Researchers use patient’s whole genome to predict his risk for 55 different health conditions
For pathologists, the day draws ever closer when they will use a patient’s whole genome sequence for diagnostic purposes. That’s the implication from research being done at the University of Stanford Medical School where scientists recently made a leap forward in advancing practical application of the human genome to patient care.
Stanford researchers recently announced that, for the first time, a healthy person’s complete DNA was sequenced, then used to create an easy-to-use, cumulative risk report. This study model could catapult patient genomic analysis into clinical laboratories even as it adds personalized medicine to the doctor’s black bag of diagnostic tools within the decade. The Stanford study team reported these findings in a recent issue of Lancet.
Stanford Bioengineering Professor Stephen Quake, Ph.D., 40, is the first person ever to have his complete DNA decoded and analyzed to predict future risk for a range of diseases. The analysis combined personal history with genetic information to produce the report. This report also included how he would respond to certain medications.
And what did Quake learn about himself? It was determined that he has a heightened risk for heart disease, cardiac arrest, diabetes and prostate cancer. The scariest of all was a 50% risk for coronary artery disease, type-2 diabetes and obesity. The analysis also revealed that Quake would respond favorably to cholesterol-reducing statin drugs. He is now taking a statin medication to lower his risk for heart disease.
“The $1,000 genome is coming fast,” said Quake’s cardiologist, Euan Ashley, M.D., a Stanford Assistant Professor of Medicine. “The challenge lies in knowing what to do with all that information. We’ve focused on establishing priorities that will be the most helpful when a patient and physician sit together and look at the computer screen.”
Based on Quake’s age and gender, researchers designed an algorithm to overlay his genetic data with what is known about the inherent risk for 55 specific health conditions. The algorithm incorporated data from various studies with Quake’s personal genomic sequence to calculate his risk for disease.
Quake, who is Stanford’s Lee Otterson Professor of Bioengineering, has already made national headlines. It was just last year when he used a technology he helped invent to sequence and publish his own complete genome for less than $50,000. Stanford scientists used Quake’s genetic data from his earlier project as the basis of the analysis in this most recent study.
The study evolved out of Quake’s concern about a snippet in his genome associated with hypertrophic cardiomyopathy, an inherited disease that causes sudden death.
When Quake asked Ashley about this, the study resulted. “Several of us had already been thinking about how you would take someone’s genomic profile and translate what’s in the billions of base pairs in that DNA to something that’s clinically useful,” recalled Ashley, who was the study team leader. “Then we realized, ‘Hey’ we already have someone’s genome.’”
Discussing the findings, Quake said, “It’s certainly been interesting. I was curious to see what would show up, but it’s important to recognize that not everyone will want to know the intimate details of their genome… There are ethical, educational and policy questions that need to be addressed going forward.”
On the other hand, he said, “Patients at risk for certain diseases could receive closer monitoring and more frequent testing, while those at a lower risk would be spared unnecessary tests. This will have important economic benefits as well, because it improves the efficiency of medicine.”
Russ B. Altman, M.D., Ph.D., Chairman, Department of Bioengineering at Stanford, pointed out, “There’s hope, too, in the promise of more effectively using available drugs to combat or prevent disease. The researchers found five to 10 previously unknown SNPs (single nucleotide polymorphisms) in genes involved in drug response. “This is really exciting because we never would have found these if we’d just relied on our usual panel of suspects.”
Pathologists and clinical laboratory managers should note that evaluation of Quake’s whole genome sequence produced clinical knowledge that was actionable by him—as the patient, along with his care team. It shows how far and how fast the field of genetic medicine is advancing. Moreover, it is widely acknowledged that acceptance of new clinical laboratory tests proceeds fastest when the information produced by the lab test can be used by physicians to select therapies which benefit the patient. —P. Kirk