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.
Harvard Researchers Are Using a Breakthrough Tool to Find the Antibodies That Best Knock Out the Coronavirus
To find a cure for a deadly infectious disease in the 1995 medical thriller Outbreak, scientists extract the virus's antibodies from its original host—an African monkey.
"When a person is infected, the immune system makes antibodies kind of blindly."
The antibodies prevent the monkeys from getting sick, so doctors use these antibodies to make the therapeutic serum for humans. With SARS-CoV-2, the original hosts might be bats or pangolins, but scientists don't have access to either, so they are turning to the humans who beat the virus.
Patients who recovered from COVID-19 are valuable reservoirs of viral antibodies and may help scientists develop efficient therapeutics, says Stephen J. Elledge, professor of genetics and medicine at Harvard Medical School in Boston. Studying the structure of the antibodies floating in their blood can help understand what their immune systems did right to kill the pathogen.
When viruses invade the body, the immune system builds antibodies against them. The antibodies work like Velcro strips—they use special spots on their surface called paratopes to cling to the specific spots on the viral shell called epitopes. Once the antibodies circulating in the blood find their "match," they cling on to the virus and deactivate it.
But that process is far from simple. The epitopes and paratopes are built of various peptides that have complex shapes, are folded in specific ways, and may carry an electrical charge that repels certain molecules. Only when all of these parameters match, an antibody can get close enough to a viral particle—and shut it out.
So the immune system forges many different antibodies with varied parameters in hopes that some will work. "When a person is infected, the immune system makes antibodies kind of blindly," Elledge says. "It's doing a shotgun approach. It's not sure which ones will work, but it knows once it's made a good one that works."
Elledge and his team want to take the guessing out of the process. They are using their home-built tool VirScan to comb through the blood samples of the recovered COVID-19 patients to see what parameters the efficient antibodies should have. First developed in 2015, the VirScan has a library of epitopes found on the shells of viruses known to afflict humans, akin to a database of criminals' mug shots maintained by the police.
Originally, VirScan was meant to reveal which pathogens a person overcame throughout a lifetime, and could identify over 1,000 different strains of viruses and bacteria. When the team ran blood samples against the VirScan's library, the tool would pick out all the "usual suspects." And unlike traditional blood tests called ELISA, which can only detect one pathogen at a time, VirScan can detect all of them at once. Now, the team has updated VirScan with the SARS-CoV-2 "mug shot" and is beginning to test which antibodies from the recovered patients' blood will bind to them.
Knowing which antibodies bind best can also help fine-tune vaccines.
Obtaining blood samples was a challenge that caused some delays. "So far most of the recovered patients have been in China and those samples are hard to get," Elledge says. It also takes a person five to 10 days to develop antibodies, so the blood must be drawn at the right time during the illness. If a person is asymptomatic, it's hard to pinpoint the right moment. "We just got a couple of blood samples so we are testing now," he said. The team hopes to get some results very soon.
Elucidating the structure of efficient antibodies can help create therapeutics for COVID-19. "VirScan is a powerful technology to study antibody responses," says Harvard Medical School professor Dan Barouch, who also directs the Center for Virology and Vaccine Research. "A detailed understanding of the antibody responses to COVID-19 will help guide the design of next-generation vaccines and therapeutics."
For example, scientists can synthesize antibodies to specs and give them to patients as medicine. Once vaccines are designed, medics can use VirScan to see if those vaccinated again COVID-19 generate the necessary antibodies.
Knowing which antibodies bind best can also help fine-tune vaccines. Sometimes, viruses cause the immune system to generate antibodies that don't deactivate it. "We think the virus is trying to confuse the immune system; it is its business plan," Elledge says—so those unhelpful antibodies shouldn't be included in vaccines.
More importantly, VirScan can also tell which people have developed immunity to SARS-CoV-2 and can return to their workplaces and businesses, which is crucial to restoring the economy. Knowing one's immunity status is especially important for doctors working on the frontlines, Elledge notes. "The resistant ones can intubate the sick."
Lina Zeldovich has written about science, medicine and technology for Popular Science, Smithsonian, National Geographic, Scientific American, Reader’s Digest, the New York Times and other major national and international publications. A Columbia J-School alumna, she has won several awards for her stories, including the ASJA Crisis Coverage Award for Covid reporting, and has been a contributing editor at Nautilus Magazine. In 2021, Zeldovich released her first book, The Other Dark Matter, published by the University of Chicago Press, about the science and business of turning waste into wealth and health. You can find her on http://linazeldovich.com/ and @linazeldovich.
As countries around the world combat the coronavirus outbreak, governments that already operated sophisticated surveillance programs are ramping up the tracking of their citizens.
"The potential for invasions of privacy, abuse, and stigmatization is enormous."
Countries like China, South Korea, Israel, Singapore and others are closely monitoring citizens to track the spread of the virus and prevent further infections, and policymakers in the United States have proposed similar steps. These shifts in policy have civil liberties defenders alarmed, as history has shown increases in surveillance tend to stick around after an emergency is over.
In China, where the virus originated and surveillance is already ubiquitous, the government has taken measures like having people scan a QR code and answer questions about their health and travel history to enter their apartment building. The country has also increased the tracking of cell phones, encouraged citizens to report people who appear to be sick, utilized surveillance drones, and developed facial recognition that can identify someone even if they're wearing a mask.
In Israel, the government has begun tracking people's cell phones without a court order under a program that was initially meant to counter terrorism. Singapore has also been closely tracking people's movements using cell phone data. In South Korea, the government has been monitoring citizens' credit card and cell phone data and has heavily utilized facial recognition to combat the spread of the coronavirus.
Here at home, the United States government and state governments have been using cell phone data to determine where people are congregating. White House senior adviser Jared Kushner's task force to combat the coronavirus outbreak has proposed using cell phone data to track coronavirus patients. Cities around the nation are also using surveillance drones to maintain social distancing orders. Companies like Apple and Google that work closely with the federal government are currently developing systems to track Americans' cell phones.
All of this might sound acceptable if you're worried about containing the outbreak and getting back to normal life, but as we saw when the Patriot Act was passed in 2001 in the wake of the 9/11 terrorist attacks, expansions of the surveillance state can persist long after the emergency that seemed to justify them.
Jay Stanley, senior policy analyst with the ACLU Speech, Privacy, and Technology Project, says that this public health emergency requires bold action, but he worries that actions may be taken that will infringe on our privacy rights.
"This is an extraordinary crisis that justifies things that would not be justified in ordinary times, but we, of course, worry that any such things would be made permanent," Stanley says.
Stanley notes that the 9/11 situation was different from this current situation because we still face the threat of terrorism today, and we always will. The Patriot Act was a response to that threat, even if it was an extreme response. With this pandemic, it's quite possible we won't face something like this again for some time.
"We know that for the last seven or eight decades, we haven't seen a microbe this dangerous become a pandemic, and it's reasonable to expect it's not going to be happening for a while afterward," Stanley says. "We do know that when a vaccine is produced and is produced widely enough, the COVID crisis will be over. This does, unlike 9/11, have a definitive ending."
The ACLU released a white paper last week outlining the problems with using location data from cell phones and how policymakers should proceed when they discuss the usage of surveillance to combat the outbreak.
"Location data contains an enormously invasive and personal set of information about each of us, with the potential to reveal such things as people's social, sexual, religious, and political associations," they wrote. "The potential for invasions of privacy, abuse, and stigmatization is enormous. Any uses of such data should be temporary, restricted to public health agencies and purposes, and should make the greatest possible use of available techniques that allow for privacy and anonymity to be protected, even as the data is used."
"The first thing you need to combat pervasive surveillance is to know that it's occurring."
Sara Collins, policy counsel at the digital rights organization Public Knowledge, says that one of the problems with the current administration is that there's not much transparency, so she worries surveillance could be increased without the public realizing it.
"You'll often see the White House come out with something—that they're going to take this action or an agency just says they're going to take this action—and there's no congressional authorization," Collins says. "There's no regulation. There's nothing there for the public discourse."
Collins says it's almost impossible to protect against infringements on people's privacy rights if you don't actually know what kind of surveillance is being done and at what scale.
"I think that's very concerning when there's no accountability and no way to understand what's actually happening," Collins says. "The first thing you need to combat pervasive surveillance is to know that it's occurring."
We should also be worried about corporate surveillance, Collins says, because the tech companies that keep track of our data work closely with the government and do not have a good track record when it comes to protecting people's privacy. She suspects these companies could use the coronavirus outbreak to defend the kind of data collection they've been engaging in for years.
Collins stresses that any increase in surveillance should be transparent and short-lived, and that there should be a limit on how long people's data can be kept. Otherwise, she says, we're risking an indefinite infringement on privacy rights. Her organization will be keeping tabs as the crisis progresses.
It's not that we shouldn't avail ourselves of modern technology to fight the pandemic. Indeed, once lockdown restrictions are gradually lifted, public health officials must increase their ability to isolate new cases and trace, test, and quarantine contacts.
But tracking the entire populace "Big Brother"-style is not the ideal way out of the crisis. Last week, for instance, a group of policy experts -- including former FDA Commissioner Scott Gottlieb -- published recommendations for how to achieve containment. They emphasized the need for widespread diagnostic and serologic testing as well as rapid case-based interventions, among other measures -- and they, too, were wary of pervasive measures to follow citizens.
The group wrote: "Improved capacity [for timely contact tracing] will be most effective if coordinated with health care providers, health systems, and health plans and supported by timely electronic data sharing. Cell phone-based apps recording proximity events between individuals are unlikely to have adequate discriminating ability or adoption to achieve public health utility, while introducing serious privacy, security, and logistical concerns."
The bottom line: Any broad increases in surveillance should be carefully considered before we go along with them out of fear. The Founders knew that privacy is integral to freedom; that's why they wrote the Fourth Amendment to protect it, and that right shouldn't be thrown away because we're in an emergency. Once you lose a right, you don't tend to get it back.