Genetically Sequencing Healthy Babies Yielded Surprising Results
Today in Melrose, Massachusetts, Cora Stetson is the picture of good health, a bubbly precocious 2-year-old. But Cora has two separate mutations in the gene that produces a critical enzyme called biotinidase and her body produces only 40 percent of the normal levels of that enzyme.
In the last few years, the dream of predicting and preventing diseases through genomics, starting in childhood, is finally within reach.
That's enough to pass conventional newborn (heelstick) screening, but may not be enough for normal brain development, putting baby Cora at risk for seizures and cognitive impairment. But thanks to an experimental study in which Cora's DNA was sequenced after birth, this condition was discovered and she is being treated with a safe and inexpensive vitamin supplement.
Stories like these are beginning to emerge from the BabySeq Project, the first clinical trial in the world to systematically sequence healthy newborn infants. This trial was led by my research group with funding from the National Institutes of Health. While still controversial, it is pointing the way to a future in which adults, or even newborns, can receive comprehensive genetic analysis in order to determine their risk of future disease and enable opportunities to prevent them.
Some believe that medicine is still not ready for genomic population screening, but others feel it is long overdue. After all, the sequencing of the Human Genome Project was completed in 2003, and with this milestone, it became feasible to sequence and interpret the genome of any human being. The costs have come down dramatically since then; an entire human genome can now be sequenced for about $800, although the costs of bioinformatic and medical interpretation can add another $200 to $2000 more, depending upon the number of genes interrogated and the sophistication of the interpretive effort.
Two-year-old Cora Stetson, whose DNA sequencing after birth identified a potentially dangerous genetic mutation in time for her to receive preventive treatment.
(Photo courtesy of Robert Green)
The ability to sequence the human genome yielded extraordinary benefits in scientific discovery, disease diagnosis, and targeted cancer treatment. But the ability of genomes to detect health risks in advance, to actually predict the medical future of an individual, has been mired in controversy and slow to manifest. In particular, the oft-cited vision that healthy infants could be genetically tested at birth in order to predict and prevent the diseases they would encounter, has proven to be far tougher to implement than anyone anticipated.
But in the last few years, the dream of predicting and preventing diseases through genomics, starting in childhood, is finally within reach. Why did it take so long? And what remains to be done?
Great Expectations
Part of the problem was the unrealistic expectations that had been building for years in advance of the genomic science itself. For example, the 1997 film Gattaca portrayed a near future in which the lifetime risk of disease was readily predicted the moment an infant is born. In the fanfare that accompanied the completion of the Human Genome Project, the notion of predicting and preventing future disease in an individual became a powerful meme that was used to inspire investment and public support for genomic research long before the tools were in place to make it happen.
Another part of the problem was the success of state-mandated newborn screening programs that began in the 1960's with biochemical tests of the "heel-stick" for babies with metabolic disorders. These programs have worked beautifully, costing only a few dollars per baby and saving thousands of infants from death and severe cognitive impairment. It seemed only logical that a new technology like genome sequencing would add power and promise to such programs. But instead of embracing the notion of newborn sequencing, newborn screening laboratories have thus far rejected the entire idea as too expensive, too ambiguous, and too threatening to the comfortable constituency that they had built within the public health framework.
"What can you find when you look as deeply as possible into the medical genomes of healthy individuals?"
Creating the Evidence Base for Preventive Genomics
Despite a number of obstacles, there are researchers who are exploring how to achieve the original vision of genomic testing as a tool for disease prediction and prevention. For example, in our NIH-funded MedSeq Project, we were the first to ask the question: "What can you find when you look as deeply as possible into the medical genomes of healthy individuals?"
Most people do not understand that genetic information comes in four separate categories: 1) dominant mutations putting the individual at risk for rare conditions like familial forms of heart disease or cancer, (2) recessive mutations putting the individual's children at risk for rare conditions like cystic fibrosis or PKU, (3) variants across the genome that can be tallied to construct polygenic risk scores for common conditions like heart disease or type 2 diabetes, and (4) variants that can influence drug metabolism or predict drug side effects such as the muscle pain that occasionally occurs with statin use.
The technological and analytical challenges of our study were formidable, because we decided to systematically interrogate over 5000 disease-associated genes and report results in all four categories of genetic information directly to the primary care physicians for each of our volunteers. We enrolled 200 adults and found that everyone who was sequenced had medically relevant polygenic and pharmacogenomic results, over 90 percent carried recessive mutations that could have been important to reproduction, and an extraordinary 14.5 percent carried dominant mutations for rare genetic conditions.
A few years later we launched the BabySeq Project. In this study, we restricted the number of genes to include only those with child/adolescent onset that could benefit medically from early warning, and even so, we found 9.4 percent carried dominant mutations for rare conditions.
At first, our interpretation around the high proportion of apparently healthy individuals with dominant mutations for rare genetic conditions was simple – that these conditions had lower "penetrance" than anticipated; in other words, only a small proportion of those who carried the dominant mutation would get the disease. If this interpretation were to hold, then genetic risk information might be far less useful than we had hoped.
Suddenly the information available in the genome of even an apparently healthy individual is looking more robust, and the prospect of preventive genomics is looking feasible.
But then we circled back with each adult or infant in order to examine and test them for any possible features of the rare disease in question. When we did this, we were surprised to see that in over a quarter of those carrying such mutations, there were already subtle signs of the disease in question that had not even been suspected! Now our interpretation was different. We now believe that genetic risk may be responsible for subclinical disease in a much higher proportion of people than has ever been suspected!
Meanwhile, colleagues of ours have been demonstrating that detailed analysis of polygenic risk scores can identify individuals at high risk for common conditions like heart disease. So adding up the medically relevant results in any given genome, we start to see that you can learn your risks for a rare monogenic condition, a common polygenic condition, a bad effect from a drug you might take in the future, or for having a child with a devastating recessive condition. Suddenly the information available in the genome of even an apparently healthy individual is looking more robust, and the prospect of preventive genomics is looking feasible.
Preventive Genomics Arrives in Clinical Medicine
There is still considerable evidence to gather before we can recommend genomic screening for the entire population. For example, it is important to make sure that families who learn about such risks do not suffer harms or waste resources from excessive medical attention. And many doctors don't yet have guidance on how to use such information with their patients. But our research is convincing many people that preventive genomics is coming and that it will save lives.
In fact, we recently launched a Preventive Genomics Clinic at Brigham and Women's Hospital where information-seeking adults can obtain predictive genomic testing with the highest quality interpretation and medical context, and be coached over time in light of their disease risks toward a healthier outcome. Insurance doesn't yet cover such testing, so patients must pay out of pocket for now, but they can choose from a menu of genetic screening tests, all of which are more comprehensive than consumer-facing products. Genetic counseling is available but optional. So far, this service is for adults only, but sequencing for children will surely follow soon.
As the costs of sequencing and other Omics technologies continue to decline, we will see both responsible and irresponsible marketing of genetic testing, and we will need to guard against unscientific claims. But at the same time, we must be far more imaginative and fast moving in mainstream medicine than we have been to date in order to claim the emerging benefits of preventive genomics where it is now clear that suffering can be averted, and lives can be saved. The future has arrived if we are bold enough to grasp it.
Funding and Disclosures:
Dr. Green's research is supported by the National Institutes of Health, the Department of Defense and through donations to The Franca Sozzani Fund for Preventive Genomics. Dr. Green receives compensation for advising the following companies: AIA, Applied Therapeutics, Helix, Ohana, OptraHealth, Prudential, Verily and Veritas; and is co-founder and advisor to Genome Medical, Inc, a technology and services company providing genetics expertise to patients, providers, employers and care systems.
Shoot for the Moon: Its Surface Contains a Pot of Gold
Here's a riddle: What do the Moon, nuclear weapons, clean energy of the future, terrorism, and lung disease all have in common?
One goal of India's upcoming space probe is to locate deposits of helium-3 that are worth trillions of dollars.
The answer is helium-3, a gas that's extremely rare on Earth but 100 million times more abundant on the Moon. This past October, the Lockheed Martin corporation announced a concept for a lunar landing craft that may return humans to the Moon in the coming decade, and yesterday China successfully landed the Change-4 probe on the far side of the Moon. Landing inside the Moon's deepest crater, the Chinese achieved a first in space exploration history.
Meanwhile, later this month, India's Chandrayaan-2 space probe will also land on the lunar surface. One of its goals is to locate deposits of helium-3 that are worth trillions of dollars, because it could be a fuel for nuclear fusion energy to generate electricity or propel a rocket.
The standard way that nuclear engineers are trying to achieve sustainable fusion uses fuels that are more plentiful on Earth: deuterium and tritium. But MIT researchers have found that adding small amounts of helium-3 to the mix could make it much more efficient, and thus a viable energy source much sooner that once thought.
Even if fusion is proven practical tomorrow, any kind of nuclear energy involves long waits for power plant construction measured in decades. However, mining helium-3 could be useful now, because of its non-energy applications. A major one is its ability to detect neutrons coming from plutonium that could be used in terrorist attacks. Here's how it works: a small amount of helium-3 is contained within a forensic instrument. When a neutron hits an atom of helium-3, the reaction produces tritium, a proton, and an electrical charge, alerting investigators to the possibility that plutonium is nearby.
Ironically, as global concern about a potential for hidden nuclear material increased in the early 2000s, so did the supply of helium-3 on Earth. That's because helium-3 comes from the decay of tritium, used in thermonuclear warheads (H-bombs). Thousands of such weapons have been dismantled from U.S. and Russian arsenals, making helium-3 available for plutonium detection, research, and other applications--including in the world of healthcare.
Helium-3 can help doctors diagnose lung diseases, since it enables imaging of the lungs in real time.
Helium-3 dramatically improves the ability of doctors to image the lungs in a range of diseases including asthma, chronic obstructive pulmonary disease and emphysema, cystic fibrosis, and bronchopulmonary dysplasia, which happens particularly in premature infants. Specifically, helium-3 is useful in magnetic resonance imaging (MRI), a procedure that creates images from within the body for diagnostic purposes.
But while a standard MRI allows doctors to visualize parts of the body like the heart or brain, it's useless for seeing the lungs. Because lungs are filled with air, which is much less dense than water or fat, effectively no signals are produced that would enable imaging.
To compensate for this problem, a patient can inhale gas that is hyperpolarized –meaning enhanced with special procedures so that the magnetic resonance signals from the lungs are finally readable. This gas is safe to breathe when mixed with enough oxygen to support life. Helium-3 is one such gas that can be hyperpolarized; since it produces such a strong signal, the MRI can literally see the air inside the lungs and in all of the airways, revealing intricate details of the bronchopulmonary tree. And it can do this in real time
The capability to show anatomic details of the lungs and airways, and the ability to display functional imaging as a patient breathes, makes helium-3 MRI far better than the standard method of testing lung function. Called spirometry, this method tells physicians how the lungs function overall, but does not home in on particular areas that may be causing a problem. Plus, spirometry requires patients to follow instructions and hold their breath, so it is not great for testing young children with pulmonary disease.
In recent years, the cost of helium-3 on Earth has skyrocketed.
Over the past several years, researchers have been developing MRI for lung testing using other hyperpolarized gases. The main alternative to helium-3 is xenon-129. Over the years, researchers have learned to overcome certain disadvantages of the latter, such as its potential to put patients to sleep. Since helium-3 provides the strongest signal, though, it is still the best gas for MRI studies in many lung conditions.
But the supply of helium-3 on Earth has been decreasing in recent years, due to the declining rate of dismantling of warheads, just as the Department of Homeland Security has required more and more of the gas for neutron detection. As a result, the cost of the gas has skyrocketed. Less is available now for medical uses – unless, of course, we begin mining it on the moon.
The question is: Are the benefits worth the 239,000-mile trip?
Should Organ Donors Be Paid?
Deanna Santana had assumed that people on organ transplant lists received matches. She didn't know some died while waiting. But in May 2011, after her 17-year-old son, Scott, was killed in a car accident, she learned what a precious gift organ and tissue donation can be.
"I would estimate it cost our family about $4,000 for me to donate a kidney to a stranger."
His heart, lungs, kidneys, liver and pancreas saved five people. His corneas enabled two others to see. And his bones, connective tissues and veins helped 73 individuals.
The donation's impact had a profound effect on his mother as well. In September 2016, she agreed to donate a kidney in a paired exchange of four people making the same sacrifice for four compatible strangers.
She gave up two weeks' worth of paid vacation to recuperate and covered lodging costs for loved ones during her transplant. Eventually, she qualified for state disability for part of her leave, but the compensation was less than her salary as public education and relations manager at Sierra Donor Services, an organ procurement organization in West Sacramento, California.
"I would estimate it cost our family about $4,000 for me to donate a kidney to a stranger," says Santana, 51. Despite the monetary hardship, she "would do it again in a heartbeat."
While some contend it's exploitative to entice organ donors and their families with compensation, others maintain they should be rewarded for extending their generosity while risking complications and recovering from donation surgery. But many agree on one point: The focus should be less on paying donors and more on removing financial barriers that may discourage interested prospects from doing a good deed.
"There's significant potential risk associated with donating a kidney, some of which we're continuing to learn," says transplant surgeon Matthew Cooper, a board member of the National Kidney Foundation and co-chair of its Transplant Task Force.
Although most kidneys are removed laparoscopically, reducing hospitalization and recuperation time, complications can occur. The risks include wound and urinary tract infections, pneumonia, blood clots, injury to local nerves causing decreased sensation in the hip or thigh, acute blood loss requiring transfusion and even death, Cooper says.
"We think that donation is a cost-neutral opportunity. It, in fact, is not."
Meanwhile, from a financial standpoint, estimates have found it costs a kidney donor in the United States an average of $3,000 to navigate the entire transplant process, which may include time off from work, travel to and from the hospital, accommodations, food and child care expenses.
"We think that donation is a cost-neutral opportunity. It, in fact, is not," says Cooper, who is also Director of Kidney and Pancreas Transplantation at MedStar Georgetown Transplant Institute in Washington, D.C.
The National Organ Transplant Act of 1984 makes it illegal to sell human organs but did not prohibit payment for the donation of human plasma, sperm and egg cells.
Unlike plasma, sperm and eggs cells—which are "renewable resources"—a kidney is irreplaceable, says John J. Friedewald, a nephrologist who is medical director of kidney transplantation at Northwestern Memorial Hospital in Chicago.
Offering some sort of incentives could lessen the overall burden on donors while benefiting many more potential recipients. "We can eliminate the people waiting on the list and dying, at least for kidneys," Friedewald says.
On the other hand, incentives may influence an individual to the point that the donation is made purely for monetary gain. "It's a delicate balance," he explains, "because so much of the transplant system has been built on altruism."
That's where doing away with the "disincentives" comes into the equation. Compensating donors for the costs they endure would be a reasonable compromise, Friedewald says.
Depending on the state, living donors may deduct up to $10,000 from their adjusted gross income under the Organ Donation Tax Deduction Act for the year in which the transplantation occurs. "Human organ" applies to all or part of a liver, pancreas, kidney, intestine, lung or bone marrow. The subtracted modification may be claimed for only unreimbursed travel and lodging expenses and lost wages.
For some or many donors, the tax credit doesn't go far enough in offsetting their losses, but they often take it in stride, says Chaya Lipschutz, a Brooklyn, N.Y.-based matchmaker for donors and recipients, who launched the website KidneyMitzvah.com in 2009.
Seeking compensation for lost wages "is extremely rare" in her experience. "In all the years of doing this," she recalls, "I only had two people who donated a kidney who needed to get paid for lost wages." She finds it "pretty amazing that mostly all who contact don't ask."
Lipschutz, an Orthodox Jew, has walked in a donor's shoes. In September 2005, at age 48, she donated a kidney to a stranger after coming across an ad in a weekly Jewish newspaper. The ad stated: "Please help save a Jewish life—New Jersey mother of two in dire need of kidney—Whoever saves one life from Israel it is as if they saved an entire nation."
To make matches, Lipschutz posts in various online groups in the United States and Israel. Donors in Israel may receive "refunds" for loss of earnings, travel expenses, psychological treatment, recovery leave, and insurance. They also qualify for visits to national parks and nature reserves without entrance fees, Lipschutz says.
"There has been an attempt to figure out what would constitute fair compensation without the appearance that people are selling their organs or their loved ones' organs."
Kidneys can be procured from healthy living donors or patients who have undergone circulatory or brain death.
"The real dilemma arises with payment for living donation, which would favor poorer individuals to donate who would not necessarily do so," says Dr. Cheryl L. Kunis, a New York-based nephrologist whose practice consists primarily of kidney transplant recipients. "In addition, such payment for living donation has not demonstrated to improve a donor's socioeconomic status globally."
Living kidney donation has the highest success rate. But organs from young and previously healthy individuals who die in accidents or from overdoses, especially in the opioid epidemic, often work just as well as kidneys from cadaveric donors who succumb to trauma, Kunis says.
In these tragic circumstances, she notes that the decision to donate is often left to an individual's grieving family members when a living will isn't available. A payment toward funeral expenses, for instance, could tip their decision in favor of organ donation.
A similar scenario presents when a patient with a beating heart is on the verge of dying, and the family is unsure about consenting to organ donation, says Jonathan D. Moreno, a professor in the department of medical ethics and health policy at the University of Pennsylvania.
"There has been an attempt to figure out what would constitute fair compensation," he says, "without the appearance that people are selling their organs or their loved ones' organs."
The overarching concern remains the same: Compensating organ donors could lead to exploitation of socioeconomically disadvantaged groups. "What's likely to finally resolve" this bioethics debate, Moreno foresees, "is patient-compatible organs grown in pigs as the basic science of xenotransplants (between species) seems to be progressing."
Cooper, the transplant surgeon at Georgetown, believes more potential donors would come forward if financial barriers weren't an issue. Of the ones who end up giving a part of themselves, with or without reimbursement, "the overwhelming majority look back upon it as an extremely positive experience," he says. After all, "they're lifesavers. They should be celebrated."