no surprises. Physicians worry about whether bad things will be uncovered with the new agents as they are used more.” Dr. Laposata, though, sees a declining future for warfarin and predicts the decline will be exponential rather than linear. “In 2009 when COAG started,” he says, “we had no idea where we were going to be with novel oral anticoagulants. So it would be hard to muster a lot of enthusiasm for trying to figure out the best way to do this with warfarin—that is, pharmacogenetics or not—when the population of people using it will be so much smaller.”

But the case for understanding the genetics of warfarin response may not be totally lost. Many pharmacogenetic tests, like that for warfarin, are standalone tests, each costing hundreds of dollars and therefore hard to justify economically. That’s unlikely to remain the case for long. “The cost-effectiveness of identifying rare variants will be modulated by more efficient, cost-effective genomic testing,” Dr. Weck says. “We should be able to identify these really important variants that are the most likely to be associated with extremes in response or adverse events. But we also need to be able to mine those data to look for new variants in different ethnic populations like African Americans or other groups.” A whole exome sequencing project is underway at the University of North Carolina, and the list of potential incidental findings to report includes pharmacogenetic variants.
In the meantime, Dr. Laposata says, “Sequencing the entire genome would be a huge plus. It does appear that a lot of drugs cluster around the cytochrome P450s. One can argue that even at this point, if you want to get a pretty good look at a lot of drugs, CYP2D6, CYP­2C19, and CYP2C9 account for about 75 percent of drugs pharmacogenomically. If we sequenced even those three genes, we’d have a pretty good sense about dozens and dozens of drugs.”

Even today Dr. Johnson sees an increasing number of patients come in with genetic data about themselves, principally from 23andme. “Right now it is about ordering a specific test and being able to justify that the cost of the test is offset by some benefit. Where we’re moving eventually is that a lot of people are going to have a lot of genetic information about themselves. At that point it’s not so much should I use the information but more can I justify ignoring the information.”

Elizabeth Silverman, of New York, NY, is a writer who covers genomics.