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.
We Pioneered a Technology to Save Millions of Poor Children, But a Worldwide Smear Campaign Has Blocked It
In a few weeks it will be 20 years that we three have been working together. Our project has been independently praised as one of the most influential of all projects of the last 50 years.
Two of us figured out how to make rice produce a source of vitamin A, and the rice becomes a golden color instead of white.
The project's objectives have been admired by some and vilified by others. It has directly involved teams of highly motivated people from a handful of nations, from both the private and public sector. A book, dedicated to the three of us, has been written about our work. Nevertheless, success has, so far, eluded us all. The story of our thwarted efforts is a tragedy that we hope will soon – finally – reach a milestone of potentially profound significance for humanity.
So, what have we been working on, and why haven't we succeeded yet?
Food: everybody needs it, and many are fortunate enough to have enough, even too much of it. Food is a highly emotional subject on every continent and in every culture. For a healthy life our food has to provide energy, as well as, in very small amounts, minerals and vitamins. A varied diet, easily achieved and common in industrialised countries, provides everything.
But poor people in countries where rice is grown often eat little else. White rice only provides energy: no minerals or vitamins. And the lack of one of the vitamins, vitamin A, is responsible for killing around 4,500 poor children every day. Lack of vitamin A is the biggest killer of children, and also the main cause of irreversible childhood blindness.
Our project is about fixing this one dietary deficiency – vitamin A – in this one crop – rice – for this one group of people. It is a huge group though: half of the world's population live by eating a lot of rice every day. Two of us (PB & IP) figured out how to make rice produce a source of vitamin A, and the rice becomes a golden color instead of white. The source is beta-carotene, which the human body converts to vitamin A. Beta-carotene is what makes carrots orange. Our rice is called "Golden Rice."
The technology has been donated to assist those rice eaters who suffer from vitamin A deficiency ('VAD') so that Golden Rice will cost no more than white rice, there will be no restrictions on the small farmers who grow it, and nothing extra to pay for the additional nutrition. Very small amounts of beta-carotene will contribute to alleviation of VAD, and even the earliest version of Golden Rice – which had smaller amounts than today's Golden Rice - would have helped. So far, though, no small farmer has been allowed to grow it. What happened?
To create Golden Rice, it was necessary to precisely add two genes to the 30,000 genes normally present in rice plants. One of the genes is from maize, also known as corn, and the other from a commonly eaten soil bacterium. The only difference from white rice is that Golden Rice contains beta-carotene.
It has been proven to be safe to man and the environment, and consumption of only small quantities of Golden Rice will combat VAD, with no chance of overdosing. All current Golden Rice results from one introduction of these two genes in 2004. But the use of that method – once, 15 years ago - means that Golden Rice is a 'GMO' ('genetically modified organism'). The enzymes used in the manufacture of bread, cheese, beer and wine, and the insulin which diabetics take to keep them alive, are all made from GMOs too.
The first GMO crops were created by agri-business companies. Suspicion of the technology and suspicion of commercial motivations merged, only for crop (but not enzymes or pharmaceutical) applications of GMO technology. Activists motivated by these suspicions were successful in getting the 'precautionary principle' incorporated in an international treaty which has been ratified by 166 countries and the European Union – The Cartagena Protocol.
The equivalent of 13 jumbo jets full of children crashes into the ground every day and kills them all, because of vitamin A deficiency.
This protocol is the basis of national rules governing the introduction of GMO crops in every signatory country. Government regulators in, and for, each country must agree before a GMO crop can be 'registered' to be allowed to be used by the public in that country. Currently regulatory decisions to allow Golden Rice release are being considered in Bangladesh and the Philippines.
The Cartagena Protocol obliges the regulators in each country to consider all possible risks, and to take no account of any possible benefits. Because the anti-gmo-activists' initial concerns were principally about the environment, the responsibility for governments' regulation for GMO crops – even for Golden Rice, a public health project delivered through agriculture – usually rests with the Ministry of the Environment, not the Ministry of Health or the Ministry of Agriculture.
Activists discovered, before Golden Rice was created, that inducing fear of GMO food crops from 'multinational agribusinesses' was very good for generating donations from a public that was largely illiterate about food technology and production. And this source of emotionally charged donations would cease if Golden Rice was proven to save sight and lives, because Golden Rice represented the opposite of all the tropes used in anti-GMO campaigns.
Golden Rice is created to deliver a consumer benefit, it is not for profit – to multinational agribusiness or anyone else; the technology originated in the public sector and is being delivered through the public sector. It is entirely altruistic in its motivations; which activists find impossible to accept. So, the activists believed, suspicion against Golden Rice had to be amplified, Golden Rice had to be stopped: "If we lose the Golden Rice battle, we lose the GMO war."
Activism continues to this day. And any Environment Ministry, with no responsibility for public health or agriculture, and of course an interest in avoiding controversy about its regulatory decisions, is vulnerable to such activism.
The anti-GMO crop campaigns, and especially anti-Golden Rice campaigns, have been extraordinarily effective. If so much regulation by governments is required, surely there must be something to be suspicious about: 'There is no smoke without fire'. The suspicion pervades research institutions and universities, the publishers of scientific journals and The World Health Organisation, and UNICEF: even the most scientifically literate are fearful of entanglement in activist-stoked public controversy.
The equivalent of 13 jumbo jets full of children crashes into the ground every day and kills them all, because of VAD. Yet the solution of Golden Rice, developed by national scientists in the counties where VAD is endemic, is ignored because of fear of controversy, and because poor children's deaths can be ignored without controversy.
Perhaps more controversy lies in not taking scientifically based regulatory decisions than in taking them.
The tide is turning, however. 151 Nobel Laureates, a very significant proportion of all Nobel Laureates, have called on the UN, governments of the world, and Greenpeace to cease their unfounded vilification of GMO crops in general and Golden Rice in particular. A recent Golden Rice article commented, "What shocks me is that some activists continue to misrepresent the truth about the rice. The cynic in me expects profit-driven multinationals to behave unethically, but I want to think that those voluntarily campaigning on issues they care about have higher standards."
The recently published book has exposed the frustrating saga in simple detail. And the publicity from all the above is perhaps starting to change the balance of where controversy lies. Perhaps more controversy lies in not taking scientifically based regulatory decisions than in taking them.
But until they are taken, while there continues a chance of frustrating the objectives of the Golden Rice project, the antagonism will continue. And despite a solution so close at hand, VAD-induced death and blindness, and the misery of affected families, will continue also.
© The Authors 2019. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver applies to the data made available in this article, unless otherwise stated.
[Ed. Note: This is the third episode in our Moonshot series, which will explore four cutting-edge scientific developments that stand to fundamentally transform our world.]
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.