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.
Short-Term Suspended Animation for Humans Is Coming Soon
At 1 a.m., Tony B. is flown to a shock trauma center of a university hospital. Five minutes earlier, he was picked up unconscious with no blood pressure, having suffered multiple gunshot wounds with severe blood loss. Standard measures alone would not have saved his life, but on the helicopter he was injected with ice-cold fluids intravenously to begin cooling him from the inside, and given special drugs to protect his heart and brain.
Suspended animation is not routine yet, but it's going through clinical trials at the University of Maryland and the University of Pittsburgh.
A surgeon accesses Tony's aorta, allowing his body to be flushed with larger amounts of cold fluids, thereby inducing profound hypothermia -- a body temperature below 10° C (50° F). This is suspended animation, a form of human hibernation, but officially the procedure is called Emergency Preservation and Resuscitation for Cardiac Arrest from Trauma (EPR-CAT).
This chilly state, which constitutes the preservation component of Tony's care, continues for an hour as surgeons repair injuries and connect his circulation to cardiopulmonary bypass (CPB). This allows blood to move through the brain delivering oxygen at low doses appropriate for the sharply reduced metabolic rate that comes with the hypothermia, without depending on the heart and lungs. CPB also enables controlled, gradual re-warming of Tony's body as fluid and appropriate amounts of red blood cells are transfused into him.
After another hour or so, Tony's body temperature reaches the range of 32-34° C (~90-93° F), called mild hypothermia. Having begun the fluid resuscitation process already, the team stops warming Tony, switches his circulation from CPB to his own heart and lungs, and begins cardiac resuscitation with electrical jolts to his heart. With his blood pressure stable, his heart rate slow but appropriate for the mild hypothermia, Tony is maintained at this intermediate temperature for 24 hours; this last step is already standard practice in treatment of people who suffer cardiac arrest without blood loss trauma.
The purpose is to prevent brain damage that might come with the rapid influx of too much oxygen, just as a feast would mean death to a starvation victim. After he is warmed to a normal temperature of 37° C (~99° F), Tony is awakened and ultimately recovers with no brain damage.
Tony's case is fictional; EPR-CAT is not routine yet, but it's going through clinical trials at the University of Maryland and the University of Pittsburgh, under the direction of trauma surgeon Dr. Samuel Tisherman, who spent many years developing the procedure in dogs and pigs. In such cases, patients undergo suspended animation for a couple of hours at most, but other treatments are showing promise in laboratory animals, like the use of hydrogen sulfide gas without active cooling to induce suspended animation in mice. Such interventions could ultimately fuse with EPR-CAT, sending the new technology further into what's still the realm of science fiction – at least for now.
Consider the scenario of a 5-year-old girl diagnosed with a progressive, incurable, terminal disease.
Experts say that extended suspended animation – cooling patients in a stable state for months or years -- could be possible at some point, although no one can predict when the technology will be clinical reality, since hydrogen sulfide and other chemical tactics would have to move into clinical use in humans and prove safe and effective in combination with EPR-CAT, or with a similar cooling approach.
How Could Long-Term Suspended Animation Impact Humanity?
Consider the scenario of a 5-year-old girl diagnosed with a progressive, incurable, terminal disease. Since available treatments would only lengthen the projected survival by a year, she is placed into suspended animation. She is revived partially every few years, as new treatments become available that can have a major impact on her disease. After 35 years of this, she is revived completely as treatments are finally adequate to cure her condition, but biologically she has aged only a few months. Physically, she is normal now, though her parents are in their seventies, and her siblings are grown and married.
Such hypothetical scenarios raise many issues: Where will the resources come from to take care of patients for that long? Who will pay? And how will patients adapt when they emerge into a completely different world?
"Heavy resource utilization is a factor if you've got people hibernating for years or decades," says Bradford Winters, an associate professor of anesthesiology and critical care medicine, and assistant professor of neurological surgery at Johns Hopkins.
Conceivably, special high-tech facilities with robots and artificial intelligence watching over the hibernators might solve the resource issue, but even then, Winters notes that long-term hibernation would entail major disparities between the wealthy and poor. "And then there is the psychological effect of being disconnected from one's family and society for a generation or more," he says. "What happens to that 5-year-old waking to her retired parents and married siblings? Will her younger sister adopt her? What would that be like?"
Probably better than dying is one answer.
Back on Earth, human hibernation would raise daunting policy questions that may take many years to resolve.
Outside of medicine, one application of human hibernation that has intrigued generations of science fiction writers is in long-duration space travel. During a voyage lasting years or decades, space explorers or colonists not only could avoid long periods of potential boredom, but also the aging process. Considering that the alternative to "sleeper ships" would be multi-generation starships so large that they'd be like small worlds, human hibernation in spaceflight could become an enabling technology for interstellar flight.
Big Questions: It's Not Too Early to Ask
Back on Earth, the daunting policy questions may take many years to resolve. Society ought to be aware of them now, before human hibernation technology outpaces its dramatic implications.
"Our current framework of ethical and legal regulation is adequate for cases like the gunshot victim who is chilled deeply for a few hours. Short-term cryopreservation is currently part of the continuum of care," notes David N. Hoffman, a clinical ethicist and health care attorney who teaches at Columbia University, and at Yeshiva University's Benjamin N. Cardozo School of Law and Albert Einstein College of Medicine.
"But we'll need a new framework when there's a capability to cryopreserve people for many years and still bring them back. There's also a legal-ethical issue involving the parties that decide to put the person into hibernation versus the patient wishes in terms of what risk benefit ratio they would accept, and who is responsible for the expense and burdens associated with cases that don't turn out just right?"
To begin thinking about practical solutions, Hoffman characterizes long-term human hibernation as an extension of the ethics of cyro-preserved embryos that are held for potential parents, often for long periods of time. But the human hibernation issue is much more complex.
"The ability of the custodian and patient to enter into a meaningful and beneficial arrangement is fraught, because medical advances necessary to address the person's illness or injury are -- by definition -- unknown," says Hoffman. "It means that you need a third party, a surrogate, to act on opportunities that the patient could never have contemplated."
Such multigenerational considerations might become more manageable, of course, in an era when gene therapy, bionic parts, and genetically engineered replacement organs enable dramatic life extension. But if people will be living for centuries regardless of whether or not they hibernate, then developing the medical technology may be the least of the challenges.
The Mind-Blowing Promise of Neural Implants
You may not have heard of DARPA, the research branch of the Pentagon. But you're definitely familiar with some of the technology it has pioneered, like the Internet, Siri, and handheld GPS.
"Now we're going to try to go from this proof-of-concept all the way to commercial technologies that can powerfully affect patients' lives."
Last week in National Harbor, Maryland, DARPA celebrated its 60th anniversary by showcasing its latest breakthroughs and emerging research programs, one of which centers around using neurotechnology to enhance the capabilities of the human brain. This technology is initially being developed to help warfighters and veterans, but its success could have enormous implications for civilian patients and, eventually, mainstream consumers.
The field is moving ahead rapidly. Fifteen years ago, a monkey named Aurora used a brain-machine interface to control a cursor on a computer screen. In 2014, DARPA's mind-controlled prosthetic arm for amputees won approval from the Food and Drug Administration.
Since then, DARPA has continued to push neurotechnology to new heights. Here are three of their research programs that are showing promise in early human testing:
1) A NEURAL IMPLANT HELP MANAGE PSYCHIATRIC ILLNESS
More than 2.2 million veterans and 44 million civilians are living with some form of psychiatric illness, and medications don't work for everyone. DARPA set out to create new options for people living with debilitating anxiety, depression, and PTSD.
"We can get somebody back to normal. It's a whole new set of tools for physicians," said Justin Sanchez, Director of the Biological Technologies Office at DARPA.
He told the audience about a woman living with both epilepsy and extreme anxiety, who has a direct neural interface that reads her brain's signals in real time and can be modulated with stimulation. He shared a recent video of her testing the device:
"Now we're going to try to go from this proof-of-concept all the way to commercial technologies that can powerfully affect patients' lives," Sanchez said.
2) A NEURAL IMPLANT TO HELP IMPROVE MEMORY
"We are right at the cusp" of improving memory recall with direct neural interfaces, Sanchez said.
All day long, our brains shift between poor and good memory states. A brain-computer interface can read the signals of populations of neurons in the lateral temporal cortex. The device continuously monitors the state of the brain and delivers stimulation within a fraction of a second after detecting a poor memory state, to improve the person's memory performance.
The improved memory lasts only seconds, so the system "delivers stimulation as needed in a closed loop to keep the performance in a good state, because of this natural variability of performance," said Dan Rizzuto, founder of NiaTherapeutics, whose technology was developed with support from DARPA and the United States BRAIN Initiative.
Check out this recently shot video of a patient testing the device, which Sanchez called "a breakthrough moment":
About 400 patients have been tested with this technology so far. In a pilot study whose data have not yet been published, patients with traumatic brain injury showed improvement in recall of around 28 percent, according to Rizzuto.
He estimates that potential FDA approval of the device for patients with traumatic brain injury is still 7 to 8 years away. The technology holds the potential to help many other kinds of patients as well.
"We believe this device could also be used to treat Alzheimer's because it's not specific to any brain pathology but based on a deep understanding of the way human memory works," Rizzuto said.
3) A NEURAL IMPLANT TO REVOLUTIONIZE PROSTHETICS FOR WARFIGHTERS AND VETERANS
Since 2006, DARPA has run a program to revolutionize prosthetics. The latest advances allow amputees to actually feel again with their bionic limbs.
Sensors in a prosthetic hand relay information to an interface in the brain that allows the person to detect which of their "fingers" are being touched, while their eyes are closed:
WHAT COMES NEXT?
DARPA is now turning its attention to non-surgical, non-invasive neurotechnology. Researchers hope to use advanced sensor technology to detect signals from neurons without putting any electrodes directly inside the brain. Under the direction of program manager Dr. Al Emondi, the N³ program is about to launch soon and plans to run for four or five years.
"We haven't even scratched the surface of what a human brain's capability is," said Dr. Geoffrey Ling, the Founding Director of the Biological Technologies Office. "When we can make this a non-invasive consumer technology, this will explode. It will take on a life of its own."
Then, inevitably, the hard questions will follow.
As Sanchez put it: "Will society consider some form of neural enhancement a personal choice like braces? Could there be a disturbing gap for people who have neurotech and those who don't? We must come together and all think over the horizon. How the story unfolds ultimately depends on all of us."
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.