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.
Men and Women Experience Pain Differently. Learning Why Could Lead to Better Drugs.
It's been more than a decade since Jeannette Rotondi has been pain-free. A licensed social worker, she lives with five chronic pain diagnoses, including migraines. After years of exploring treatment options, doctors found one that lessened the pain enough to allow her to "at least get up."
"With all that we know now about genetics and the immune system, I think the future of pain medicine is more precision-based."
Before she says, "It was completely debilitating. I was spending time in dark rooms. I got laid off from my job." Doctors advised against pregnancy; she and her husband put off starting a family for almost a decade.
"Chronic pain is very unpredictable," she says. "You cannot schedule when you'll be in debilitative pain or cannot function. You don't know when you'll be hit with a flare. It's constantly in your mind. You have to plan for every possibly scenario. You need to carry water, medications. But you can't plan for everything." Even odors can serve as a trigger.
According to the CDC, one fifth of American adults live with chronic pain, and women are affected more than men. Do men and women simply vary in how much pain they can handle? Or is there some deeper biological explanation? The short answer is it's a little of both. But understanding the biological differences can enable researchers to develop more effective treatments.
While studies in animals are straightforward (they either respond to pain or they don't), humans are more complex. Social and psychological factors can affect the outcome. For example, one Florida study found that gender role expectations influenced pain sensitivity.
"If you are a young male and you believe very strongly that men are tougher than women, you will have a much higher threshold and will be less sensitive to pain," says Robert Sorge, an associate professor at the University of Alabama at Birmingham whose lab researches the immune system's involvement in pain and addiction.
He also notes, "We looked at transgender women and their pain sensitivity in comparison to cis men and women. They show very similar pain sensitivity to cis women, so that may reduce the impact of genetic sex in terms of what underlies that sensitivity."
But the difference goes deeper than gender expectations. There are biological differences as well. In 2015, Sorge and his team discovered that pain stimuli activated different immune cells in male and female rodents and that the presence of testosterone seemed to be a factor in the response.
More recently, Ted Price, professor of neuroscience at University of Texas, Dallas, examined pain at a genetic level, specifically looking at the patterns of RNA, which are single-stranded molecules that act as a messenger for DNA. Price noted that there were differences in these patterns that coincided with whether an individual experienced pain.
Price explains, "Every cell in your body has DNA, but the RNA that is in the cells is different for every cell type. The RNA in any particular cell type, like a neuron, can change as a result of some environmental influence like an injury. We found a number of genes that are potentially causative factors for neuropathic pain. Those, interestingly, seemed to be different between men and women."
Differences in treatment also affect pain response. Sorge says, "Women are experiencing more pain dismissal and more hostility when they report chronic pain. Women are more likely to have their pain associated with psychological issues." He adds that this dismissal may require women to exaggerate symptoms in order to be believed.
This can impact pain management. "Women are more likely to be prescribed and to use opioids," says Dr. Roger B. Fillingim, Director of Pain Research and Intervention Center of Excellence at the University of Florida. Yet, when self-administering pain meds, "women used significantly less opioids after surgery than did men." He also points out that "men are at greater risk for dose escalation and for opioid-related death than are women. So even though more women are using opioids, men are more likely to die from opioid-related causes."
Price acknowledges that other drugs treat pain, but "unfortunately, for chronic pain, none of these drugs work very well. We haven't yet made classes of drugs that really target the underlying mechanism that causes people to have chronic pain."
New drugs are now being developed that "might be particularly efficacious in women's chronic pain."
Sorge points out that there are many variables in pain conditions, so drugs that work for one may be ineffective for another. "With all that we know now about genetics and the immune system, I think the future of pain medicine is more precision-based, where based on your genetics, your immune status, your history, we may eventually get to the point where we can say [certain] drugs have a much bigger chance of working for you."
It will take some time for these new discoveries to translate into effective treatments, but Price says, "I'm excited about the opportunities. DNA and RNA sequencing totally changes our ability to make these therapeutics. I'm very hopeful." New drugs are now being developed that "might be particularly efficacious in women's chronic pain," he says, because they target specific receptors that seem to be involved when only women experience pain.
Earlier this year, three such drugs were approved to treat migraines; Rotondi recently began taking one. For Rotondi, improved treatments would allow her to "show up for life. For me," she says, "it would mean freedom."
Deaf Scientists Just Created Over 1000 New Signs to Dramatically Improve Ability to Communicate
For the deaf, talent and hard work may not be enough to succeed in the sciences. According to the National Science Foundation, deaf Americans are vastly underrepresented in the STEM fields, a discrepancy that has profound economic implications.
The problem with STEM careers for the deaf and hard-of-hearing is that there are not enough ASL signs available.
Deaf and hard-of-hearing professionals in the sciences earn 31 percent more than those employed in other careers, according to a 2010 study by the National Technical Institute for the Deaf (NTID) in Rochester, N.Y., the largest technical college for deaf and hard-of-hearing students. But at the same time, in 2017, U.S. students with hearing disabilities earned only 1.1 percent of the 39,435 doctoral degrees awarded in science and engineering.
One reason so few deaf students gravitate to science careers and may struggle to complete doctoral programs is the communication chasm between deaf and hard-of-hearing scientists and their hearing colleagues.
Lorne Farovitch is a doctoral candidate in biomedical science at the University of Rochester of New York. Born deaf and raised by two deaf parents, he communicated solely in American Sign Language (ASL) until reaching graduate school. There, he became frustrated at the large chunk of his workdays spent communicating with hearing lab mates and professors, time he would have preferred spending on his scientific work.
The problem with STEM careers for the deaf and hard-of-hearing is that there are not enough ASL signs available, says Farovitch. Names, words, or phrases that don't exist in ASL must be finger spelled — the signer must form a distinct hand shape to correspond with each letter of the English alphabet, a tedious and time-consuming process. For instance, it requires 12 hand motions to spell out the word M-I-T-O-C-H-O-N-D-R-I-A. Imagine repeating those motions countless times a day.
To bust through this linguistic quagmire, Farovitch, along with a team of deaf STEM professionals, linguists, and interpreters, have been cooking up signs for terms like Anaplasma phagocytophilum, the tick-borne bacterium Farovitch studies. The sign creators are then videotaped performing the new signs. Those videos are posted on two crowd-sourcing sites, ASLcore.org and ASL Clear.
The beauty of ASL is you can express an entire concept in a single sign, rather than by the name of a word.
"If others don't pick it up and use it, a sign goes extinct," says Farovitch. Thus far, more than 1,000 STEM terms have been developed on ASL Clear and 500 vetted and approved by the deaf STEM community, according to Jeanne Reis, project director of the ASL Clear Project, based at The Learning Center for the Deaf in Framingham, Mass.
The beauty of ASL is you can express an entire concept in a single sign, rather than by the name of a word. The signs are generally intuitive and wonderfully creative. To express "DNA" Farovitch uses two fingers of each hand touching the tips of the opposite hand; then he draws both the hands away to suggest the double helix form of the hereditary material present in most organisms.
"If you can show it, you can understand the concept better,'' says the Canadian-born scientist. "I feel I can explain science better now."
The hope is that as ASL science vocabulary expands more, deaf and hard-of-hearing students will be encouraged to pursue the STEM fields. "ASL is not just a tool; it's a language. It's a vital part of our lives," Farovitch explains through his interpreter.
The deaf community is diverse—within and beyond the sciences. Sarah Latchney, PhD, an environmental toxicologist, is among the approximately 90 percent of deaf people born to hearing parents. Hers made sure she learned ASL at an early age but they also sent Latchney to a speech therapist to learn to speak and read lips. Latchney is so adept at both that she can communicate one-on-one with a hearing person without an interpreter.
Like Favoritch, Latchney has developed "conceptually accurate" ASL signs but she has no plans to post them on the crowd-sourcing sites. "I don't want to fix [my signs]; it works for me," she explains.
Young scientists like Farovitch and Latchney stress the need for interpreters who are knowledgeable about science. "When I give a presentation I'm a nervous wreck that I'll have an interpreter who may not have a science background," Latchney explains. "Many times what I've [signed] has been misinterpreted; either my interpreter didn't understand the question or didn't frame it correctly."
To enlarge the pool of science-savvy interpreters, the University of Rochester will offer a new masters degree program: ASL Interpreting in Medicine and Science (AIMS), which will train interpreters who have a strong background in the biological sciences.
Since the Americans with Disabilities Act was enacted in 1990, opportunities in higher education for deaf and hard-of-hearing students have opened up in the form of federally funded financial aid and the creation of student disability services on many college campuses. Still, only 18 percent of deaf adults have graduated from college, compared to 33 percent of the general population, according to a survey by the U.S. Census Bureau in 2015.
The University of Rochester and the Rochester Institute of Technology, home to NTID, have jointly created two programs to increase the representation of deaf and hard-of-hearing professionals in the sciences. The Rochester Bridges to the Doctorate Program, which Farovitch is enrolled in, prepares deaf scholars for biomedical PhD programs. The Rochester Postdoctoral Partnership readies deaf postdoctoral scientists to successfully attain academic research and teaching careers. Both programs are funded by the National Institutes of Science. In the last five years, the University of Rochester has gone from zero deaf postdoctoral and graduate students to nine.
"Deafness is not a problem, it's just a difference."
It makes sense for these two private universities to support strong programs for the deaf: Rochester has the highest per capita population of deaf or hard-of-hearing adults younger than 65 in the nation, according to the U.S. Census. According to the U.S. Department of Education, there are about 136,000 post-secondary level students who are deaf or hard of hearing.
"Deafness is not a problem, it's just a difference," says Farovitch. "We just need a different way to communicate. It doesn't mean we require more work."