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.
“Jurassic Park Without the Scary Parts” Is Actually Happening
[Editor's Note: This video is the first of a five-part series titled "The Future Is Now: The Revolutionary Power of Stem Cell Research." Produced in partnership with the Regenerative Medicine Foundation, and filmed at the annual 2019 World Stem Cell Summit, this series illustrates how stem cell research will profoundly impact life on earth. A new video will be published every Monday this month.]
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.
Forcing Vaccination on Every Child Undermines Civil Liberties
[Editor's Note: This opinion essay is in response to our current Big Question, which we posed to experts with different viewpoints: "Where should society draw the line between requiring vaccinations for children and allowing parental freedom of choice?"]
Our children are the future. The survival of humanity is advanced by the biological imperative that mothers and fathers want and need to protect their children and other children from being harmed for any reason.
Science is not perfect, doctors are not infallible, and medical interventions come with risks.
In the 21st century, consensus science considers vaccination to be one of the greatest inventions in the history of medicine and the greatest achievement of public health programs. The national vaccination rate for U.S. kindergarten children is 94 percent and most children today receive 69 doses of 16 federally recommended vaccines. However, public health is not simply measured by high vaccination rates and absence of infectious disease, which is evidenced by the chronic inflammatory disease and disability epidemic threatening to bankrupt the U.S. health care system.
Science is not perfect, doctors are not infallible, and medical interventions come with risks, which is why parents have the power to exercise informed consent to medical risk taking on behalf of their minor children.
As a young mother, I learned that vaccine risks are 100 percent for some children because, while we are all born equal under the law, we are not born all the same. Each one of us enters this world with different genes, a unique microbiome and epigenetic influences that affect how we respond to the environments in which we live. We do not all respond the same way to infectious diseases or to pharmaceutical products like vaccines.
Few parents were aware of vaccine side effects in 1980, when my bright, healthy two-and-a-half year-old son, Chris, suffered a convulsion, collapse, and state of unconsciousness (encephalopathy) within hours of his fourth DPT shot, and then regressed physically, mentally and emotionally and became a totally different child. Chris was eventually diagnosed with multiple learning disabilities and confined to a special education classroom throughout his public school education, but he and I both know his vaccine reaction could have been much worse. Today, Chris is an independent adult but many survivors of brain injury are not.
Barbara Loe Fisher and her son, Chris, in December 1981 after his fourth DPT shot.
(Courtesy Fisher)
The public conversation about several hundred cases of measles reported in the U.S. this year is focused on whether every parent has a social obligation to vaccinate every child to maintain "community immunity," but vaccine failures are rarely discussed. Emerging science reveals that there are differences in naturally and vaccine acquired immunity, and both vaccinated and unvaccinated children and adults transmit infections, sometimes with few or no symptoms.
Nearly 40 percent of cases reported in the 2015 U.S. measles outbreak occurred in recently vaccinated individuals who developed vaccine reactions that appeared indistinguishable from measles. Outbreaks of pertussis (whooping cough) in highly vaccinated child populations have been traced to waning immunity and evolution of the B. pertussis microbe to evade the vaccines. Influenza vaccine effectiveness was less than 50 percent in 11 of the past 15 flu seasons.
Vaccine policymakers recognize that children with severe combined immune deficiency or those undergoing chemotherapy or organ transplants are at increased risk for complications of infectious diseases and vaccines. However, there is no recognition of the risks to healthy infants and children with unidentified susceptibility to vaccine reactions, including children whose health suddenly deteriorates without explanation after vaccination. Medical care is being denied to children and adults in the U.S. if even one government recommended vaccination is declined, regardless of health or vaccine reaction history.
When parents question the risks and failures of a commercial pharmaceutical product being mandated for every child, the answer is not more force but better science and respect for the informed consent ethic.
The social contract we have with each other when we live in communities, whether we belong to the majority or a minority, is to care about and protect every individual living in the community. One-size-fits-all vaccine policies and laws, which fail to respect biodiversity and force everyone to be treated the same, place an unequal risk burden on a minority of unidentified individuals unable to survive vaccination without being harmed.
A law that requires certain minorities to bear a greater risk of injury or sacrifice their lives in service to the majority is not just or moral.
Between 1991 and 2013, the Institute of Medicine (IOM) published reports documenting that vaccines can cause brain inflammation and other serious reactions, injuries and death. A 2012 IOM report acknowledged that there are genetic, biological, and environmental risk factors that make some individuals more susceptible to adverse responses to vaccines but often doctors cannot identify who they are because of gaps in vaccine science. Congress acknowledged this fact a quarter century earlier in the 1986 National Childhood Vaccine Injury Act, which created a federal vaccine injury compensation program alternative to a lawsuit that has awarded more than $4 billion to vaccine-injured children and adults.
We give up the human right to autonomy and informed consent at our peril, no matter where or in what century we live.
Vaccine manufacturers and administrators have liability protection, yet today almost no health condition qualifies for a medical vaccine exemption under government guidelines. Now, there is a global call by consensus science advocates for elimination of all personal belief vaccine exemptions and censorship of books and public conversations that criticize vaccine safety or government vaccine policy. Some are calling for quarantine of all who refuse vaccinations and criminal prosecution, fines and imprisonment of parents with unvaccinated children, as well as punishment of doctors who depart from government policy.
There is no civil liberty more fundamentally a natural, inalienable right than exercising freedom of thought and conscience when deciding when and for what reason we are willing to risk our life or our child's life. That is why voluntary, informed consent to medical risk-taking has been defined as a human right governing the ethical practice of modern medicine.
In his first Presidential inaugural address, Thomas Jefferson warned:
"All, too, will bear in mind this sacred principle, that though the will of the majority is in all cases to prevail, that will to be rightful must be reasonable; that the minority posses their equal rights, which equal law must protect, and to violate would be oppression."
The seminal 1905 U.S. Supreme Court decision, Jacobson v. Massachusetts, affirmed the constitutional authority of states to enact mandatory smallpox vaccination laws. However, the justices made it clear that implementation of a vaccination law should not become "cruel and inhuman to the last degree." They warned, "All laws, this court has said, should receive a sensible construction. General terms should be so limited in their application as not to lead to injustice, oppression, or an absurd consequence. It will always, therefore, be presumed that the legislature intended exceptions to its language, which would avoid results of this character."
Mothers and fathers, who know and love their children better than anyone else, depend upon sound science and compassionate public health policies to help them protect their own and other children from harm. If individuals susceptible to vaccine injury cannot be reliably identified, the accuracy of vaccine benefit and risk calculations must be reexamined. Yet, consensus science and medicine around vaccination discourages research into the biological mechanisms of vaccine injury and death and identification of individual risk factors to better inform public health policy.
A critic of consensus science, physician and author Michael Crichton said, "Let's be clear: the work of science has nothing whatever to do with consensus. Consensus is the business of politics. Period."
Condoning elimination of civil liberties, including freedom of speech and the right to dissent guaranteed under the First Amendment of the U.S. Constitution, to enforce vaccination creates a slippery slope. Coercion, punishment and censorship will destroy, not instill, public trust in the integrity of medical practice and public health laws.
There are more than a dozen new vaccines being fast tracked to market by industry and governments. Who in society should be given the power to force all children to use every one of them without parental consent regardless of how small or great the risk?
We give up the human right to autonomy and informed consent at our peril, no matter where or in what century we live. Just and compassionate public health laws that protect parental and human rights will include flexible medical, religious and conscientious belief vaccine exemptions to affirm the informed consent ethic and prevent discrimination against vulnerable minorities.
[Editor's Note: Read the opposite viewpoint here.]