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.
In The Fake News Era, Are We Too Gullible? No, Says Cognitive Scientist
One of the oddest political hoaxes of recent times was Pizzagate, in which conspiracy theorists claimed that Hillary Clinton and her 2016 campaign chief ran a child sex ring from the basement of a Washington, DC, pizzeria.
To fight disinformation more effectively, he suggests, humans need to stop believing in one thing above all: our own gullibility.
Millions of believers spread the rumor on social media, abetted by Russian bots; one outraged netizen stormed the restaurant with an assault rifle and shot open what he took to be the dungeon door. (It actually led to a computer closet.) Pundits cited the imbroglio as evidence that Americans had lost the ability to tell fake news from the real thing, putting our democracy in peril.
Such fears, however, are nothing new. "For most of history, the concept of widespread credulity has been fundamental to our understanding of society," observes Hugo Mercier in Not Born Yesterday: The Science of Who We Trust and What We Believe (Princeton University Press, 2020). In the fourth century BCE, he points out, the historian Thucydides blamed Athens' defeat by Sparta on a demagogue who hoodwinked the public into supporting idiotic military strategies; Plato extended that argument to condemn democracy itself. Today, atheists and fundamentalists decry one another's gullibility, as do climate-change accepters and deniers. Leftists bemoan the masses' blind acceptance of the "dominant ideology," while conservatives accuse those who do revolt of being duped by cunning agitators.
What's changed, all sides agree, is the speed at which bamboozlement can propagate. In the digital age, it seems, a sucker is born every nanosecond.
The Case Against Credulity
Yet Mercier, a cognitive scientist at the Jean Nicod Institute in Paris, thinks we've got the problem backward. To fight disinformation more effectively, he suggests, humans need to stop believing in one thing above all: our own gullibility. "We don't credulously accept whatever we're told—even when those views are supported by the majority of the population, or by prestigious, charismatic individuals," he writes. "On the contrary, we are skilled at figuring out who to trust and what to believe, and, if anything, we're too hard rather than too easy to influence."
He bases those contentions on a growing body of research in neuropsychiatry, evolutionary psychology, and other fields. Humans, Mercier argues, are hardwired to balance openness with vigilance when assessing communicated information. To gauge a statement's accuracy, we instinctively test it from many angles, including: Does it jibe with what I already believe? Does the speaker share my interests? Has she demonstrated competence in this area? What's her reputation for trustworthiness? And, with more complex assertions: Does the argument make sense?
This process, Mercier says, enables us to learn much more from one another than do other animals, and to communicate in a far more complex way—key to our unparalleled adaptability. But it doesn't always save us from trusting liars or embracing demonstrably false beliefs. To better understand why, leapsmag spoke with the author.
How did you come to write Not Born Yesterday?
In 2010, I collaborated with the cognitive scientist Dan Sperber and some other colleagues on a paper called "Epistemic Vigilance," which laid out the argument that evolutionarily, it would make no sense for humans to be gullible. If you can be easily manipulated and influenced, you're going to be in major trouble. But as I talked to people, I kept encountering resistance. They'd tell me, "No, no, people are influenced by advertising, by political campaigns, by religious leaders." I started doing more research to see if I was wrong, and eventually I had enough to write a book.
With all the talk about "fake news" these days, the topic has gotten a lot more timely.
Yes. But on the whole, I'm skeptical that fake news matters very much. And all the energy we spend fighting it is energy not spent on other pursuits that may be better ways of improving our informational environment. The real challenge, I think, is not how to shut up people who say stupid things on the internet, but how to make it easier for people who say correct things to convince people.
"History shows that the audience's state of mind and material conditions matter more than the leader's powers of persuasion."
You start the book with an anecdote about your encounter with a con artist several years ago, who scammed you out of 20 euros. Why did you choose that anecdote?
Although I'm arguing that people aren't generally gullible, I'm not saying we're completely impervious to attempts at tricking us. It's just that we're much better than we think at resisting manipulation. And while there's a risk of trusting someone who doesn't deserve to be trusted, there's also a risk of not trusting someone who could have been trusted. You miss out on someone who could help you, or from whom you might have learned something—including figuring out who to trust.
You argue that in humans, vigilance and open-mindedness evolved hand-in-hand, leading to a set of cognitive mechanisms you call "open vigilance."
There's a common view that people start from a state of being gullible and easy to influence, and get better at rejecting information as they become smarter and more sophisticated. But that's not what really happens. It's much harder to get apes than humans to do anything they don't want to do, for example. And research suggests that over evolutionary time, the better our species became at telling what we should and shouldn't listen to, the more open to influence we became. Even small children have ways to evaluate what people tell them.
The most basic is what I call "plausibility checking": if you tell them you're 200 years old, they're going to find that highly suspicious. Kids pay attention to competence; if someone is an expert in the relevant field, they'll trust her more. They're likelier to trust someone who's nice to them. My colleagues and I have found that by age 2 ½, children can distinguish between very strong and very weak arguments. Obviously, these skills keep developing throughout your life.
But you've found that even the most forceful leaders—and their propaganda machines—have a hard time changing people's minds.
Throughout history, there's been this fear of demagogues leading whole countries into terrible decisions. In reality, these leaders are mostly good at feeling the crowd and figuring out what people want to hear. They're not really influencing [the masses]; they're surfing on pre-existing public opinion. We know from a recent study, for instance, that if you match cities in which Hitler gave campaign speeches in the late '20s through early '30s with similar cities in which he didn't give campaign speeches, there was no difference in vote share for the Nazis. Nazi propaganda managed to make Germans who were already anti-Semitic more likely to express their anti-Semitism or act on it. But Germans who were not already anti-Semitic were completely inured to the propaganda.
So why, in totalitarian regimes, do people seem so devoted to the ruler?
It's not a very complex psychology. In these regimes, the slightest show of discontent can be punished by death, or by you and your whole family being sent to a labor camp. That doesn't mean propaganda has no effect, but you can explain people's obedience without it.
What about cult leaders and religious extremists? Their followers seem willing to believe anything.
Prophets and preachers can inspire the kind of fervor that leads people to suicidal acts or doomed crusades. But history shows that the audience's state of mind and material conditions matter more than the leader's powers of persuasion. Only when people are ready for extreme actions can a charismatic figure provide the spark that lights the fire.
Once a religion becomes ubiquitous, the limits of its persuasive powers become clear. Every anthropologist knows that in societies that are nominally dominated by orthodox belief systems—whether Christian or Muslim or anything else—most people share a view of God, or the spirit, that's closer to what you find in societies that lack such religions. In the Middle Ages, for instance, you have records of priests complaining of how unruly the people are—how they spend the whole Mass chatting or gossiping, or go on pilgrimages mostly because of all the prostitutes and wine-drinking. They continue pagan practices. They resist attempts to make them pay tithes. It's very far from our image of how much people really bought the dominant religion.
"The mainstream media is extremely reliable. The scientific consensus is extremely reliable."
And what about all those wild rumors and conspiracy theories on social media? Don't those demonstrate widespread gullibility?
I think not, for two reasons. One is that most of these false beliefs tend to be held in a way that's not very deep. People may say Pizzagate is true, yet that belief doesn't really interact with the rest of their cognition or their behavior. If you really believe that children are being abused, then trying to free them is the moral and rational thing to do. But the only person who did that was the guy who took his assault weapon to the pizzeria. Most people just left one-star reviews of the restaurant.
The other reason is that most of these beliefs actually play some useful role for people. Before any ethnic massacre, for example, rumors circulate about atrocities having been committed by the targeted minority. But those beliefs aren't what's really driving the phenomenon. In the horrendous pogrom of Kishinev, Moldova, 100 years ago, you had these stories of blood libel—a child disappeared, typical stuff. And then what did the Christian inhabitants do? They raped the [Jewish] women, they pillaged the wine stores, they stole everything they could. They clearly wanted to get that stuff, and they made up something to justify it.
Where do skeptics like climate-change deniers and anti-vaxxers fit into the picture?
Most people in most countries accept that vaccination is good and that climate change is real and man-made. These ideas are deeply counter-intuitive, so the fact that scientists were able to get them across is quite fascinating. But the environment in which we live is vastly different from the one in which we evolved. There's a lot more information, which makes it harder to figure out who we can trust. The main effect is that we don't trust enough; we don't accept enough information. We also rely on shortcuts and heuristics—coarse cues of trustworthiness. There are people who abuse these cues. They may have a PhD or an MD, and they use those credentials to help them spread messages that are not true and not good. Mostly, they're affirming what people want to believe, but they may also be changing minds at the margins.
How can we improve people's ability to resist that kind of exploitation?
I wish I could tell you! That's literally my next project. Generally speaking, though, my advice is very vanilla. The mainstream media is extremely reliable. The scientific consensus is extremely reliable. If you trust those sources, you'll go wrong in a very few cases, but on the whole, they'll probably give you good results. Yet a lot of the problems that we attribute to people being stupid and irrational are not entirely their fault. If governments were less corrupt, if the pharmaceutical companies were irreproachable, these problems might not go away—but they would certainly be minimized.
“Virtual Biopsies” May Soon Make Some Invasive Tests Unnecessary
At his son's college graduation in 2017, Dan Chessin felt "terribly uncomfortable" sitting in the stadium. The bouts of pain persisted, and after months of monitoring, a urologist took biopsies of suspicious areas in his prostate.
This innovation may enhance diagnostic precision and promptness, but it also brings ethical concerns to the forefront.
"In my case, the biopsies came out cancerous," says Chessin, 60, who underwent robotic surgery for intermediate-grade prostate cancer at University Hospitals Cleveland Medical Center.
Although he needed a biopsy, as most patients today do, advances in radiologic technology may make such invasive measures unnecessary in the future. Researchers are developing better imaging techniques and algorithms—a form of computer science called artificial intelligence, in which machines learn and execute tasks that typically require human brain power.
This innovation may enhance diagnostic precision and promptness. But it also brings ethical concerns to the forefront of the conversation, highlighting the potential for invasion of privacy, unequal patient access, and less physician involvement in patient care.
A National Academy of Medicine Special Publication, released in December, emphasizes that setting industry-wide standards for use in patient care is essential to AI's responsible and transparent implementation as the industry grapples with voluminous quantities of data. The technology should be viewed as a tool to supplement decision-making by highly trained professionals, not to replace it.
MRI--a test that uses powerful magnets, radio waves, and a computer to take detailed images inside the body--has become highly accurate in detecting aggressive prostate cancer, but its reliability is more limited in identifying low and intermediate grades of malignancy. That's why Chessin opted to have his prostate removed rather than take the chance of missing anything more suspicious that could develop.
His urologist, Lee Ponsky, says AI's most significant impact is yet to come. He hopes University Hospitals Cleveland Medical Center's collaboration with research scientists at its academic affiliate, Case Western Reserve University, will lead to the invention of a virtual biopsy.
A National Cancer Institute five-year grant is funding the project, launched in 2017, to develop a combined MRI and computerized tool to support more accurate detection and grading of prostate cancer. Such a tool would be "the closest to a crystal ball that we can get," says Ponsky, professor and chairman of the Urology Institute.
In situations where AI has guided diagnostics, radiologists' interpretations of breast, lung, and prostate lesions have improved as much as 25 percent, says Anant Madabhushi, a biomedical engineer and director of the Center for Computational Imaging and Personalized Diagnostics at Case Western Reserve, who is collaborating with Ponsky. "AI is very nascent," Madabhushi says, estimating that fewer than 10 percent of niche academic medical centers have used it. "We are still optimizing and validating the AI and virtual biopsy technology."
In October, several North American and European professional organizations of radiologists, imaging informaticists, and medical physicists released a joint statement on the ethics of AI. "Ultimate responsibility and accountability for AI remains with its human designers and operators for the foreseeable future," reads the statement, published in the Journal of the American College of Radiology. "The radiology community should start now to develop codes of ethics and practice for AI that promote any use that helps patients and the common good and should block use of radiology data and algorithms for financial gain without those two attributes."
Overreliance on new technology also poses concern when humans "outsource the process to a machine."
The statement's leader author, radiologist J. Raymond Geis, says "there's no question" that machines equipped with artificial intelligence "can extract more information than two human eyes" by spotting very subtle patterns in pixels. Yet, such nuances are "only part of the bigger picture of taking care of a patient," says Geis, a senior scientist with the American College of Radiology's Data Science Institute. "We have to be able to combine that with knowledge of what those pixels mean."
Setting ethical standards is high on all physicians' radar because the intricacies of each patient's medical record are factored into the computer's algorithm, which, in turn, may be used to help interpret other patients' scans, says radiologist Frank Rybicki, vice chair of operations and quality at the University of Cincinnati's department of radiology. Although obtaining patients' informed consent in writing is currently necessary, ethical dilemmas arise if and when patients have a change of heart about the use of their private health information. It is likely that removing individual data may be possible for some algorithms but not others, Rybicki says.
The information is de-identified to protect patient privacy. Using it to advance research is akin to analyzing human tissue removed in surgical procedures with the goal of discovering new medicines to fight disease, says Maryellen Giger, a University of Chicago medical physicist who studies computer-aided diagnosis in cancers of the breast, lung, and prostate, as well as bone diseases. Physicians who become adept at using AI to augment their interpretation of imaging will be ahead of the curve, she says.
As with other new discoveries, patient access and equality come into play. While AI appears to "have potential to improve over human performance in certain contexts," an algorithm's design may result in greater accuracy for certain groups of patients, says Lucia M. Rafanelli, a political theorist at The George Washington University. This "could have a disproportionately bad impact on one segment of the population."
Overreliance on new technology also poses concern when humans "outsource the process to a machine." Over time, they may cease developing and refining the skills they used before the invention became available, said Chloe Bakalar, a visiting research collaborator at Princeton University's Center for Information Technology Policy.
"AI is a paradigm shift with magic power and great potential."
Striking the right balance in the rollout of the technology is key. Rushing to integrate AI in clinical practice may cause harm, whereas holding back too long could undermine its ability to be helpful. Proper governance becomes paramount. "AI is a paradigm shift with magic power and great potential," says Ge Wang, a biomedical imaging professor at Rensselaer Polytechnic Institute in Troy, New York. "It is only ethical to develop it proactively, validate it rigorously, regulate it systematically, and optimize it as time goes by in a healthy ecosystem."