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.
Scientists Used Fruit Flies to Quickly Develop a Personalized Cancer Treatment for a Dying Man
Imagine a man with colorectal cancer that has spread throughout his body. His tumor is not responding to traditional chemotherapy. He needs a radically effective treatment as soon as possible and there's no time to wait for a new drug or a new clinical trial.
A plethora of novel combinations of treatments can be screened quickly on as many as 400,000 flies at once.
This was the very real, and terrifying, situation of a recent patient at Mount Sinai Medical Center in New York City. So his doctors turned to a new tactic to speed up the search for a treatment that would save him: Fruit flies.
Yes, fruit flies. Those annoying little buggers that descend on opened food containers are actually leading scientists to fully personalized cancer treatments. Oncology advances often are more about about utilizing old drugs in new combinations than about adding new drugs. But classically, the development of each new chemotherapy drug combination has required studies involving numerous patients spread over many years or decades.
With the fruit fly method, however, a novel treatment -- in the sense that a particular combination of drugs and the timing of their administration has never been used before -- is developed for each patient, almost like on Star Trek, when, faced suddenly with an unknown disease, a futuristic physician researches it and develops a cure quickly enough to save the patient's life.
How It Works
Using genetic engineering techniques, researchers produce a population of fruit fly embryos, each of which is programmed to develop a replica of the patient's cancer.
Since a lot of genetically identical fly embryos can be created, and since they hatch from eggs within 30 hours and then mature within days, a plethora of novel combinations of treatments can be screened quickly on as many as 400,000 flies at once. Then, only the regimens that are effective are administered to the patient.
Biotech entrepreneur Laura Towart, CEO of the UK- and Ireland-based company, My Personal Therapeutics, is partnering with Mount Sinai to develop and test the fruit fly tactic. The researchers recently published a paper demonstrating that the tumor of the man with metastatic colorectal cancer had shrunk considerably following the treatment, and remained stable for 11 months, although he eventually succumbed to his illness.
Open Questions
Cancer is in fact many different diseases, even if it strikes two people in the same place, and both cancers look the same under a microscope. At the level of DNA, RNA, proteins, and other molecular factors, each cancer is unique – and may require a unique treatment approach.
Determining the true impact on cancer mortality will require clinical trials involving many more patients.
"Anatomy of a cancer still plays a major role, if you're a surgeon or radiation oncologist, but the medical approach to cancer therapy is moving toward treatments that are personalized based on other factors," notes Dr. Howard McLeod, an internationally recognized expert on cancer genetics at the Moffitt Cancer Center, in Tampa, Florida. "We are also headed into an era when even the methods for monitoring patients are individualized."
One big unresolved question about the fruit fly screening approach is how effective it will be in terms of actually extending life. Determining the true impact on cancer mortality will require clinical trials involving many more patients.
Next Up
Using machine learning and artificial intelligence, Towart is now working to build a service called TuMatch that will offer rapid and affordable personalized treatment recommendations for all genetically driven cancers. "We hope to have TuMatch available to patients with colorectal/GI cancers by January 2020," she says. "We are also offering [the fruit fly approach] for patients with rare genetic diseases and for patients who are diabetic."
Are Towart's fruit flies the answer to why the man's tumor shrunk? To be sure, the definitive answer will come from further research that is expected soon, but it's also clear that, prior to the treatment, there was nothing left to do for that particular patient. Thus, although it's early in the game, there's a pretty good rationale for optimism.
A Million Patients Have Innovated Their Own Medical Solutions, And Doctors Are Terrified
In the fall of 2017, patient advocate Renza Scibilia told a conference of endocrinologists in Australia about new, patient-developed artificial pancreas technology that helped her manage her Type 1 diabetes.
"Because it's not a regulated product, some [doctors] were worried and said 'What if it goes wrong?'"
"They were in equal measure really interested and really scared," recalled Scibilia. "Because it's not a regulated product, some were worried and said 'What if it goes wrong? What is my liability going to be?'"
That was two years ago. Asked if physicians have been more receptive to the same "looping" technology now that its benefits have been supported by considerable data (as Leapsmag pointed out in May), Scibilia said, "No. Clinicians are still really insecure. They're always going to be reluctant to accept consumer-driven technology."
This exemplifies a major challenge to the growing Do-It-Yourself (DIY) biohealth movement: physicians are unnerved and worried about innovations developed by patients and other consumers that haven't been tested in elaborate clinical trials or sanctioned by regulatory authorities.
"It's difficult for patients who develop new health technology to demonstrate the advantage in a way that physicians would accept." said Howard DeMonaco, visiting scientist at MIT's Sloan School of Management. "New approaches to the treatment of diseases are by definition suspect to clinicians. Most are risk averse unless there is a substantial advantage to the new approach and the risks in doing so appear to be minimized."
Nevertheless, the DIY biohealth movement is booming. About a million people reported that they created medical innovations to address their own medical needs in surveys conducted from 2010-2015 in the U.S., U.K., Finland, Canada and South Korea.
Add in other DIY health innovations created in homes, community biolabs and "Maker" health fairs, and it's clear that health care providers are increasingly confronted with medical devices, information technology, and even medications that were developed in unconventional settings and lack the blessing of regulatory authorities.
Researchers in Portugal have tried to spread the word about many of these solutions on the Patent Innovations website, which has more than 500 examples, ranging from a 3-D printed arm and hand to a sensor device that warns someone when an osteomy bag is full.
When Reddit asked medical professionals, "What is the craziest DIY health treatment you've seen a patient attempt?" thousands shared horror stories.
But even in this era of patient empowerment, more widespread use of DIY health solutions still depends upon the approval and cooperation of physicians, nurses and other caregivers. And health care providers still lack awareness of promising patient-developed innovations, according to Dr. Joyce Lee, a pediatric endocrinologist at the University of Michigan who advocates involving patients in the design of healthcare technology. "Most physicians are scared of what they don't know," she said.
They're also understandably worried about patients who don't know what they're doing and make irresponsible decisions. When Reddit asked medical professionals, "What is the craziest DIY health treatment you've seen a patient attempt?" thousands shared horror stories, including a man who poked a hole in his belly button with a knitting needle to relieve gas.
Yet DeMonaco and Lee think it's possible to start bridging the gaps between responsible patient innovators and skeptical doctors as well as unprepared regulatory systems.
One obstacle to consumer-driven health innovations is that clinical trials to prove their safety and effectiveness are expensive and time-consuming, as De Monaco points out in a recent article. He and his colleagues suggested that low-cost clinical trials by and for patients could help address this challenge. They urged patients to publish their own research and detail the impact of innovations on their own health, and create databases that incorporate the findings of other patients.
For example, Adam Brown, who has Type 1 diabetes, compared the effects of low and high carbohydrate diets on his blood sugar management, and conveyed the results in an online journal. "Sharing the information allowed others to copy the experiment," the article noted, suggesting that this could be a model to create multi-patient trials that could be "analyzed by expert patients and/or by professionals."
Asked how to convince health care providers to consider such research, DeMonaco cited the example of doctors prescribing "off label" drugs for purposes that aren't approved by the FDA. "The secret to off label use, like any other user innovation, is dissemination," he said. Sharing case reports and other low-cost research serves to disseminate the information "in a way that is comfortable for physicians," he said, and urged patient innovators to take the same approach.
The FDA regulates commercial products and has no authority if consumers want to use medical devices, medications, or information systems that they find on their own.
Physicians should also be encouraged to engage in patient-driven research, said Dr. Lee. She suggests forming "maker spaces in which patients and physicians are involved in designing personalized technology for chronic diseases. In my vision, patient peers would build, iterate, and learn from each other and the doctor would be part of the team, constantly assessing and evaluating the technology and facilitating the process."
Some kind of regulatory oversight of DIY health technology is also necessary, said Todd Kuiken, senior research scholar at NC State and former principal investigator at the Woodrow Wilson Center's Synthetic Biology Project.
The FDA regulates commercial products and has no authority if consumers want to use medical devices, medications, or information systems that they find on their own. But that doesn't stop regulators from worrying about patients who use them. For example, the FDA issued a warning about diabetes looping technology earlier this year after one diabetic was hospitalized with hypoglycemia.
Kuiken, for one, believes that citizen-driven innovation requires oversight "to move forward." He suggested that Internal Review Boards, with experts on medical technology, safety and ethics, could play a helpful role in validating the work of patient innovators and others engaged in DIY health research. "As people are developing health products, there would be experts available to take a look and check in," he said.
Kuiken pointed out that in native American territories, tribally based IRBs working with the national Indian Health Services help to oversee new health science research. The model could be applied more broadly.
He also offered hope to those who want to integrate the current health regulatory structure into the ecosystem of DIY health innovations. "I didn't expect people from the FDA or NIH to show up" he said about a workshop on citizen-driven biomedical research that he helped organize at the Wilson Center last year. But senior officials from both agencies attended.
He indicated they "were open to new ideas." While he wouldn't disclose contributions made by individual participants in the workshop, he said the government staffers were "very interested in figuring out how to engage with citizen health innovators, to build bridges with the DIY community."
"Why should we wait for regulatory bodies? Why wait for trials that take too long?"
Time will tell whether those bridges will be built quickly enough to increase the comfort of physicians with health innovations developed by patients and other consumers. In the meantime, DIY health innovators like patient advocate Scibilia are undeterred.
"Why should we wait for regulatory bodies?" she asked. "Why wait for trials that take too long? There are plenty of data out there indicating the [diabetes looping] technology works. So we're just going to do it. We're not waiting."