Simple genetic probes
Such testing isn’t for the typical, older cardiac patient who comes in with chest pain, the result of a lifetime of poor diet and little exercise. “Those patients can be treated with standard treatments, such as surgical interventions. But what if a 30-year-old woman comes in with chest pain and her doctors can’t find any obvious reason why she should be having heart problems at such a young age?” said Wu, who is also the director of Stanford’s Cardiovascular Institute. That could be the moment for doctors to break out the complementary long padlock probes for inherited heart disease.
Complementary long padlock probes, or cLPPs, were developed at the Stanford Genome Technology Center. These simple probes accurately target specific parts of the genome and can be made in large batches at low cost. Because of their simplicity, they are easily customized to target different genes. Wilson and Wu spearheaded the effort to put cLPPs to work diagnosing cardiac diseases.
A preliminary test of the assay on blood samples and some skin samples from 29 participants from families with inherited heart disease validated the cLPP approach, the researchers said. The heart disease cLPP assay was cheaper, faster and more accurate than whole-genome assays.
The Stanford team next plans to test the technique on a group of 200-300 patients. In the meantime, Wilson and Wu are offering the test free to any research lab that wants to try it. “They can just email me,” said Wilson, “and we’ll send them the assay, and then they can do it in their own lab — as long as they have some experience with next-generation sequencing.”
The assay will shorten the time it takes to diagnose difficult or unusual heart disease cases, Wu said. “Suppose you have a 60-year-old patient who comes in with heart failure,” he said. “We do the angiogram and we find he has no history of heart attack or other issues, and yet the heart is not performing well. We also find that several of his family members have similar heart conditions. So if we run the new genetic test and find the man’s illness has a genetic cause, such as dilated cardiomyopathy, we now have both a cause and a diagnosis, and we can initiate treatment right away.”
Avoiding a ‘fishing expedition’
“Not having that result delays diagnosis and increases costs because you’re going through a whole bunch of tests — sometimes it becomes a fishing expedition, which can be frustrating to both the physician and the patient,” Wu added. “But perhaps the most important benefit is that you can give the patient accurate answers about his or her disease.”
Wilson and Wu said the genome technology group has been working on the cLPP technique for a long time. “Our goal is to make genetic testing more accessible to more people,” Wilson said. “We want to democratize it. For now, we’re going to release it free of charge: Researchers can get samples of the assay so they can run it themselves. We’re also releasing all of the technical data for the probes so researchers can recreate and modify the probes themselves. In some ways it’s making genetic testing open source.”
Our goal is to make genetic testing more accessible to more people.
The development of the new test is an example of Stanford Medicine’s focus on precision health, which aims to enable researchers and physicians to better predict individual risks for specific diseases, develop approaches to early detection and prevention, and help clinicians make real-time decisions about the best way to care for patients.
Other Stanford-affiliated authors of the paper are Peidong Shen, PhD, research scientist; Eula Fung, MS, clinical data analyst; Ioannis Karakikes, PhD, instructor in cardiovascular medicine; Stanford undergraduate Angela Zhang; Kolsoum InanlooRahatloo, PhD, postdoctoral scholar; Justin Odegaard, MD, PhD, instructor of pathology; Karim Sallam, MD, cardiovascular medical fellow; Ronald Davis, PhD, professor of biochemistry and of genetics; George Lui, MD, professor of cardiovascular medicine and of pediatrics; and Euan Ashley, MD, PhD, professor of cardiovascular medicine.
This work was supported by the National Institutes of Health (grants R01HD081355, R01HL126527, R01HL113006 and R24HL117756), the Stanford Cardiovascular Institute, the Steven M. Gootter Foundation and the American Heart Association.
Information about Stanford’s departments of Pathology, Medicine and Radiology, which also supported the work, is available at http://pathology.stanford.edu, http://medicine.stanford.edu and http://med.stanford.edu/radiology.html.
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