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 use AI to predict how hospital stays will go
The Friday Five covers five stories in research that you may have missed this week. There are plenty of controversies and troubling ethical issues in science – and we get into many of them in our online magazine – but this news roundup focuses on scientific creativity and progress to give you a therapeutic dose of inspiration headed into the weekend.
Here are the promising studies covered in this week's Friday Five:
- The problem with bedtime munching
- Scientists use AI to predict how stays in hospitals will go
- How to armor the shields of our livers against cancer
- One big step to save the world: turn one kind of plastic into another
- The perfect recipe for tiny brains
And an honorable mention this week: Bigger is better when it comes to super neurons in super agers
The Toxic Effects of Noise and What We’re Not Doing About It
Erica Walker had a studio in her Brookline, Mass. apartment where she worked as a bookbinder and furniture maker. That was until a family with two rowdy children moved in above her.
The kids ran amuck, disrupting her sleep and work. Ear plugs weren’t enough to blot out the commotion. Aside from anger and a sense of lost control, the noise increased her heart rate and made her stomach feel like it was dropping, she says.
That’s when Walker realized that noise is a public health problem, not merely an annoyance. She set up her own “mini study” on how the clamor was affecting her. She monitored sound levels in her apartment and sent saliva samples to a lab to measure her stress levels.
Walker ultimately sold her craft equipment and returned to school to study public health. Today she is assistant professor of epidemiology and director of the Community Noise Lab at the Brown University School of Public Health. “We treat noise like a first world problem—like a sacrifice we should have to make for modern conveniences. But it’s a serious environmental stressor,” she asserts.
Our daily soundscape is a cacophony of earsplitting jets, motorcycles, crying babies, construction sites or gunshots if you’re in the military. Noise exposure is the primary cause of preventable hearing loss. Researchers have identified links between excessive noise and a heightened risk of heart disease, metabolic disorders, anxiety, depression, sleep disorders, and impaired cognition. Even wildlife suffers. Blasting oil drills and loud shipping vessels impede the breeding, feeding and migration of whales and dolphins.
At one time, the federal government had our back… and our ears. Congress passed the Noise Control Act in 1972. The Environmental Protection Agency set up the Office of Noise Abatement and Control (ONAC) to launch research, explore solutions and establish noise emission standards. But ONAC was defunded in 1981 amidst a swirl of antiregulatory sentiment.
Impossibly Loud and Unhealthy
Daniel Fink. a physician, WHO consultant, and board chair of The Quiet Coalition, a program of the nonprofit Quiet Communities, likens the effect of noise to the invisible but cumulative harm of second-hand smoke. About 1 in 4 adults in the U.S. who report excellent to good hearing already have some hearing loss. The injury can happen after one loud concert or from years with a blaring TV. Some people are more genetically susceptible to noise-related hearing loss than others.
“People say noise isn’t a big deal but it bothers your body whether you realize it or not,” says Ted Rueter, director of Noise Free America: A Coalition to Promote Quiet. Noise can chip away at your ears or cardiovascular system even while you’re sleeping. Rueter became a “quiet advocate” while a professor at UCLA two decades ago. He was plagued by headaches, fatigue and sleep deprivation caused by the hubbub of Los Angeles, he says.
The louder a sound is, and the longer you are exposed to it, the more likely it will cause nerve damage and harmful fluid buildup in your inner ear. Normal speech is 50-60 decibels (dBs). The EPA recommends that 24-hour exposure to noise should be no higher than 70 weighted decibels over 24 hours (weighted to approximate how the human ear perceives the sound) to prevent hearing loss but a 55 dB limit is recommended to protect against other harms from noise, too.
The decibel scale is logarithmic. That means 80 dB is 10 times louder than 70 dB. Trucks and motorcycles run 90 dBs. A gas-powered leaf blower, jackhammer or snow blower will cost you 100 dBs. A rock concert is in the 110 dB range. Aircraft takeoffs or sirens? 120 dBs.
Walker, the Brown professor, says that sound measurements often use misleading metrics, though, because they don’t include low frequency sound that disturb the body. The high frequency of a screeching bus will register in decibels but the sound that makes your chest reverberate is not accounted for, she explains. ‘How loud?’ is a superficial take when it comes to noise, Walker says.
After realizing the impact of noise on her own health, Erica Walker was inspired to change careers and become director of the Community Noise Lab at the Brown University School of Public Health.
Erica Walker
Fink adds that the extent to which noise impairs hearing is underestimated. People assume hearing loss is due to age but it’s not inevitable, he says. He cites studies of older people living in quiet, isolated areas who maintain excellent hearing. Just like you can prevent wrinkles by using sunscreen, you can preserve hearing by using ear plugs when attending fireworks or hockey games.
You can enable push notifications on a Smart Watch to alert you at a bar exceeding healthy sound levels. Free apps like SoundPrint, iHEARu, or NoiseTube can do decibel checks, too, but you don’t need one, says Fink. “If you can’t carry a conversation at normal volume, it’s too loud and your auditory health is at risk,” he says.
About 40 million U.S. adults, ages 20-69, have noise-induced hearing loss. Fink is among them after experiencing tinnitus (ringing or buzzing in the ears) on leaving a raucous New Year’s Eve party in 2007. The condition is permanent and he wears earplugs now for protection.
Fewer are aware of the link between noise pollution and heart disease. Piercing noise is stressful, raising blood pressure and heart rate. If you live near a freeway or constantly barking dog, the chronic sound stress can trigger systemic inflammation and the vascular changes associated with heart attacks and stroke.
Researchers at Rutgers University’s Robert Wood Johnson Medical School, working with data from the state’s Bureau of Transportation, determined that 1 in 20 heart attacks in New Jersey during 2018 were due to noise from highways, trains and air traffic. That’s 800 heart attack hospitalizations in the state that year.
Another study showed that incidence of hypertension and hardening arteries decreased during the Covid-19 air lockdown among Poles in Krakow routinely exposed to aircraft noise. The authors, comparing their pre-pandemic 2015 results to 2020 data, concluded it was no coincidence.
Mental health takes a hit, too. Chronic noise can provoke anxiety, depression and violence. Cognitively, there is ample evidence that noise disturbance lowers student achievement and worker productivity, and hearing loss among older people can speed up cognitive decline.
Noise also contributes to health disparities. People in neighborhoods with low socioeconomic status and a higher percentage of minority residents bear the brunt of noise. Affluent people have the means to live far from airports, factories, and honking traffic.
Out, Out, Damn Noise
Europe is ahead of the U.S. in tackling noise pollution. The World Health Organization developed policy guidelines used by the European Environment Agency to establish noise regulations and standards, and progress reports are issued.
Americans are relying too much on personal protective equipment (PPE) instead of eliminating or controlling noise. The Centers of Disease Control and Prevention rank PPE as the least useful response. Earplugs and muffs are effective, says Walker, but these devices are “a band-aid on a waterfall.”
Editing out noise during product design is the goal. Engineers have an arsenal of techniques and know-how for that. The problem is that these solutions aren’t being applied.
A better way to lower the volume is by maintaining or substituting equipment intended for common use. Piercing building alarms can be replaced with visual signals that flash alerts. Clanking chain and gear drives can be swapped out with belt drives. Acoustical barriers can wall off highway noise. Hospitals can soften beeping monitors and limit loudspeaker blasts. Double paned windows preserve quiet.
Editing out noise during product design is the goal. Engineers have an arsenal of techniques and know-how for that. The problem is that these solutions aren’t being applied, says Jim Thompson, an engineer and editor of the Noise Control Engineering Journal, published by the Institute of Noise Control Engineering of the USA
Engineers have materials to insulate, absorb, reflect, block, seal or diffuse noise. Building walls can be padded. Metal gears and parts can be replaced with plastic. Clattering equipment wheels can be rubberized. In recent years, building certifications such as LEED have put more emphasis on designs that minimize harmful noise.
Walker faults urban planners, too. A city’s narrow streets and taller buildings create a canyon effect which intensifies noise. City planners could use bypasses, rerouting, and other infrastructure strategies to pump down traffic volume. Sound-absorbing asphalt pavement exists, too.
Some municipalities are taking innovative measures on their own. Noise cameras have been installed in Knoxville, Miami and New York City this year and six California cities will join suit next year. If your muffler or audio system registers 86 dB or higher, you may receive a warning, fine or citation, similar to how a red-light camera works. Rueter predicts these cameras will become commonplace.
Based on understanding how metabolic processes affect noise-induced hearing loss in animal models, scientists are exploring whether pharmacological interventions might work to inhibit cellular damage or improve cellular defenses against noise.
Washington, DC, and the University of Southern California have banned gas-powered leaf blowers in lieu of quieter battery-powered models to reduce both noise and air pollution. California will be the first state to ban the sale of gas-powered lawn equipment starting 2024.
New York state legislators enacted the SLEEP (Stop Loud and Excessive Exhaust Pollution) Act in 2021. This measure increases enforcement and fines against motorists and repair shops that illegally modify mufflers and exhaust systems for effect.
“A lot more basic science and application research is needed [to control noise],” says Thompson, noting that funding for this largely dried up after the 1970s. Based on understanding how metabolic processes affect noise-induced hearing loss in animal models, scientists are exploring whether pharmacological interventions might work to inhibit cellular damage or improve cellular defenses against noise.
Studying biochemical or known genetic markers for noise risk could lead to other methods for preventing hearing loss. This would offer an opportunity to identify people with significant risk so those more susceptible to hearing loss could start taking precautions to avoid noise or protect their ears in childhood.
These efforts could become more pressing in the near future, with the anticipated onslaught of drones, rising needs for air conditioners, and urban sprawl boding poorly for the soundscape. This, as deforestation destroys natural carbon absorption reservoirs and removes sound-buffering trees.
“Local and state governments don’t have a plan to deal with [noise] now or in the future,” says Walker. “We need to think about this with intentionality.”