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.
The Best Coronavirus Experts to Follow on Twitter
As the coronavirus tears across the globe, the world's anxiety is at a fever-pitch, and we're all craving information to stay on top of the crisis.
But turning to the Internet for credible updates isn't as simple as it sounds, since we have an invisible foe spreading as quickly as the virus itself: misinformation. From wild conspiracy theories to baseless rumors, an infodemic is in full swing.
For the latest official information, you should follow the CDC, WHO, and FDA, in addition to your local public health department. But it's also helpful to pay attention to the scientists, doctors, public health experts and journalists who are sharing their perspectives in real time as new developments unfold. Here's a handy guide to get you started:
VIROLOGY
Dr. Trevor Bedford/@trvrb: Scientist at the Fred Hutchinson Cancer Research Center studying viruses, evolution and immunity.
Dr. Benhur Lee/@VirusWhisperer: Professor of microbiology at the Icahn School of Medicine at Mount Sinai
Dr. Angela Rasmussen/@angie_rasmussen: Virologist and associate research scientist at Columbia University
Dr. Florian Krammer/@florian_krammer: Professor of Microbiology at the Icahn School of Medicine at Mount Sinai
EPIDEMIOLOGY:
Dr. Alice Sim/@alicesim: Infectious disease epidemiologist and consultant at the World Health Organization
Dr. Tara C. Smith/@aetiology: Infectious disease specialist and professor at Kent State University
Dr. Caitlin Rivers/@cmyeaton: Epidemiologist and assistant professor at the Johns Hopkins Bloomberg School of Public Health
Dr. Michael Mina/@michaelmina_lab: Physician and Assistant Professor of Epidemiology & Immunology at the Harvard TH Chan School of Public Health
INFECTIOUS DISEASE:
Dr. Nahid Bhadelia/@BhadeliaMD: Infectious diseases physician and the medical director of Special Pathogens Unit at Boston University School of Medicine
Dr. Paul Sax/@PaulSaxMD: Clinical Director of the Division of Infectious Diseases at Brigham and Women's Hospital
Dr. Priya Sampathkumar/@PsampathkumarMD: Infectious Disease Specialist at the Mayo Clinic
Dr. Krutika Kuppalli/@KrutikaKuppalli: Medical doctor and Infectious Disease Specialist based in Palo Alto, CA
PANDEMIC PREP:
Dr. Syra Madad/@syramadad: Senior Director, System-wide Special Pathogens Program at New York City Health + Hospitals
Dr Sylvie Briand/@SCBriand: Director of Pandemic and Epidemic Diseases Department at the World Health Organization
Jeremy Konyndyk/@JeremyKonyndyk: Senior Policy Fellow at the Center for Global Development
Amesh Adalja/@AmeshAA: Senior Scholar at the Johns Hopkins University Center for Health Security
PUBLIC HEALTH:
Scott Becker/@scottjbecker: CEO of the Association of Public Health Laboratories
Dr. Scott Gottlieb/@ScottGottliebMD: Physician, former commissioner of the Food and Drug Administration
APHA Public Health Nursing/@APHAPHN: Public Health Nursing Section of the American Public Health Association
Dr. Tom Inglesby/@T_Inglesby: Director of the Johns Hopkins SPH Center for Health Security
Dr. Nancy Messonnier/@DrNancyM_CDC: Director of the Center for the National Center for Immunization and Respiratory Diseases (NCIRD)
Dr. Arthur Caplan/@ArthurCaplan: Professor of Bioethics at New York University Langone Medical Center
SCIENCE JOURNALISTS:
Laura Helmuth/@laurahelmuth: Incoming Editor in Chief of Scientific American
Helen Branswell/@HelenBranswell: Infectious disease and public health reporter at STAT
Sharon Begley/@sxbegle: Senior writer at STAT
Carolyn Johnson/@carolynyjohnson: Science reporter at the Washington Post
Amy Maxmen/@amymaxmen: Science writer and senior reporter at Nature
Laurie Garrett/@Laurie_Garrett: Pulitzer-prize winning science journalist, author of The Coming Plague, former senior fellow for global health at the Council on Foreign Relations
Soumya Karlamangla/@skarlamangla: Health writer at the Los Angeles Times
André Picard/@picardonhealth: Health Columnist, The Globe and Mail
Caroline Chen/@CarolineYLChen: Healthcare reporter at ProPublica
Andrew Jacobs/@AndrewJacobsNYT: Science reporter at the New York Times
Meg Tirrell/@megtirrell: Biotech and pharma reporter for CNBC
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.
One of the main factors that will influence the ultimate trajectory of the novel coronavirus pandemic will be the availability of a vaccine.
Vaccine development has traditionally been a process measured in years and even decades.
Vaccines are incontrovertibly the best means to control infectious diseases and there are no human vaccines against any of the (now) 7 known human coronaviruses. As soon as the gravity of this outbreak was recognized, several companies, along with governmental and non-governmental partners, have embarked on a rapid development program to develop a vaccine targeted at this virus.
Vaccine development has traditionally been a process measured in years and even decades as scientists tinker with a pathogen trying to weaken or dissemble it to render it capable of creating an effective immune response with acceptable levels of side effects. However, in 2020, powerful new vaccine technologies are available to augment traditional vaccine development and are responsible for the rapid delivery of a vaccine candidate for the start of clinical trials.
Vaccine Platforms: A Game-Changing Technology
The new technologies that are being harnessed are what are known as vaccine platform technologies. Vaccine platforms, as my colleagues and I wrote in a report assessing their promise, offer a means to use the same building blocks to make more than one vaccine. To slightly oversimply, a vaccine platform confers the ability to switch out the pathogen being targeted very rapidly, akin to changing a video game cartridge. Indeed, the recently FDA-licensed Ebola vaccine uses another virus as a platform with the requisite Ebola protein inserted.
Because of this rapid availability to utilize platforms for a variety of different targets, the initial development process can be significantly shortened. This is especially true for vaccines utilizing the genetic material of the target alone. These DNA and RNA vaccines basically can be "printed" once the genetic sequence of the target is known.
An RNA vaccine is the approach being used by the Cambridge-based biotech company Moderna – which took just 42 days to produce an experimental vaccine candidate. Clinical testing is expected to begin next month on 45 healthy volunteers.
Another biotech, the Pennsylvania-based Inovio, is using a DNA approach. In essence, such vaccines involve the genetic material being injected and translated into a viral protein by human cells, which then prompt the immune system to make antibodies.
There are other approaches as well. One company, the Maryland-based Novavax, will use nanoparticles, while another is attempting to adapt an orally administered avian coronavirus vaccine and Johnson & Johnson is using different virus platforms to deliver coronavirus proteins (similar to their experimental Ebola vaccine).
At this stage, it is important for all approaches to be on the table in the hope that at least one makes it through clinical trials. There also may be a need for different types of vaccines for different populations.
Vaccines Will Still Take Time
Despite the quick development time made possible by the use of vaccine platforms, clinical testing for safety, efficacy, and dosing schedules will still take months to complete. After this process, the vaccine will need to be mass produced in large quantities to vaccinate, basically, the world. So, for all intents and purposes, we cannot expect to see an approved vaccine for at least a year or maybe longer if everything does not go perfectly well in clinical trials.
Vaccine platform technologies offer a bright ray of hope in the bleak shadow of the pandemic.
Once a vaccine is available, it will likely appear in batches to be distributed to those at highest risk for severe disease, such as the elderly and those with underlying conditions, as well as healthcare workers, first. At this time, it appears children are less likely to experience severe illness and they may not be the first targets for the vaccine but, if this virus is with us (as is predicted), coronavirus vaccination could become part of routine childhood vaccinations.
Changing Pandemic Trajectory
Vaccination will not come fast enough to impact the initial wave of the novel virus which may continue until summer approaches in temperate climates. However, it will be a crucial tool to blunt the impact of a future appearance in the following respiratory virus season. This reappearance is all but assured as this virus has adeptly established itself in human populations and is behaving like the community-acquired coronavirus that it is.
A Glimmer of Hope
When looking at the trajectory of the virus, it can appear, thus far, that no public health effort has made a substantial impact on the spread of the virus. However, that trajectory will change with the advent of an efficacious vaccine. Such a vaccine, especially if conferring protection against other human coronaviruses, may result in coronaviruses being taken off the table of biological threats altogether in the future.
Vaccine platform technologies offer a bright ray of hope in the bleak shadow of the pandemic and, if successful, will change the way the world approaches future pandemic threats with more rapid deployment of platform-based vaccines.
Dr. Adalja is focused on emerging infectious disease, pandemic preparedness, and biosecurity. He has served on US government panels tasked with developing guidelines for the treatment of plague, botulism, and anthrax in mass casualty settings and the system of care for infectious disease emergencies, and as an external advisor to the New York City Health and Hospital Emergency Management Highly Infectious Disease training program, as well as on a FEMA working group on nuclear disaster recovery. Dr. Adalja is an Associate Editor of the journal Health Security. He was a coeditor of the volume Global Catastrophic Biological Risks, a contributing author for the Handbook of Bioterrorism and Disaster Medicine, the Emergency Medicine CorePendium, Clinical Microbiology Made Ridiculously Simple, UpToDate's section on biological terrorism, and a NATO volume on bioterrorism. He has also published in such journals as the New England Journal of Medicine, the Journal of Infectious Diseases, Clinical Infectious Diseases, Emerging Infectious Diseases, and the Annals of Emergency Medicine. He is a board-certified physician in internal medicine, emergency medicine, infectious diseases, and critical care medicine. Follow him on Twitter: @AmeshAA