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 Death Predictor: A Helpful New Tool or an Ethical Morass?
Whenever Eric Karl Oermann has to tell a patient about a terrible prognosis, their first question is always: "how long do I have?" Oermann would like to offer a precise answer, to provide some certainty and help guide treatment. But although he's one of the country's foremost experts in medical artificial intelligence, Oermann is still dependent on a computer algorithm that's often wrong.
Doctors are notoriously terrible at guessing how long their patients will live.
Artificial intelligence, now often called deep learning or neural networks, has radically transformed language and image processing. It's allowed computers to play chess better than the world's grand masters and outwit the best Jeopardy players. But it still can't precisely tell a doctor how long a patient has left – or how to help that person live longer.
Someday, researchers predict, computers will be able to watch a video of a patient to determine their health status. Doctors will no longer have to spend hours inputting data into medical records. And computers will do a better job than specialists at identifying tiny tumors, impending crises, and, yes, figuring out how long the patient has to live. Oermann, a neurosurgeon at Mount Sinai, says all that technology will allow doctors to spend more time doing what they do best: talking with their patients. "I want to see more deep learning and computers in a clinical setting," he says, "so there can be more human interaction." But those days are still at least three to five years off, Oermann and other researchers say.
Doctors are notoriously terrible at guessing how long their patients will live, says Nigam Shah, an associate professor at Stanford University and assistant director of the school's Center for Biomedical Informatics Research. Doctors don't want to believe that their patient – whom they've come to like – will die. "Doctors over-estimate survival many-fold," Shah says. "How do you go into work, in say, oncology, and not be delusionally optimistic? You have to be."
But patients near the end of life will get better treatment – and even live longer – if they are overseen by hospice or palliative care, research shows. So, instead of relying on human bias to select those whose lives are nearing their end, Shah and his colleagues showed that they could use a deep learning algorithm based on medical records to flag incoming patients with a life expectancy of three months to a year. They use that data to indicate who might need palliative care. Then, the palliative care team can reach out to treating physicians proactively, instead of relying on their referrals or taking the time to read extensive medical charts.
But, although the system works well, Shah isn't yet sure if such indicators actually get the appropriate patients into palliative care. He's recently partnered with a palliative care doctor to run a gold-standard clinical trial to test whether patients who are flagged by this algorithm are indeed a better match for palliative care.
"What is effective from a health system perspective might not be effective from a treating physician's perspective and might not be effective from the patient's perspective," Shah notes. "I don't have a good way to guess everybody's reaction without actually studying it." Whether palliative care is appropriate, for instance, depends on more than just the patient's health status. "If the patient's not ready, the family's not ready and the doctor's not ready, then you're just banging your head against the wall," Shah says. "Given limited capacity, it's a waste of resources" to put that person in palliative care.
The algorithm isn't perfect, but "on balance, it leads to better decisions more often."
Alexander Smith and Sei Lee, both palliative care doctors, work together at the University of California, San Francisco, to develop predictions for patients who come to the hospital with a complicated prognosis or a history of decline. Their algorithm, they say, helps decide if this patient's problems – which might include diabetes, heart disease, a slow-growing cancer, and memory issues – make them eligible for hospice. The algorithm isn't perfect, they both agree, but "on balance, it leads to better decisions more often," Smith says.
Bethany Percha, an assistant professor at Mount Sinai, says that an algorithm may tell doctors that their patient is trending downward, but it doesn't do anything to change that trajectory. "Even if you can predict something, what can you do about it?" Algorithms may be able to offer treatment suggestions – but not what specific actions will alter a patient's future, says Percha, also the chief technology officer of Precise Health Enterprise, a product development group within Mount Sinai. And the algorithms remain challenging to develop. Electronic medical records may be great at her hospital, but if the patient dies at a different one, her system won't know. If she wants to be certain a patient has died, she has to merge social security records of death with her system's medical records – a time-consuming and cumbersome process.
An algorithm that learns from biased data will be biased, Shah says. Patients who are poor or African American historically have had worse health outcomes. If researchers train an algorithm on data that includes those biases, they get baked into the algorithms, which can then lead to a self-fulfilling prophesy. Smith and Lee say they've taken race out of their algorithms to avoid this bias.
Age is even trickier. There's no question that someone's risk of illness and death goes up with age. But an 85-year-old who breaks a hip running a marathon should probably be treated very differently than an 85-year-old who breaks a hip trying to get out of a chair in a dementia care unit. That's why the doctor can never be taken out of the equation, Shah says. Human judgment will always be required in medical care and an algorithm should never be followed blindly, he says.
Experts say that the flaws in artificial intelligence algorithms shouldn't prevent people from using them – carefully.
Researchers are also concerned that their algorithms will be used to ration care, or that insurance companies will use their data to justify a rate increase. If an algorithm predicts a patient is going to end up back in the hospital soon, "who's benefitting from knowing a patient is going to be readmitted? Probably the insurance company," Percha says.
Still, Percha and others say, the flaws in artificial intelligence algorithms shouldn't prevent people from using them – carefully. "These are new and exciting tools that have a lot of potential uses. We need to be conscious about how to use them going forward, but it doesn't mean we shouldn't go down this road," she says. "I think the potential benefits outweigh the risks, especially because we've barely scratched the surface of what big data can do right now."
“Young Blood” Transfusions Are Not Ready For Primetime – Yet
The world of dementia research erupted into cheers when news of the first real victory in a clinical trial against Alzheimer's Disease in over a decade was revealed last October.
By connecting the circulatory systems of a young and an old mouse, the regenerative potential of the young mouse decreased, and the old mouse became healthier.
Alzheimer's treatments have been famously difficult to develop; 99 percent of the 200-plus such clinical trials since 2000 have utterly failed. Even the few slight successes have failed to produce what is called 'disease modifying' agents that really help people with the disease. This makes the success, by the midsize Spanish pharma company Grifols, worthy of special attention.
However, the specifics of the Grifols treatment, a process called plasmapheresis, are atypical for another reason - they did not give patients a small molecule or an elaborate gene therapy, but rather simply the most common component of normal human blood plasma, a protein called albumin. A large portion of the patients' normal plasma was removed, and then a sterile solution of albumin was infused back into them to keep their overall blood volume relatively constant.
So why does replacing Alzheimer's patients' plasma with albumin seem to help their brains? One theory is that the action is direct. Alzheimer's patients have low levels of serum albumin, which is needed to clear out the plaques of amyloid that slowly build up in the brain. Supplementing those patients with extra albumin boosts their ability to clear the plaques and improves brain health. However, there is also evidence suggesting that the problem may be something present in the plasma of the sick person and pulling their plasma out and replacing it with a filler, like an albumin solution, may be what creates the purported benefit.
This scientific question is the tip of an iceberg that goes far beyond Alzheimer's Disease and albumin, to a debate that has been waged on the pages of scientific journals about the secrets of using young, healthy blood to extend youth and health.
This debate started long before the Grifols data was released, in 2014 when a group of researchers at Stanford found that by connecting the circulatory systems of a young and an old mouse, the regenerative potential of the young mouse decreased, and the old mouse became healthier. There was something either present in young blood that allowed tissues to regenerate, or something present in old blood that prevented regeneration. Whatever the biological reason, the effects in the experiment were extraordinary, providing a startling boost in health in the older mouse.
After the initial findings, multiple research groups got to work trying to identify the "active factor" of regeneration (or the inhibitor of that regeneration). They soon uncovered a variety of compounds such as insulin-like growth factor 1 (IGF1), CCL11, and GDF11, but none seemed to provide all the answers researchers were hoping for, with a number of high-profile retractions based on unsound experimental practices, or inconclusive data.
Years of research later, the simplest conclusion is that the story of plasma regeneration is not simple - there isn't a switch in our blood we can flip to turn back our biological clocks. That said, these hypotheses are far from dead, and many researchers continue to explore the possibility of using the rejuvenating ability of youthful plasma to treat a variety of diseases of aging.
But the bold claims of improved vigor thanks to young blood are so far unsupported by clinical evidence.
The data remain intriguing because of the astounding results from the conjoined circulatory system experiments. The current surge in interest in studying the biology of aging is likely to produce a new crop of interesting results in the next few years. Both CCL11 and GDF11 are being researched as potential drug targets by two startups, Alkahest and Elevian, respectively.
Without clarity on a single active factor driving rejuvenation, it's tempting to try a simpler approach: taking actual blood plasma provided by young people and infusing it into elderly subjects. This is what at least one startup company, Ambrosia, is now offering in five commercial clinics across the U.S. -- for $8,000 a liter.
By using whole plasma, the idea is to sidestep our ignorance, reaping the benefits of young plasma transfusion without knowing exactly what the active factors are that make the treatment work in mice. This space has attracted both established players in the plasmapheresis field – Alkahest and Grifols have teamed up to test fractions of whole plasma in Alzheimer's and Parkinson's – but also direct-to-consumer operations like Ambrosia that just want to offer patients access to treatments without regulatory oversight.
But the bold claims of improved vigor thanks to young blood are so far unsupported by clinical evidence. We simply haven't performed trials to test whether dosing a mostly healthy person with plasma can slow down aging, at least not yet. There is some evidence that plasma replacement works in mice, yes, but those experiments are all done in very different systems than what a human receiving young plasma might experience. To date, I have not seen any plasma transfusion clinic doing young blood plasmapheresis propose a clinical trial that is anything more than a shallow advertisement for their procedures.
The efforts I have seen to perform prophylactic plasmapheresis will fail to impact societal health. Without clearly defined endpoints and proper clinical trials, we won't know whether the procedure really lowers the risk of disease or helps with conditions of aging. So even if their hypothesis is correct, the lack of strong evidence to fall back on means that the procedure will never spread beyond the fringe groups willing to take the risk. If their hypothesis is wrong, then people are paying a huge amount of money for false hope, just as they do, sadly, at the phony stem cell clinics that started popping up all through the 2000s when stem cell hype was at its peak.
Until then, prophylactic plasma transfusions will be the domain of the optimistic and the gullible.
The real progress in the field will be made slowly, using carefully defined products either directly isolated from blood or targeting a bloodborne factor, just as the serious pharma and biotech players are doing already.
The field will progress in stages, first creating and carefully testing treatments for well-defined diseases, and only then will it progress to large-scale clinical trials in relatively healthy people to look for the prevention of disease. Most of us will choose to wait for this second stage of trials before undergoing any new treatments. Until then, prophylactic plasma transfusions will be the domain of the optimistic and the gullible.