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.
Here's something to chew on. Can a gulp of water help save the planet? If you're drinking *and* eating your water at the same time, the answer may be yes.
The tasteless packaging is made from brown seaweed that biodegrades naturally in four to six weeks.
The Lowdown
A start-up company called Skipping Rocks Lab has created a "water bubble" encased in an edible sachet that you can pop in your mouth whole. Or if you're not into swallowing it, you can tear off the edge, drink up, and toss the rest in a composter. The tasteless packaging is made from brown seaweed that biodegrades naturally in four to six weeks, whereas plastic water bottles can linger for hundreds of years.
The founders of the London-based company are determined to "make plastic packaging disappear." They had two foodie inspirations: molecular gastronomists and fruit. They tried to emulate the way chefs used edible membranes to encase bubbles of liquid to make things like fake caviar and fake egg yolks; and they also considered the peel of an orange or banana, which protects the tasty insides but can be composted.
The sachets can also contain other liquids that come in single-serve plastic containers -- think packets of condiments with takeout meals, specialty cocktails at parties, and especially single servings of water for sporting events. The London Marathon last month gave out the water bubble pods at a station along the route, using them to replace 200,000 plastic bottles that would have likely ended up first in the street, and ultimately in the ocean.
Next Up
The engineers and chemists at Skipping Rocks intend to lease their machines to others who can then manufacture their own sachets on-site to fill with whatever they desire. The new material, which is dubbed "Notpla" (not plastic), also has other applications beyond holding liquids. It can be used to replace the plastic lining in cardboard takeout boxes, for example. And the startup is working on additional materials to replace other types of ubiquitous plastic packaging, like the netting that encases garlic and onions, and the sachets that hold nails and screws.
Edible water bubbles may be the future of drinks at sporting events and festivals.
Open Questions
One hurdle is that the pods are not very hardy, so while they work fine to hand out along a marathon route, they wouldn't really be viable for a hiker to throw in her backpack. Another issue concerns the retail market: to be stable on a shelf, they'd have to be protected from all that handling, which brings us back to the problem the engineers tried to solve in the first place -- disposable packaging.
So while Skipping Rocks may not achieve their ultimate goal of ridding the world of plastic waste, a little progress can still go a long way. If edible water bubbles are the future of drinks at sporting events and festivals, the environment will certainly benefit from their presence -- and absence.
The Internet has made it easier than ever to misguide people. The anti-vaxx movement, climate change denial, protests against stem cell research, and other movements like these are rooted in the spread of misinformation and a distrust of science.
"I had been taught intelligent design and young-earth creationism instead of evolution, geology, and biology."
Science illiteracy is pervasive in the communities responsible for these movements. For the mainstream, the challenge lies not in sharing the facts, but in combating the spread of misinformation and facilitating an open dialogue between experts and nonexperts.
I grew up in a household that was deeply skeptical of science and medicine. My parents are evangelical Christians who believe the word of the Bible is law. To protect my four siblings and me from secular influence, they homeschooled some of us and put the others in private Christian schools. When my oldest brother left for a Christian college and the tuition began to add up, I was placed in a public charter school to offset the costs.
There, I became acutely aware of my ignorant upbringing. I had been taught intelligent design and young-earth creationism instead of evolution, geology, and biology. My mother skipped over world religions, and much of my history curriculum was more biblical-based than factual. She warned me that stem cell research, vaccines, genetic modification of crops, and other areas of research in biological science were examples of humans trying to be like God. At the time, biologist Richard Dawkins' The God Delusion was a bestseller and science seemed like an excuse to not believe in God, so she and my father discouraged me from studying it.
The gaps in my knowledge left me feeling frustrated and embarrassed. The solution was to learn about the things that had been censored from my education, but several obstacles stood in the way.
"When I first learned about fundamentalism, my parents' behavior finally made sense."
I lacked a good foundation in basic mathematics after being taught by my mother, who never graduated college. My father, who holds a graduate degree in computer science, repeatedly told me that I inherited my mother's "bad math genes" and was therefore ill-equipped for science. While my brothers excelled at math under his supervision and were even encouraged toward careers in engineering and psychology, I was expected to do well in other subjects, such as literature. When I tried to change this by enrolling in honors math and science classes, they scolded me -- so reluctantly, I dropped math. By the time I graduated high school, I was convinced that math and science were beyond me.
When I look back at my high school transcripts, that sense of failure was unfounded: my grades were mostly A's and B's, and I excelled in honors biology. Even my elementary standardized test scores don't reflect a student disinclined toward STEM, because I consistently scored in the top percentile for sciences. Teachers often encouraged me to consider studying science in college. Why then, I wondered, did my parents reject that idea? Why did they work so hard to sway me from that path? It wasn't until I moved away from my parents' home and started working to put myself through community college that I discovered my passion for both biology and science writing.
As a young adult venturing into the field of science communication, I've become fascinated with understanding communities that foster antagonistic views toward science. When I first learned about fundamentalism, my parents' behavior finally made sense. It is the foundation of the Religious Right, a right-wing Christian group which heavily influences the Republican party in the United States. The Religious Right crusades against secular education, stem cell research, abortion, evolution, and other controversial issues in science and medicine on the basis that they contradict Christian beliefs. They are quietly overturning the separation of church and state in order to enforce their religion as policy -- at the expense of science and progress.
Growing up in this community, I learned that strong feelings about these issues arise from both a lack of science literacy and a distrust of experts. Those who are against genetic modification of crops don't understand that GMO research aims to produce more, and longer-lasting, food for a growing planet. The anti-vaxx movement is still relying on a deeply flawed study that was ultimately retracted. Those who are against stem cell research don't understand how it works or the important benefits it provides the field of medicine, such as discovering new treatment methods.
In fact, at one point the famous Christian radio show Focus on the Family spread anti-vaxx mentality when they discussed vaccines that, long ago, were derived from aborted fetal cells. Although Focus on the Family now endorses vaccines, at the time it was enough to convince my own mother, who listened to the show every morning, not to vaccinate us unless the law required it.
"In everyday interactions with skeptics, science communicators need to shift their focus from convincing to discussing."
We can help clear up misunderstandings by sharing the facts, but the real challenge lies in willful ignorance. It was hard for me to accept, but I've come to understand that I'm not going to change anyone's mind. It's up to an individual to evaluate the facts, consider the arguments for and against, and make his or her own decision.
As my parents grew older and my siblings and I introduced them to basic concepts in science, they came around to trusting the experts a little more. They now see real doctors instead of homeopathic practitioners. They acknowledge our world's changing climate instead of denying it. And they even applaud two of their children for pursuing careers in science. Although they have held on to their fundamentalism and we still disagree on many issues, these basic changes give me hope that people in deeply skeptical communities are not entirely out of reach.
In everyday interactions with skeptics, science communicators need to shift their focus from convincing to discussing. This means creating an open dialogue with the intention of being understanding and helpful, not persuasive. This approach can be beneficial in both personal and online interactions. There are people within these movements who have doubts, and their doubts will grow as we continue to feed them through discussion.
People will only change their minds when it is the right time for them to do so. We need to be there ready to hold their hand and lead them toward truth when they reach out. Until then, all we can do is keep the channels of communication open, keep sharing the facts, and fight the spread of misinformation. Science is the pursuit of truth, and as scientists and science communicators, sometimes we need to let the truth speak for itself. We're just there to hold the megaphone.