What Are Liquid Biopsies Useful For?
The most important recent innovation in diagnostics is proving to have a remarkable number of applications.
A “liquid biopsy” is a way of using high-speed sequencing machines to measure small fragments of DNA floating in a person’s bloodstream. These fragments are probably released by dying cells. The tests are informative in any situation where a person has “foreign” DNA in the body—from a growing baby, a tumor, or a transplanted organ. Liquid biopsies permit scientists to locate, study, and monitor these genetic interlopers via a simple blood draw, and the applications of such tests are growing rapidly.
So far, the major commercial use for liquid biopsies is during pregnancy. Starting in 2011, several companies launched “non-invasive prenatal tests” (NIPTs for short) to detect Down syndrome in a fetus by examining the mother’s blood. The tests typically work by counting DNA fragments and determining if the fetus has too many or too few chromosomes. Down syndrome is caused by an extra copy of chromosome 21.
The tests have proved popular: more than a million NIPTs are performed each year, according to Diana Bianchi, executive director of the Mother Infant Research Center at Tufts University. The tests can cost $1,000 or more; companies that offer them include Berry Genomics in China and Natera, Sequenom, and Verinata in the United States.
To confidently confirm a diagnosis of Down syndrome, it’s still necessary to perform a biopsy of the amniotic sac (amniocentesis) or of the placenta (a chorionic villus sampling, or CVS). But the number of invasive tests is plummeting because NIPTs are very good at ruling out problems. The frequency with which amniocentesis is performed in the United States has fallen by 80 percent in four years, according to Bianchi.
Rare birth disorders
NIPTs can reveal much more about the fetal genome than just extra chromosomes. They can also spot small missing chunks of DNA, called microdeletions, that cause rare ailments such as cri-du-chat syndrome. Companies have begun offering tests for a few microdeletion syndromes. But these conditions are so rare that the chance of a “false positive” is high. The problem is that the underlying error rate of the technology is similar to the rate at which the conditions are found in the population (around 1 in 20,000). In some cases, half the positive results turn out to be incorrect.
Even so, it looks inevitable that we’ll know more and more about the DNA of the unborn. Researchers at Stanford have shown that with enough effort, they can sequence a fetus’s entire genome from a mother’s blood. Already, one area of investigation in liquid-biopsy research is how to spot the DNA differences, as small as mutations in one genetic letter, that cause single-gene disorders like cystic fibrosis and thalassemia, a blood disorder. This year a team at Berry Genomics, working with Chinese academics, used blood tests to detect Wilson disease in several fetuses. In that disease, the body accumulates dangerous amounts of copper.
If you are a pregnant woman and there are fragments of Y chromosomes in your blood, then it’s a boy. If not, it’s a girl. Gender determination is one of the simplest uses of liquid biopsies. It’s so easy that companies have started selling direct-to-consumer tests. One, called Sneakpeek, retails for $169. Consumers simply send in a drop of blood. The results are available at nine weeks—well before a baby’s sex can typically be known by ultrasound. (These tests can be thrown off if a woman has cells with a Y chromosome, as sometimes occurs.)
The testing company Natera and a partner, the DNA Diagnostics Center, offer a liquid biopsy to determine the father of a fetus. This test also works as early as nine weeks into the pregnancy. It costs $795. (Before liquid biopsies, the only way to do a paternity test on a fetus was via a biopsy after the 15th week of gestation.) One hitch is that for this test to work, Natera also requires a blood sample from “all the alleged fathers.”
Last year, companies including Guardant Health and Personal Genome Diagnostics began selling tests that create a genetic profile of a person’s cancer from mutated DNA fragments found in a blood sample. Such “theragnostic” tests are used to determine which drugs to give a patient, since cancers caused by specific mutations respond better to certain medications. The test can be repeated to spot any new mutations.
Because the amount of DNA in the blood from a tumor is roughly proportional to the size and stage of the cancer, such tests can also be used to judge the effects of surgery or drug treatment. Liquid biopsies are particularly useful in assessing lung cancer, where an ordinary biopsy is hard to do.
In the future, the most dramatic use of liquid biopsies will be to spot cancer before any symptoms arise. Research has shown that in many cases, blood tests can pick up cancer before it can be seen on an imaging machine. Such screening tests are still in early development, and it may take years of study to demonstrate their value. Natera says it is working on such tests to detect early-stage cancers in long-term smokers and women with a family risk of breast and ovarian cancer.
An organ transplant—a kidney, heart, or liver—can be viewed as a genome transplant. The recipient now has cells with someone else’s DNA in them. Doctors think tracking this DNA via liquid biopsies could determine whether the organ is being rejected: too much DNA from the donated organ could mean it is being attacked by the recipient’s immune system. In 2014, researchers at Stanford took blood samples from 44 adult and 21 pediatric heart transplant patients and found that they could spot signs of organ rejection. The test worked about as well as a biopsy of heart tissue. Liquid biopsies could also prove helpful in monitoring patients who have received bone marrow transplants.
Type 1 diabetes
In type 1 diabetes, the body kills its own insulin-making beta cells because of an immune reaction. Often, the disease is well under way before a patient knows it. This year a team of U.S. scientists searched the blood of 50 people at risk for the disease, trying to spot excess DNA from beta cells—a sign that those cells were dying.
The scientists employed an interesting and important trick to spot the DNA from beta cells. In these cells, the insulin gene has undergone a biochemical alteration called demethylation, which turns it on. In other tissues the insulin gene is methylated and turned off. Sequencing machines can measure whether a strand of DNA is methylated. That allowed the scientists to roughly track how much DNA was shed by beta cells. For early detection of cancer, analyzing methylation patterns could permit scientists to determine the location of a cancer, since each organ has its own pattern of genes that are on or off.
Tests that can measure DNA fragments in a person’s blood have become a commercial success in prenatal medicine and are likely to become important in cancer testing. The tests have many other uses that are still being explored.
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