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.
BREAKING: The First U.S. Test to Detect If a Person Has Potential Immunity to COVID-19 Was Just Developed
While testing for COVID-19 ramps up around the country, there's another kind of testing that will prove equally important to combating the pandemic: one that can detect whether someone has already been infected.
"The idea is that this assay can be established anywhere in the world following these steps."
Why is this important? As former FDA commissioner Scott Gottlieb wrote in today's Wall Street Journal: "If a sizable portion of a local community has some protection, authorities can be more confident in relying less on invasive measures. Once deployed, serological tests are cheap, straightforward, and easy to scale."
Now, a microbiology lab at the Icahn School of Medicine at Mount Sinai, led by Dr. Florian Krammer, has just announced the development of this serological test. Leapsmag spoke with Daniel Stadlbauer, a post-doctoral fellow in the lab who helped lead the work.
Is yours the first serological test available?
They did something similar in South Korea. In the U.S., it's the first of these tests.
How close are we to rolling this test out to the public?
Last week, we started this process and we finished the protocol today. Mount Sinai is trying to roll this out in the next few days in the clinic to see which patients have been infected with coronavirus recently or have been infected at all.
The protocol we uploaded today can be used as a template for other research labs or hospitals to follow the steps we provided and they should then be able to set up the antibody test. The idea is that this assay can be established anywhere in the world following these steps.
Are there any bottlenecks to getting this rolled out – supply chain or regulation obstacles?
There are no regulations that say you can't do it. Research labs and hospitals for sure can do it. I'm not aware of supply chain issues because you need basic lab equipment and materials, but I don't think those are in short supply right now.
How does the test work?
People coming to the hospital who are suspected to have infection with coronavirus, their blood gets taken routinely. This blood can be used for our test, too. The test will tell you if this person has antibodies against coronavirus. You can also test the blood of people who are not currently sick to see if this person was infected, say, a month ago. If there are antibodies in the blood, you can say this person is probably immune to getting it again.
It will be essential workers who need to be tested first, like nurses, firefighters, and doctors. It will be great to know that they would not put themselves or others at risk by going back to work because they cannot spread the disease.
"People probably cannot get reinfected once they mount a good immune response and have good antibody levels."
How soon after infection does the test detect if you have antibodies?
Usually after 7 days of infection.
How long do the antibodies last to confer immunity?
Those studies need to be done – right now it's unclear. People probably cannot get reinfected once they mount a good immune response and have good antibody levels. How long those level last still needs to be investigated. But they won't get reinfected in the next, I would say, six months.
How accurate is the test?
Very accurate. The advantage – which is bad for us but good for the test – is that humans have no baseline immunity to this coronavirus. It means that when you have not been infected, you have pretty much no antibodies, which is why it can spread so easily. But once you have antibodies in your blood, we can detect them and it's a clear difference between antibodies or no antibodies.
Where should hospitals and labs go for more information on how to build their own tests from your work?
They should check out our lab website to find the detailed protocol to download.
If I am a person who just wants to take this test to find out if I've already been infected, what should I do?
It will be done soon in the clinical setting. I don't know yet how widely it will be available. The more research labs and hospitals that set up this testing, the more people who can be tested in the future.
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.
Blood Donated from Recovered Coronavirus Patients May Soon Yield a Stopgap Treatment
In October 1918, Lieutenant L.W. McGuire of the United States Navy sent a report to the American Journal of Public Health detailing a promising therapy that had already saved the lives of a number of officers suffering from pneumonia complications due to the Spanish influenza outbreak.
"These antibodies then become essentially drugs."
McGuire described how transfusions of blood from recovered patients – an idea which had first been trialed during a polio epidemic in 1916 – had led to rapid recovery in a series of severe pneumonia cases at a Naval Hospital in Massachusetts. "It is believed the serum has a decided influence in shortening the course of the disease, and lowering the mortality," he wrote.
Now more than a century on, this treatment – long forgotten in the western world - is once again coming to the fore during the current COVID-19 pandemic. With fatalities continuing to rise, and no vaccine expected for many months, experts are urging medical centers across the U.S. and Europe to initiate collaborations between critical care and transfusion services to offer this as an emergency treatment for those who need it most.
As of March 20, there are more than 90,000 individuals globally who have recovered from the disease. Some scientists believe that the blood of many of these people contains high levels of neutralizing antibodies that can kill the virus.
"These antibodies then become essentially drugs," said Arturo Casadevall, professor of Molecular Microbiology & Immunology at John Hopkins Bloomberg School of Public Health, who is currently co-ordinating a clinical trial of convalescent serum for COVID-19 involving 20 institutions across the US.
"We're talking about preparing a therapy right out of the serum of those that have recovered. It could also be used in patients who are already sick, but have not progressed to respiratory failure, to treat them before they enter intensive care units. That will provide a lot of support because there's a limited number of respirators and resources."
The first conclusive data on how the blood of recovered patients can help tackle COVID-19 is set to come out of China, where it was also used as an emergency treatment during the SARS and MERS outbreaks. On February 9, a severely ill patient in Wuhan was treated with convalescent serum and since then, hospitals across China have used the therapy on a total of 245 patients, with 91 reportedly showing an improvement in symptoms.
In China alone, more than 58,000 patients have now recovered from COVID-19. Casadevall said that last week the country shipped 90 tons of serum and plasma from these patients to Italy – the center of the pandemic in Europe – for emergency use.
Some of the first people to be treated are likely to be doctors and nurses in hospitals who are most at risk of exposure.
A current challenge, however, is that the blood donation from the recovered patients must be precisely timed in order to maximize the number of antibodies a future patient receives. Doctors in China say that obtaining the necessary blood samples at the right time is one of the major barriers to applying the treatment on a larger scale.
"It's difficult to get the donations," said Dr. Yuan Shi of Chongqing Medical University. "When patients have recovered from the disease, we would like to collect their blood two to four weeks afterwards. We try our best to call back the patients, but it's sometimes difficult to get them to come back within that time period."
Because of such hurdles, Japan's largest drugmaker, Takeda Pharmaceuticals, is now working to turn neutralizing antibodies from recovered COVID-19 patients into a standardized drug product. They hope to launch a clinical trial for this in the next few months.
In the U.S., Casadevall hopes blood transfusions from recovered patients can become clinically available as a therapy within the next four weeks, once regulatory approval has been received. Some of the first people to be treated are likely to be doctors and nurses in hospitals who are most at risk of exposure, to provide a protective boost in their immunity.
"A lot of healthcare workers in the U.S. have already been asked to quarantine, and you can imagine what effect that's going to have on the healthcare system," he said. "It can't take large numbers of people staying home; there's not the capacity."
But not all medical experts are convinced it's the way to go, especially when it comes to the most severe cases of COVID-19. "There's no knowing whether that treatment would be useful or not," warned Dr. Andrew Freedman, head of Cardiff University's School of Medicine in the U.K.
"There are going to be better things available in a few months, but we are facing, 'What do you do now?'"
However, Casadevall says that the treatment is not envisioned as a panacea to treating coronavirus, but simply a temporary measure which could give doctors some options until stronger options such as vaccines or new drugs are available.
"This is a stopgap option," he said. "There are going to be better things available in a few months, but we are facing, 'What do you do now?' The only thing we can offer severely ill people at the moment is respiratory support and oxygen, and we don't have anything to prevent those exposed from going on and getting ill."