Simple testing: This disposable cartridge can detect genetic variations from blood samples. The circles lining the top and bottom are loaded with reagents for different chemical reactions. DNA is isolated from white blood cells and captured on a glass slide within the cartridge.   Credit: Nanosphere 


A new device rapidly analyzes blood for medically relevant genetic variations. 


MIT Technology Review, December 3, 2009, by Emily Singer  —  A desktop instrument recently approved by the U.S. Food and Drug Administration might finally bring pharmacogenomic testing–the use of a patient’s genetic information for drug prescription decisions–to the mainstream. The device, made by Nanosphere, a startup based in Northbrook, IL, can, in a matter of hours, detect genetic variations in blood that modulate the effectiveness of some drugs. Dubbed Verigene, the technology employs a combination of microfluidics and nanotechnology, housed in a single plastic cartridge, to pull DNA from a blood sample and then screen it for the relevant sequences.

“We believe the benefit of our system is that this simple cartridge format could be run in any hospital, even a doctor’s office,” says William Moffitt, chief executive at Nanosphere. “We’re moving complex testing to the point of patient care.” Moffitt says Verigene is the first nanotechnology-based microfluidics product capable of analyzing DNA directly from a blood sample.

People can respond to drugs very differently, thanks in part to commonly occurring genetic variations in enzymes that metabolize some of the mostly highly prescribed compounds, such as heart medicines, pain medicines, and antidepressants. While doctors have widely adopted pharmacogenomic testing for prescribing some cancer drugs, such testing hasn’t yet taken hold for many other drugs whose effectiveness is modulated by genetics, including those for HIV, pain control, and epilepsy. The technology needed to detect these variations in patients has been available for years, but the process is often time-consuming and expensive. Physicians typically must send patients’ saliva or blood samples to a central lab, where the DNA is isolated, amplified, and analyzed. That process can take days or weeks.

“In some cases, it doesn’t matter if it takes a week to get a result. But in some cases we would like to have the information to choose a drug during the office visit, when the patient is right there,” says Howard McLeod, director of the Institute for Pharmacogenomics and Individualized Therapy at the University of North Carolina, Chapel Hill. “That way we can say, this drug is the one your DNA says will most likely be beneficial.”

The anticoagulant warfarin, for example, is frequently prescribed to prevent blood clots. But people metabolize the drug differently, meaning patients must be carefully monitored to make sure they don’t suffer dangerous bleeding. The FDA changed the drug’s label in 2007 to note that two specific genetic variations affect a patient’s sensitivity to the drug, but broad gene testing has not yet caught on. “Currently, available genotyping tests for warfarin pharmacogenomics require isolation of DNA from blood and testing in a molecular diagnostics laboratory certified for high-complexity testing,” says Karen Weck, director of the molecular genetics laboratory at the University of North Carolina, Chapel Hill.

Nanosphere is developing a test that can detect these variations in blood samples in an hour or two. A patient’s blood is injected into a disposable cartridge, which holds a glass slide dotted with DNA. The plastic frame also houses a system of microfluidics chambers containing the reagents for a number of chemical reactions. When the cartridge is inserted into the Verigene instrument, mechanical valves and air pressure mix the reagents in different chambers, triggering a series of reactions.

Magnetic beads first pull out white blood cells, which are burst open using sonic energy, releasing fragments of DNA. Everything but the DNA is then washed away, and a solution of these DNA fragments flows over the glass slide. Target DNA binds to spots on the slide that have been printed with DNA sequences complementary to those of the target sequence. Gold nanoparticles, about 13 nanometers in diameter, then attach to the other end of captured DNA fragments, sandwiching the target. Each gold nanoparticle is coated with silver, expanding the diameter to half a micron, thus allowing it to be easily detected when hit with light.

“If it works, this could be a convenient way for physicians and coagulation clinics to incorporate pharmacogenomic information into warfarin dosing,” says Weck. However, she adds, “the accuracy of the test should be carefully compared to more traditional molecular tests before it is widely used.” Nanosphere already has FDA approval for a warfarin test used in an older version of its system and plans to file for regulatory approval for its new test next year.

The company is also developing a pharmacogenomics test for use with the anticlotting drug Plavix, which is prescribed to people given heart stents. The drug must be metabolized into its active form, and scientists recently discovered that about 30 percent of Caucasians have a poorly functioning variant of the enzyme that metabolizes the drug and are thus less likely to benefit from it. While it’s currently possible to identify these patients through mail-order testing, “we want to know the answer before the patient goes home,” says Marc Sabatine, a cardiologist at Brigham and Women’s Hospital in Boston.

Nanosphere’s device is one of a number of microfluidics technologies in development for so-called “point of care” genetic testing–diagnostics that can be performed in the hospital or doctor’s office while the patient is there. Verigene, which was approved by the FDA in October, can come with different modules, ranging from $40,000 to $80,000, designed for different types of testing.

“You could have a version of our system in a molecular diagnostics lab running genetic assays, like those for cystic fibrosis and warfarin, or in a microbiology lab running virus assays, or in a stat lab for ER running tests, like the cardiac troponin test, a biomarker to diagnose heart attack, and pharmacogenomic testing for [Plavix metabolism],” says Moffitt. The Verigene system can also detect respiratory viruses, such as the H1N1 flu. Over the past month, the company has been installing the systems in medical centers ranging from typical community hospitals to large academic research hospitals.

Researchers hope the availability of this type of testing will enable the discovery of new applications in pharmacogenomic testing. “There are also drugs we use in [intensive care units] that would benefit from genetic-guided therapy, but because of the absence of technology [for quick pharmacogenomic] testing, no one is really trying,” says McLeod.

New research reveals more than you ever wanted to know about the bacteria inhabiting your body.

MIT Technology Review, December 3, 2009, by Emily Singer  —  The back of your knee probably has more microbes than your mouth or your gut–that’s just one of the somewhat disturbing revelations from a study published in Nov 2009, online in Science. Researchers from the University of Colorado, Boulder have developed the most complete map yet of the microbes that dwell on and in us. “The highest diversity skin sites were the forearms, palm, index finger, back of the knee and sole of the foot. The armpits and soles of the feet showed some similarities, perhaps because they are from dark and moist environments,” said Noah Fierer, one of the study’s authors, in a statement.

Scientists are mapping our microbial inhabitants in order to better understand their role in human health and disease.

Each of us contains roughly 10 times as many microbial cells as human ones. And while some microbes make us sick, many play vital roles in our physiology. They give us the ability to digest foods whose nutrients would otherwise be lost to us, and they make essential vitamins and amino acids our bodies can’t. And yet, because the vast majority of these microbes die when extracted from their native habitat, they have been impossible to study and have remained a mystery…

New ultrafast DNA-sequencing technologies allow scientists to study the genetic makeup of entire microbial communities, each of which may contain hundreds or thousands of different species. For the first time, microbiologists can compare genetic snapshots of all the microbes inhabiting people who differ by age, origin, and health status. By analyzing the functions of those microbes’ genes, they can figure out the main roles the organisms play in our bodies.

The new study, which analyzed 27 sites on the body of nine different volunteers, found that microbial diversity varies highly, both between individuals and from place to place in the same person. According to a release from the University of Colorado, Boulder:

The study showed humans carry “personalized” communities of bacteria around that vary widely from our foreheads and feet to our noses and navels, said CU-Boulder’s Rob Knight, senior author on the paper. “This is the most complete view we have yet of the microbial side of ourselves, one that our group and others will be adding to over the coming years,” said Knight, an assistant professor in CU-Boulder’s chemistry and biochemistry department. “The goal is to find out what is normal for a healthy person, which will provide a baseline for further studies to look at people with diseased states. One of the biggest surprises was how much variation there was from person to person in a healthy group of subjects.”

“We have an immense number of questions to answer,” said Fierer, an assistant professor in CU-Boulder’s ecology and evolutionary biology department who was a co-author on the study. “Why do healthy people have such different microbial communities? Do we each have distinct microbial signatures at birth, or do they evolve as we age? And how much do they matter? We just don’t know yet.”

ScienceDaily (Dec. 2, 2009) – Previous studies have shown a link between low vitamin D status and heart disease. Now a new study shows that patients with high blood pressure who possess a gene variant that affects an enzyme critical to normal vitamin D activation are twice as likely as those without the variant to have congestive heart failure.


“This study is the first indication of a genetic link between vitamin D action and heart disease,” says Robert U. Simpson, professor of pharmacology at the University of Michigan Medical School and one of the authors of the study in the journal Pharmacogenomics.


“This study revealed that a critical enzyme absolutely required for production of the vitamin D hormone has a genetic variant associated with the development of congestive heart failure,” Simpson says. “If subsequent studies confirm this finding and demonstrate a mechanism, this means that in the future, we may be able to screen earlier for those most vulnerable and slow the progress of the disease.” Such a screening test would be years away.


Study co-authors Russel A. Wilke of the Medical College of Wisconsin and Catherine A. McCarthy of the Marshfield Clinic Research Foundation in Marshfield, Wis., analyzed the genetic profiles of 617 subjects from the Marshfield Clinic Personalized Medicine Project, a large DNA biobank. They looked for variants in five candidate genes chosen for their roles in vitamin D regulation and hypertension. One-third of the subjects had both hypertension and congestive heart failure, one-third had hypertension alone and one-third were included as healthy controls.


The results showed that a variant in the CYP27B1 gene was associated with congestive heart failure in patients with hypertension. It is already known that mutations that inactivate this gene reduce the required conversion of vitamin D into an active hormone.

“This initial study needs to be confirmed with a larger study that would permit analysis of the full cardiovascular profile of the population possessing the gene variant,” Simpson says. A future study also would need to include people of more diverse origins than this study’s population of mostly European ancestry, the authors say.


Citation: Pharmacogenomics, (2009) 10(11):1789-97

Additional authors: Bikol N. Mukesh, Satya V. Bhupathi, Richard A. Dart and Nader R. Ghebranious, Center for Human Genetics, Marshfield Clinic Research Foundation

Funding: was provided by the National Institutes of Health, Marshfield Clinic Personalized Medicine Research Project, Abbott Laboratories and the Michigan Institute for Clinical and Health Research.

The research was funded in part by donors to cardiology research at Marshfield Clinic. Robert Simpson has a financial interest in and is president of Cardiavent, Inc., a company that is developing an analog (CARDO24) of vitamin D to treat cardiovascular diseases.



Inadequate Levels of Vitamin D May Significantly Increase Risk of Stroke, Heart Disease and Death

ScienceDaily.com  –  While mothers have known that feeding their kids milk builds strong bones, a new study by researchers at the Heart Institute at Intermountain Medical Center in Salt Lake City suggests that Vitamin D contributes to a strong and healthy heart as well — and that inadequate levels of the vitamin may significantly increase a person’s risk of stroke, heart disease, and death, even among people who’ve never had heart disease.


For more than a year, the Intermountain Medical Center research team followed 27,686 patients who were 50 years of age or older with no prior history of cardiovascular disease. The participants had their blood Vitamin D levels tested during routine clinical care. The patients were divided into three groups based on their Vitamin D levels — normal (over 30 nanograms per milliliter), low (15-30 ng/ml), or very low (less than 15 ng/ml). The patients were then followed to see if they developed some form of heart disease.


Researchers found that patients with very low levels of Vitamin D were 77 percent more likely to die, 45 percent more likely to develop coronary artery disease, and 78 percent were more likely to have a stroke than patients with normal levels. Patients with very low levels of Vitamin D were also twice as likely to develop heart failure than those with normal Vitamin D levels.


Findings from the study were presented at the American Heart Association’s Scientific Conference on Nov. 16 in Orlando, Florida.


“This was a unique study because the association between Vitamin D deficiency and cardiovascular disease has not been well-established,” says Brent Muhlestein, MD, director of cardiovascular research of the Heart Institute at Intermountain Medical Center and one of the authors of the new study. “Its conclusions about how we can prevent disease and provide treatment may ultimately help us save more lives.”


A wealth of research has already shown that Vitamin D is involved in the body’s regulation of calcium, which strengthens bones — and as a result, its deficiency is associated with musculoskeletal disorders. Recently, studies have also linked Vitamin D to the regulation of many other bodily functions including blood pressure, glucose control, and inflammation, all of which are important risk factors related to heart disease. From these results, scientists have postulated that Vitamin D deficiency may also be linked to heart disease itself.


“Utah’s population gave us a unique pool of patients whose health histories are different than patients in previous studies,” Dr. Muhlestein says. “For example, because of Utah’s low use of tobacco and alcohol, we were able to narrow the focus of the study to the effects of Vitamin D on the cardiovascular system.”


The results were quite surprising and very important, says Heidi May, PhD, MS, an epidemiologist with the Intermountain Medical Center research team and one of the study authors.


“We concluded that among patients 50 years of age or older, even a moderate deficiency of Vitamin D levels was associated with developing coronary artery disease, heart failure, stroke, and death,” she says. “This is important because Vitamin D deficiency is easily treated. If increasing levels of Vitamin D can decrease some risk associated with these cardiovascular diseases, it could have a significant public health impact. When you consider that cardiovascular disease is the leading cause of death in America, you understand how this research can help improve the length and quality of people’s lives.”


Because the study was only observational, definitive links between Vitamin D deficiency and heart disease could not be assigned — but the findings create an impetus for further study, says Dr. Muhlestein.


“We believe the findings are important enough to now justify randomized treatment trials of supplementation in patients with Vitamin D deficiency to determine for sure whether it can reduce the risk of heart disease,” he says.

ScienceDaily (Dec. 3, 2009) – Dentists can help to identify patients who are in danger of dying of a heart attack or stroke, reveals a new study from the Sahlgrenska Academy. Thanks to the study, six men who thought they were completely healthy were able to start preventive treatment in time. 

“Dentists are really proud of their profession and feel no need to encroach upon doctors’ territory,” says senior dental officer and professor Mats Jontell at the Sahlgrenska Academy. “However, we wanted to find out if we as a profession could identify patients at risk of cardiovascular disease.” 

The study involved 200 men and women over the age of 45 who did not have any known cardiovascular problems. During a routine visit to their normal dentists in Borås and Gothenburg they were also checked out for known risk factors for cardiovascular disease. 

“These risk factors are not normally manifested in the mouth, which is why the dentists went beyond their normal check-up routine,” says Jontell. “They also took the patients’ blood pressure and checked total cholesterol and blood sugar levels.” 

The risk of a fatal cardiovascular disease was calculated using a software known as HeartScore. The dentists felt that twelve men had a ten per cent risk of developing a fatal cardiovascular disease over the next ten years and advised them to see their doctors. Six of the twelve were subsequently prescribed medication to lower their blood pressure.

“Dentists regularly see a very large percentage of the Swedish population, and if there is sufficient interest they could also screen for cardiovascular risk factors which, untreated, could lead to a heart attack or stroke,” says Jontell.