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.
These Sisters May Change the Way You Think About Dying
For five weeks, Anita Freeman watched her sister writhe in pain. The colon cancer diagnosed four years earlier became metastatic.
"I still wouldn't wish that ending on my worst enemy."
At this tormenting juncture, her 66-year-old sister, Elizabeth Martin, wanted to die comfortably in her sleep. But doctors wouldn't help fulfill that final wish.
"It haunts me," Freeman, 74, who lives in Long Beach, California, says in recalling the prolonged agony. Her sister "was breaking out of the house and running in her pajamas down the sidewalk, screaming, 'Help me. Help me.' She just went into a total panic."
Finally, a post-acute care center offered pentobarbital, a sedative that induced a state of unconsciousness, but only after an empathetic palliative care doctor called and insisted on ending the inhumane suffering. "We even had to fight the owners of the facility to get them to agree to the recommendations," Freeman says, describing it as "the only option we had at that time; I still wouldn't wish that ending on my worst enemy."
Her sister died a week later, in 2014. That was two years before California's medical aid-in-dying law took effect, making doctors less reliant on palliative sedation to peacefully end unbearable suffering for terminally ill patients. Now, Freeman volunteers for Compassion & Choices, a national grassroots organization based in Portland, Oregon, that advocates for expanding end-of-life options.
Palliative sedation involves medicating a terminally ill patient into lowered awareness or unconsciousness in order to relieve otherwise intractable suffering at the end of life. It is not intended to cause death, which occurs due to the patient's underlying disease.
In contrast, euthanasia involves directly and deliberately ending a patient's life. Euthanasia is legal only in Canada and some European countries and requires a health care professional to administer the medication. In the United States, laws in seven states and Washington, D.C. give terminally ill patients the option to obtain prescription medication they can take to die peacefully in their sleep, but they must be able to self-adminster it.
Recently, palliative sedation has been gaining more acceptance among medical professionals as an occasional means to relieve suffering, even if it may advance the time of death, as some clinicians believe. However, studies have found no evidence of this claim. Many doctors and bioethicists emphasize that intent is what distinguishes palliative sedation from euthanasia. Others disagree. It's common for controversy to swirl around when and how to apply this practice.
Elizabeth Martin with her sister Anita Freeman in happier times, before metastatic cancer caused her tremendous suffering at the end of her life.
(Courtesy Anita Freeman)
"Intent is everything in ethics. The rigor and protocols we have around palliative sedation therapy also speaks to it being an intervention directed to ease refractory distress," says Martha Twaddle, medical director of palliative medicine and supportive care at Northwestern University's Lake Forest Hospital in Lake Forest, Illinois.
Palliative sedation should be considered only when pain, shortness of breath, and other unbearable symptoms don't respond to conventional treatments. Left to his or her own devices, a patient in this predicament could become restless, Twaddle says, noting that "agitated delirium is a horrible symptom for a family to witness."
At other times, "we don't want to be too quick to sedate," particularly in cases of purely "existential distress"—when a patient experiences anticipatory grief around "saying goodbye" to loved ones, she explains. "We want to be sure we're applying the right therapy for the problem."
Encouraging patients to reconcile with their kin may help them find inner peace. Nonmedical interventions worth exploring include quieting the environment and adjusting lighting to simulate day and night, Twaddle says.
Music-thanatology also can have a calming effect. It is live, prescriptive music, mainly employing the harp or voice, tailored to the patient's physiological needs by tuning into vital signs such as heart rate, respiration, and temperature, according to the Music-Thanatology Association International.
"When we integrated this therapeutic modality in 2003, our need for using palliative sedation therapy dropped 75 percent and has remained low ever since," Twaddle observes. "We have this as part of our care for treating refractory symptoms."
"If palliative sedation is being employed properly with the right patient, it should not hasten death."
Ethical concerns surrounding euthanasia often revolve around the term "terminal sedation," which "can entail a physician deciding that the patient is a lost cause—incurable medically and in substantial pain that cannot adequately be relieved," says John Kilner, professor and director of the bioethics programs at Trinity International University in Deerfield, Illinois.
By halting sedation at reasonable intervals, the care team can determine whether significant untreatable pain persists. Periodic discontinuation serves as "evidence that the physician is still working to restore the patient rather than merely to usher the patient painlessly into death," Kilner explains. "Indeed, sometimes after a period of unconsciousness, with the body relieved of unceasing pain, the body can recover enough to make the pain treatable."
The medications for palliative sedation "are tried and true sedatives that we've had for a long time, for many years, so they're predictable," says Joe Rotella, chief medical officer at the American Academy of Hospice and Palliative Medicine.
Some patients prefer to keep their eyes open and remain conscious to answer by name, while others tell their doctors in advance that they want to be more heavily sedated while receiving medications to manage pain and other symptoms. "We adjust the dosage until the patient is sleeping at a desired level of sedation," Rotella says.
Sedation is an intrinsic side effect of most medications prescribed to control severe symptoms in terminally ill patients. In general, most people die in a sleepy state, except for instances of sudden, dramatic death resulting from a major heart attack or stroke, says Ryan R. Nash, a palliative medicine physician and director of The Ohio State University Center for Bioethics in Columbus.
"Using those medications to treat pain or shortness of breath is not palliative sedation," Nash says. In addition, providing supplemental nutrition and hydration in situations where death is imminent—with a prognosis limited to hours or days—generally doesn't help prolong life. "If palliative sedation is being employed properly with the right patient," he adds, "it should not hasten death."
Nonetheless, hospice nurses sometimes feel morally distressed over carrying out palliative sedation. Implementing protocols at health systems would help guide them and alleviate some of their concerns, says Gregg VandeKieft, medical director for palliative care at Providence St. Joseph Health's Southwest Washington Region in Olympia, Washington. "It creates guardrails by sort of standardizing and normalizing things," he says.
"Our goal is to restore our patient. It's never to take their life."
The concept of proportionality weighs heavily in the process of palliative sedation. But sometimes substantial doses are necessary. For instance, an opioid-tolerant patient recently needed an unusually large amount of medication to control symptoms. She was in a state of illness-induced confusion and pain, says David E. Smith, a palliative medicine physician at Baptist Health Supportive Care in Little Rock, Arkansas.
Still, "we are parsimonious in what we do. We only use as much therapeutic force as necessary to achieve our goals," Smith says. "Our goal is to restore our patient. It's never to take their life."
Steven Pinker: Data Shows That Life Today Is Better Than Ever
The government shutdown. A volatile stock market. Climate change.
It's so easy to get discouraged by the latest headlines, argues Steven Pinker, that we lose sight of the bigger picture: life today is actually improving.
"To appreciate the world, we've got to look at numbers and trends."
Pinker, a cognitive psychologist from Harvard, says in his book "Enlightenment Now" that we're living at the greatest moment of progress in history, thanks to reason, science, and humanism. But today, he says, these ideals are under-appreciated, and we ignore them at our peril.
So he set out to provide a vigorous moral defense of the values of the Enlightenment by examining the evidence for their effectiveness. Across a range of categories from happiness and health to peace and safety, Pinker examines the data and reassures readers that this is a pretty great time to be alive. As we kick off the new year, he's hopeful that our embrace of science and reason will lead to an even more prosperous future. But political and cultural hurdles must still be overcome before the heroic story of human progress can continue to unfold.
Pinker spoke with our Editor-in-Chief Kira Peikoff in advance of the book's paperback release, which hits stores next Tuesday. This interview has been edited and condensed for clarity.
One anecdote you describe in the book was particularly striking: how the public reacted when the polio vaccine was announced. People took the day off work to celebrate, they smiled at each other in the streets, they offered to throw parades. Today, it's hard to imagine such prevalent enthusiasm for a new advance. How can we bring back a culture of respect and gratitude for science?
That's such a good question. And I wish I knew the answer. My contribution is just to remind people of how much progress we've made. It's easy to ignore if your view of the world comes from headlines, but there are some built-in biases in journalism that we have to counteract. Most things that happen all of a sudden are bad things: wars break out, terrorists attack, rampage shootings occur, whereas a lot of the things that make us better off creep up by stealth. But we have to become better aware of them.
It's unlikely that we're going to have replications of the great Salk event, which happened on a particular day, but I think we have to take lessons from cognitive science, from the work of people like Daniel Kahneman and Amos Tversky, showing how misled we can be by images and narratives and that to appreciate the world, we've got to look at numbers and trends.
The cover of "Enlightenment Now," which comes out in paperback next week.
You mention that the President's Bioethics Council under Bush was appointed to deal with "the looming threat of biomedical advances." Do you think that professional bioethicists are more of a hindrance than a help when it comes to creating truly enlightened science policy?
I do. I think that there are some problems in the culture of bioethics. And of course, I would not argue against that the concept of bioethics. Obviously, we have to do biomedical research and applications conscientiously and ethically. But the field called Bioethics tends to specialize in exotic thought experiments that tend to imagine the worst possible things that can happen, and often mire research in red tape that results in a net decrease in human welfare, whereas the goal of bioethics should be to enhance human welfare.
In an op-ed that I published in the Boston Globe a few years ago, I said, deliberately provocatively, that the main moral imperative of bioethics is to get out of the way since there's so much suffering that humans endure from degenerative diseases, from cancer, from heart disease and stroke. The potential for increasing happiness and well-being from biomedical research is just stupendous. So before we start to drag out Brave New World for the umpteenth time, or compare every advance in genetics to the Nazis, we should remember the costs of people dying prematurely from postponing advances in biomedical research.
Later in the book, you mention how much more efficient the production of food has become due to high-tech agriculture. But so many people today are leery of advances in the food industry, like GMOs. And we will have to feed 10 billion people in 2050. Are you concerned about how we will meet that challenge?
Yes, I think anyone has to be, and all the more reason we should be clear about what is simultaneously best for humans and for the planet, which is to grow as much food on this planet as possible. That ideal of density -- the less farmland the better -- runs up against the ideal of the organic farming and natural farming, which use lots of land. So genetically modified organisms and precision agriculture of the kind that is sometimes associated with Israel -- putting every last drop of water to use, delivering it when it's needed, using the minimum amount of fertilizer -- all of these technologically driven developments are going to be necessary to meet that need.
"The potential for increasing happiness and well-being from biomedical research is just stupendous."
You also mention "sustainability" as this big buzz word that you say is based on a flawed assumption that we will run out of resources rather than pivot to ingenious alternatives. What's the most important thing we can do as a culture to encourage innovation?
It has to be an ideal. We have restore it as what we need to encourage, to glorify in order to meet the needs of humanity. Governments have to play a role because lots of innovation is just too risky with benefits that are too widely diffuse for private companies and individuals to pursue. International cooperation has to play a role. And also, we need to change our environmental philosophy from a reflexive rejection of technology to an acknowledgement that it will be technology that is our best hope for staving off environmental problems.
And yet innovation and technology today are so often viewed fearfully by the public -- just look at AI and gene editing. If we need science and technology to solve our biggest challenges, how do we overcome this disconnect?
Part of it is simply making the argument that is challenging the ideology and untested assumptions behind traditional Greenism. Also, on the part of the promoters of technology themselves, it's crucial to make it not just clear, but to make it a reality that technology is going to be deployed to enhance human welfare.
That of course means an acknowledgement of the possible harms and limitations of technology. The fact that the first widely used genetically modified crop was soybeans that were resistant to herbicides, to Roundup -- that was at the very least a public relations disaster for genetically modified organisms. As opposed to say, highlighting crops that require less insecticide, less chemical fertilizers, less water level. The poster children for technology should really be cases that quite obviously benefit humanity.
"One of the surprises from 'Enlightenment Now' was how much moral progress depends on economic progress."
Finally, what is one emerging innovation that you're excited about for 2019?
I would say 4th generation nuclear power. Small modular reactors. Because everything depends on energy. For poor countries to get rich, they are going to have to consume far more energy than they do now and if they do it via fossil fuels, especially coal, that could spell disaster. Zero-carbon energy will allow poor countries to get richer -- and rich countries to stay rich without catastrophic environmental damage.
One of the surprises from "Enlightenment Now" was how much moral progress depends on economic progress. Rich countries not only allow the citizens to have cool gadgets, but all kinds of good things happen when a country gets rich, like Norway, Netherlands, Switzerland. Countries that are richer on average are more democratic, are less likely that to fight wars, are more feminist, are more environmentally conscientious, are smarter -- that is, they have a greater increase in IQ. So anything that makes a country get richer, and that's going to include a bunch of energy, is going to make humanity better off.
Kira Peikoff was the editor-in-chief of Leaps.org from 2017 to 2021. As a journalist, her work has appeared in The New York Times, Newsweek, Nautilus, Popular Mechanics, The New York Academy of Sciences, and other outlets. She is also the author of four suspense novels that explore controversial issues arising from scientific innovation: Living Proof, No Time to Die, Die Again Tomorrow, and Mother Knows Best. Peikoff holds a B.A. in Journalism from New York University and an M.S. in Bioethics from Columbia University. She lives in New Jersey with her husband and two young sons. Follow her on Twitter @KiraPeikoff.