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.
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.
With a deadly pandemic sweeping the planet, many are questioning the comfort and security we have taken for granted in the modern world.
A century ago, when an influenza pandemic struck, we barely knew what viruses were.
More than a century after the germ theory, we are still at the mercy of a microbe we can neither treat, nor control, nor immunize against. Even more discouraging is that technology has in some ways exacerbated the problem: cars and air travel allow a new disease to quickly encompass the globe.
Some say we have grown complacent, that we falsely assume the triumphs of the past ensure a happy and prosperous future, that we are oblivious to the possibility of unpredictable "black swan" events that could cause our destruction. Some have begun to lose confidence in progress itself, and despair of the future.
But the new coronavirus should not defeat our spirit—if anything, it should spur us to redouble our efforts, both in the science and technology of medicine, and more broadly in the advance of industry. Because the best way to protect ourselves against future disasters is more progress, faster.
Science and technology have overall made us much better able to deal with disease. In the developed world, we have already tamed most categories of infectious disease. Most bacterial infections, such as tuberculosis or bacterial pneumonia, are cured with antibiotics. Waterborne diseases such as cholera are eliminated through sanitation; insect-borne ones such as malaria through pest control. Those that are not contagious until symptoms appear, such as SARS, can be handled through case isolation and contact tracing. For the rest, such as smallpox, polio, and measles, we develop vaccines, given enough time. COVID-19 could start a pandemic only because it fits a narrow category: a new, viral disease that is highly contagious via pre-symptomatic droplet/aerosol transmission, and that has a high mortality rate compared to seasonal influenza.
A century ago, when an influenza pandemic struck, we barely knew what viruses were; no one had ever seen one. Today we know what COVID-19 is down to its exact genome; in fact, we have sequenced thousands of COVID-19 genomes, and can track its history and its spread through their mutations. We can create vaccines faster today, too: where we once developed them in live animals, we now use cell cultures; where we once had to weaken or inactivate the virus itself, we can now produce vaccines based on the virus's proteins. And even though we don't yet have a treatment, the last century-plus of pharmaceutical research has given us a vast catalog of candidate drugs, already proven safe. Even now, over 50 candidate vaccines and almost 100 candidate treatments are in the research pipeline.
It's not just our knowledge that has advanced, but our methods. When smallpox raged in the 1700s, even the idea of calculating a case-fatality rate was an innovation. When the polio vaccine was trialled in the 1950s, the use of placebo-controlled trials was still controversial. The crucial measure of contagiousness, "R0", was not developed in epidemiology until the 1980s. And today, all of these methods are made orders of magnitude faster and more powerful by statistical and data visualization software.
If you're seeking to avoid COVID-19, the hand sanitizer gel you carry in a pocket or purse did not exist until the 1960s. If you start to show symptoms, the pulse oximeter that tests your blood oxygenation was not developed until the 1970s. If your case worsens, the mechanical ventilator that keeps you alive was invented in the 1950s—in fact, no form of artificial respiration was widely available until the "iron lung" used to treat polio patients in the 1930s. Even the modern emergency medical system did not exist until recently: if during the 1918 flu pandemic you became seriously ill, there was no 911 hotline to call, and any ambulance that showed up would likely have been a modified van or hearse, with no equipment or trained staff.
As many of us "shelter in place", we are far more able to communicate and collaborate, to maintain some semblance of normal life, than we ever would have been. To compare again to 1918: long-distance telephone service barely existed at that time, and only about a third of homes in the US even had electricity; now we can videoconference over Zoom and Skype. And the enormous selection and availability provided by online retail and food delivery have kept us stocked and fed, even when we don't want to venture out to the store.
Let the virus push us to redouble our efforts to make scientific, technological, and industrial progress on all fronts.
"Black swan" calamities can strike without warning at any time. Indeed, humanity has always been subject to them—drought and frost, fire and flood, war and plague. But we are better equipped now to deal with them than ever before. And the more progress we make, the better prepared we'll be for the next one. The accumulation of knowledge, technology, industrial infrastructure, and surplus wealth is the best buffer against any shock—whether a viral pandemic, a nuclear war, or an asteroid impact. In fact, the more worried we are about future crises, the more energetically we should accelerate science, technology and industry.
In this sense, we have grown complacent. We take the modern world for granted, so much so that some question whether further progress is even still needed. The new virus proves how much we do need it, and how far we still have to go. Imagine how different things would be if we had broad-spectrum antiviral drugs, or a way to enhance the immune system to react faster to infection, or a way to detect infection even before symptoms appear. These technologies may seem to belong to a Star Trek future—but so, at one time, did cell phones.
The virus reminds us that nature is indifferent to us, leaving us to fend entirely for ourselves. As we go to war against it, let us not take the need for such a war as reason for despair. Instead, let it push us to redouble our efforts to make scientific, technological, and industrial progress on all fronts. No matter the odds, applied intelligence is our best weapon against disaster.