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.
Ethan Lindenberger, the Ohio teenager who sought out vaccinations after he was denied them as a child, recently testified before Congress about why his parents became anti-vaxxers. The trouble, he believes, stems from the pervasiveness of misinformation online.
There is evidence that 'educating' people with facts about the benefits of vaccination may not be effective.
"For my mother, her love and affection and care as a parent was used to push an agenda to create a false distress," he told the Senate Committee. His mother read posts on social media saying vaccines are dangerous, and that was enough to persuade her against them.
His story is an example of how widespread and harmful the current discourse on vaccinations is—and more importantly—how traditional strategies to convince people about the merits of vaccination have largely failed.
As responsible members of society, all of us have implicitly signed on to what ethicists call the "Social Contract" -- we agree to abide by certain moral and political rules of behavior. This is what our societal values, norms, and often governments are based upon. However, with the unprecedented rise of social media, alternative facts, and fake news, it is evident that our understanding—and application—of the social contract must also evolve.
Nowhere is this breakdown of societal norms more visible than in the failure to contain the spread of vaccine-preventable diseases like measles. What started off as unexplained episodes in New York City last October, mostly in communities that are under-vaccinated, has exploded into a national epidemic: 880 cases of measles across 24 states in 2019, according to the CDC (as of May 17, 2019). In fact, the Unites States is only eight months away from losing its "measles free" status, joining Venezuela as the second country out of North and South America with that status.
The U.S. is not the only country facing this growing problem. Such constant and perilous reemergence of measles and other vaccine-preventable diseases in various parts of the world raises doubts about the efficacy of current vaccination policies. In addition to the loss of valuable life, these outbreaks lead to loss of millions of dollars in unnecessary expenditure of scarce healthcare resources. While we may be living through an age of information, we are also navigating an era whose hallmark is a massive onslaught on truth.
There is ample evidence on how these outbreaks start: low-vaccination rates. At the same time, there is evidence that 'educating' people with facts about the benefits of vaccination may not be effective. Indeed, human reasoning has a limit, and facts alone rarely change a person's opinion. In a fascinating report by researchers from the University of Pennsylvania, a small experiment revealed how "behavioral nudges" could inform policy decisions around vaccination.
In the reported experiment, the vaccination rate for employees of a company increased by 1.5 percent when they were prompted to name the date when they planned to get their flu shot. In the same experiment, when employees were prompted to name both a date and a time for their planned flu shot, vaccination rate increased by 4 percent.
A randomized trial revealed the subtle power of "announcements" – direct, brief, assertive statements by physicians that assumed parents were ready to vaccinate their children.
This experiment is a part of an emerging field of behavioral economics—a scientific undertaking that uses insights from psychology to understand human decision-making. The field was born from a humbling realization that humans probably do not possess an unlimited capacity for processing information. Work in this field could inform how we can formulate vaccination policy that is effective, conserves healthcare resources, and is applicable to current societal norms.
Take, for instance, the case of Human Papilloma Virus (HPV) that can cause several types of cancers in both men and women. Research into the quality of physician communication has repeatedly revealed how lukewarm recommendations for HPV vaccination by primary care physicians likely contributes to under-immunization of eligible adolescents and can cause confusion for parents.
A randomized trial revealed the subtle power of "announcements" – direct, brief, assertive statements by physicians that assumed parents were ready to vaccinate their children. These announcements increased vaccination rates by 5.4 percent. Lengthy, open-ended dialogues demonstrated no benefit in vaccination rates. It seems that uncertainty from the physician translates to unwillingness from a parent.
Choice architecture is another compelling concept. The premise is simple: We hardly make any of our decisions in vacuum; the environment in which these decisions are made has an influence. If health systems were designed with these insights in mind, people would be more likely to make better choices—without being forced.
This theory, proposed by Richard Thaler, who won the 2017 Nobel Prize in Economics, was put to the test by physicians at the University of Pennsylvania. In their study, flu vaccination rates at primary care practices increased by 9.5 percent all because the staff implemented "active choice intervention" in their electronic health records—a prompt that nudged doctors and nurses to ask patients if they'd gotten the vaccine yet. This study illustrated how an intervention as simple as a reminder can save lives.
To be sure, some bioethicists do worry about implementing these policies. Are behavioral nudges akin to increased scrutiny or a burden for the disadvantaged? For example, would incentives to quit smoking unfairly target the poor, who are more likely to receive criticism for bad choices?
The measles outbreak is a sober reminder of how devastating it can be when the social contract breaks down.
While this is a valid concern, behavioral economics offers one of the only ethical solutions to increasing vaccination rates by addressing the most critical—and often legal—challenge to universal vaccinations: mandates. Choice architecture and other interventions encourage and inform a choice, allowing an individual to retain his or her right to refuse unwanted treatment. This distinction is especially important, as evidence suggests that people who refuse vaccinations often do so as a result of cognitive biases – systematic errors in thinking resulting from emotional attachment or a lack of information.
For instance, people are prone to "confirmation bias," or a tendency to selectively believe in information that confirms their preexisting theories, rather than the available evidence. At the same time, people do not like mandates. In such situations, choice architecture provides a useful option: people are nudged to make the right choice via the design of health delivery systems, without needing policies that rely on force.
The measles outbreak is a sober reminder of how devastating it can be when the social contract breaks down and people fall prey to misinformation. But all is not lost. As we fight a larger societal battle against alternative facts, we now have another option in the trenches to subtly encourage people to make better choices.
Using insights from research in decision-making, we can all contribute meaningfully in controversial conversations with family, friends, neighbors, colleagues, and our representatives — and push for policies that protect those we care about. A little more than a hundred years ago, thousands of lives were routinely lost to preventive illnesses. We've come too far to let ignorance destroy us now.
New Tech Can Predict Breast Cancer Years in Advance
Every two minutes, a woman is diagnosed with breast cancer. The question is, can those at high risk be identified early enough to survive?
New AI software has predicted risk equally well in both white and black women for the first time.
The current standard practice in medicine is not exactly precise. It relies on age, family history of cancer, and breast density, among other factors, to determine risk. But these factors do not always tell the whole story, leaving many women to slip through the cracks. In addition, a racial gap persists in breast cancer treatment and survival. African-American women are 42 percent more likely to die from the disease despite relatively equal rates of diagnosis.
But now those grim statistics could be changing. A team of researchers from MIT's Computer Science and Artificial Intelligence Laboratory have developed a deep learning model that can more accurately predict a patient's breast cancer risk compared to established clinical guidelines – and it has predicted risk equally well in both white and black women for the first time.
The Lowdown
Study results published in Radiology described how the AI software read mammogram images from more than 60,000 patients at Massachusetts General Hospital to identify subtle differences in breast tissue that pointed to potential risk factors, even in their earliest stages. The team accessed the patients' actual diagnoses and determined that the AI model was able to correctly place 31 percent of all cancer patients in the highest-risk category of developing breast cancer within five years of the examination, compared to just 18 percent for existing models.
"Each image has hundreds of thousands of pixels identifying something that may not necessarily be detected by the human eye," said MIT professor Regina Barzilay, one of the study's lead authors. "We all have limited visual capacities so it seems some machines trained on hundreds of thousands of images with a known outcome can capture correlations the human eye might not notice."
Barzilay, a breast cancer survivor herself, had abnormal tissue patterns on mammograms in 2012 and 2013, but wasn't diagnosed until after a 2014 image reading, illustrating the limitations of human processing alone.
MIT professor Regina Barzilay, a lead author on the new study and a breast cancer survivor herself.
(Courtesy MIT)
Next up: The MIT team is looking at training the model to detect other cancers and health risks. Barzilay recalls how a cardiologist told her during a conference that women with heart diseases had a different pattern of calcification on their mammograms, demonstrating how already existing images can be used to extract other pieces of information about a person's health status.
Integration of the AI model in standard care could help doctors better tailor screening and prevention programs based on actual instead of perceived risk. Patients who might register as higher risk by current guidelines could be identified as lower risk, helping resolve conflicting opinions about how early and how often women should receive mammograms.
Open Questions: While the results were promising, it's unknown how well the model will work on a larger scale, as the study looked at data from just one institution and used mammograms supplied by just one hospital. Some risk factor information was also unavailable for certain patients during the study, leaving researchers unable to fully compare the AI model's performance to that of the traditional standard.
One incentive to wider implementation and study, however, is the bonus that no new hardware is required to use the AI model. With other institutions now showing interest, this software could lead to earlier routine detection and treatment of breast cancer — resulting in more lives saved.