New Tests Advance the Promise of Personalized Medicine

February 5, 2012

In less than a decade, the search for common genetic variations that alter people’s risk of disease has changed the way we think about genetic risk. In the world of cardiovascular medicine, 36 single-nucleotide polymorphisms (SNPs)—the tiny genetic changes that help to differentiate one individual’s genome from another—have been found that associate with an increased risk of coronary artery disease (see “What’s Next for Genetic Risk” below).

Other newly discovered genetic variations associate with cholesterol levels, hypertension, diabetes and other risk factors for cardiovascular disease. However, a lack of clinical applications for this information has led some to question the value of such genetic discoveries for improving patient care and how long it will take for this research to translate to the clinic.

Now, with two teams at the University of Ottawa Heart Institute validating clinical genetic tests, the first answers to these questions are arriving.

Bedside Decisions

A significant barrier to the use of genetic screening in clinical settings has been the long turnaround times. Results tend to take days to come back, making point-of-care testing impractical or impossible. For patients about to receive a stent to open a blocked artery, having a point-of-care test would be hugely beneficial.

Clopidogrel is a drug widely given to patients with stents to prevent blood clots. A significant portion of the population carries a common genetic variation (CYP2C19*2) that prevents proper metabolizing of the drug. That portion varies by race but ranges from 25 to 40% of individuals. For emergency stent procedures, this can lead to dangerous outcomes, even death, for these patients. Today, there is no screening method available. The only way for doctors to know if clopidogrel will help thin a patient’s blood is to try it.

A team led by Dr. Derek So, a Heart Institute cardiologist, aims to change the way clopidogrel is given to patients requiring emergency stenting. In the process, this research has marked two firsts. The team’s RAPID GENE study validated the first-ever point-of-care genetic test for guiding and improving treatment of patients undergoing stent procedures. The study also showed that guiding patients to tailored blood-thinning treatment based on their genetic profiles helped prevent the propensity to form blood clots.

Previous studies had shown that patients unable to metabolize clopidogrel have worse outcomes after stenting, Dr. So explained, but until now, no trials had shown that altering anti-clotting therapy based on genetic information can potentially improve these outcomes.

The RAPID GENE study validated the first-ever point-of-care genetic test for guiding and improving treatment of patients undergoing stent procedures.

The Heart Institute investigators partnered with Spartan Bioscience, to design and validate the novel bedside genetic testing machine for the trial. Dr. So and his colleagues recruited 200 patients undergoing stenting at the Heart Institute for acute coronary syndrome or stable angina, and randomly assigned them to either a point-of-care genotyping strategy or to standard therapy with daily clopidogrel. All patients in the genotyping group were tested using the bedside screening system. Those with the gene variation making them unable to metabolize clopidogrel were given an alternate drug, prasugrel (Effient). Prasugrel is a more potent drug but carries a higher chance of bleeding.

The results confirmed the test’s value in guiding care: no patients in the genotyping group who carried the CYP2C19*2 gene variation showed a propensity to form blood clots, while 30.4% of patients with the gene variation in the standard care arm did. At 30-day follow-up, no major adverse cardiovascular events had been seen in either group.

“The advantage of being able to perform personalized therapy is that we get the best of both worlds,” said Dr. So. “For the people who do react properly to clopidogrel, we give them clopidogrel. And for the people who don’t, we give them the stronger medications. By doing that in the general population, you could actually prevent more bleeding outcomes, and at the same time, also decrease costs by directing the right medication to the right people.”

Also important was the limited technical knowledge needed to conduct the screening. “All genetic testing in the trial was done by clinical nurses who had only a half-hour training session on how to use the machine, and with that minimal training, we could identify at-risk variants very quickly and alter therapy,” added Dr. So.

“I think that with this proof-of-concept, this technology is going to be applied to other areas of cardiology, and other areas of medicine as well. That’s why these results are so exciting,” he explained.

Dr. So’s team is currently performing a follow-up trial, looking at whether measuring three gene variations instead of only one can better guide anti-platelet therapy. “I think that’s the future of cardiovascular genetics: that we’re going to be able to look at multiple genes very quickly and make decisions based on multiple genes at the same time,” he concluded.

A Marker for Risk

The 9p21 genetic variant, discovered by Heart Institute researchers, is by far the most significant for increasing an individual’s risk for coronary artery disease. A simple screening test for 9p21 could have a major impact in preventing heart disease in up to a fifth of the population. Alexandre Stewart (left), Principal Investigator in the Ruddy Canadian Cardiovascular Genetics Centre, and PhD student Naif Almontashiri (right) are now working to validate a blood test to identify carriers of 9p21.

Another area of cardiology in which rapid genetic testing could have a profound impact is determining which patients are at high risk for coronary artery disease (CAD) before symptoms develop. With the new knowledge of more than 35 genetic variations that contribute to the risk of CAD (see “What’s Next for Genetic Risk” on this page), researchers are actively looking at how testing for those genes could improve patient care. While many of those variants, on their own, are associated with only small increases in risk, the situation can become more serious when several are present. It is also possible that risk could be amplified when certain combinations of SNPs are present.  

There is one common genetic variation, though, that greatly increases the risk of CAD all by itself. Discovered at the Heart Institute in 2007, 9p21 was the first common risk variant for CAD. People with one copy of 9p21 have a 15 to 20% increased risk of CAD, while people with two copies have a 30 to 40% increased risk. The number of copies also predicts severity of disease; people with two copies are more likely to have severe plaque deposits at a younger age.

Heart Institute researchers have recently discovered a biomarker for 9p21 that can be screened for with a blood test. This approach holds promise for the early diagnosis of CAD, before symptoms develop, in up to a fifth of the world’s population.

The biomarker, an immune system protein called interferon alpha-21 (IFNα-21), is found in the blood of people who carry two copies of 9p21 at concentrations of up to 30 times higher than in people with no copies. A team led by Alexandre Stewart, Principal Investigator in the Heart Institute’s Ruddy Canadian Cardiovascular Genetics Centre presented this finding last year at the Canadian Cardiovascular Conference, the annual meeting of the American Society for Human Genetics and the Scientific Sessions of the American Heart Association.

“That result was very exciting because it suggested that not only is this a marker of the disease in people who have two copies of this risk locus, but if we found a way to block this interferon, we might be able to find a new therapy to reduce the progression or even stop the progression of coronary artery disease,” explained Stewart.

The result also points to a possibility as to how 9p21 increases the likelihood of CAD. “By cranking up this alpha interferon, 9p21 could actually be promoting atherosclerosis in these patients,” Stewart speculated, “particularly if their lifestyles also promote heart disease.” Inflammation, including the type of immune reaction promoted by IFNα-21, has long been suspected to contribute to coronary artery disease.

“A blood test for IFNα-21 would be reliable in detecting CAD in about a fifth of the world’s population without having to do an angiogram.” – Alexandre Stewart, Principal Investigator, Ruddy Canadian Cardiovascular Genetics Centre, UOHI

Stewart and his colleagues in the Ruddy Centre were intrigued by new information coming out of the University of California, San Diego, indicating that 9p21 may control several genes located far away in the genome that are involved in the body’s response to inflammation.

“We’ve known for years that regions of DNA can have an influence far, far away because of the way the DNA is packaged in the cell,” Stewart explained. Because the strands of DNA are wrapped so tightly within a cell’s nucleus, areas of the genome that are linearly far away from one another can end up physically abutting when wound up for storage, like thread on a spool.

Heart Institute team members took a closer look at the expression of one of these genes—IFNα-21—in patients who carry two copies of 9p21. Using a genetic test approved for laboratory research purposes, they found the strong correlation between 9p21 and elevated levels of IFNα-21. The team is now looking at whether that test can be adapted for diagnosing patients. “The question is, can we develop this into a clinically applicable test?” said Stewart.

Since individuals with high levels of IFNα-21 are likely to carry two copies of 9p21 and be at significantly higher risk, they would be appropriate targets for early preventive measures. Right now, the only way to diagnose early heart disease is a coronary angiogram, a costly and invasive procedure only performed on patients who exhibit symptoms of disease.

Findings from the Ruddy Centre and others suggest that “a blood test for IFNα-21 would be reliable in detecting CAD in about a fifth of the world’s population without having to do an angiogram. These people could immediately be targeted for aggressive [preventive] therapy,” Stewart said.

Other research from late 2011 has shown that having a high genetic risk profile does not mean a person’s future health is written in stone. A study of carriers of the 9p21 risk variant, published in PLoS Medicine, indicated that those individuals can still reduce their risk of heart disease substantially through a “prudent diet” high in fruits and vegetables. “We have to always think in terms of these risk variants interacting with the environment. If you modify your environment, you affect your risk. Our genes only mean something when they interact with the environment,” said Dr. Robert Roberts, President and CEO of the Heart Institute.

What’s Next for Genetic Risk

The total number of gene variants associated with coronary artery disease (CAD) has risen to 36 thanks to another 13 SNPs identified by the Heart Institute and its partners in the international CARDIoGRAM consortium. Although more will likely be found by the large international working groups, the research focus is now shifting toward understanding how these genetic variations exert their effects. Only 13 of the 36 operate through known molecular mechanisms.

When 9p21 became the first associated SNP to be found, the researchers were surprised that it appeared to function independently of all known risk factors for CAD. “There was surprise, as well as excitement,” said Dr. Robert Roberts, “because it meant, clearly, if there is a risk factor other than conventional risk factors, we need to know what it is.”

“I think the biggest realization that’s dawned on the research community is that we didn’t know what we thought we knew about these risk factors,” agreed Alexandre Stewart. “There’s something we’ve overlooked.”

One overlooked factor will likely turn out to be inflammation and other immune system involvement. While they have been suspected to play a role, they are far from understood. In the quest to sort out the cellular and molecular pathways through which genetic variation drives risk, some researchers are starting to approach the problem from different angles. Computer modelling and systems biology approaches may help to identify other unknown relationships across the genome similar to the one between 9p21 and an interferon (see the main story).

“We use risk models all the time to identify who is at higher risk of heart disease. So incorporating a genetic piece into that will be something people will eventually become comfortable with. It’s not something that’s ready for clinical use now, but the hope is that this type of personalized medicine will come,” commented Julie Rutberg, the Heart Institute’s Genetic Counsellor.

As for when new treatments will arrive, Dr. Roberts urges patience. As he reminded a recent audience of cardiovascular professionals in Ottawa, cholesterol was known to be a risk factor for coronary artery disease since the 1950s, but the first statin drug to treat high blood cholesterol was not available until almost 40 years later. Targeting newly discovered genes with the technology available today will move much more rapidly. “It won’t take 40 years,” he concluded, “but give us 10 or 15. We’ve had less than five since the discovery of 9p21.”