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.
A Team of Israeli Students Just Created Honey Without Bees
Can you make honey without honeybees? According to 12 Israeli students who took home a gold medal in the iGEM (International Genetically Engineered Machine) competition with their synthetic honey project, the answer is yes, you can.
The honey industry faces serious environmental challenges, like the mysterious Colony Collapse Disorder.
For the past year, the team from Technion-Israel Institute of Technology has been working on creating sustainable, artificial honey—no bees required. Why? As the team explains in a video on the project's website, "Studies have shown the amazing nutritional values of honey. However, the honey industry harms the environment, and particularly the bees. That's why vegans don't use honey and why our honey will be a great replacement."
Indeed, honey has long been a controversial product in the vegan community. Some say it's stealing an animal's food source (though bees make more honey than they can possibly use). Some avoid eating honey because it is an animal product and bees' natural habitats are disturbed by humans harvesting it. Others feel that because bees aren't directly killed or harmed in the production of honey, it's not actually unethical to eat.
However, there's no doubt that the honey industry faces some serious environmental challenges. Colony Collapse Disorder, a mysterious phenomenon in which worker bees in colonies disappear in large numbers without any real explanation, came to international attention in 2006. Several explanations from poisonous pesticides to immune-suppressing stress to new or emerging diseases have been posited, but no definitive cause has been found.
There's also the problem of human-managed honey farms having a negative impact on the natural honeybee population.
So how can honey be made without honeybees? It's all about bacteria and enzymes.
The way bees make honey is by collecting nectar from flowers, transporting it in their "honey stomach" (which is separate from their food stomach), and bringing it back to the hive, where it gets transferred from bee mouth to bee mouth. That transferal process reduces the moisture content from about 70 percent to 20 percent, and honey is formed.
The product is still currently under development.
The Technion students created a model of a synthetic honey stomach metabolic pathway, in which the bacterium Bacillus subtilis "learns" to produce honey. "The bacteria can independently control the production of enzymes, eventually achieving a product with the same sugar profile as real honey, and the same health benefits," the team explains. Bacillus subtilis, which is found in soil, vegetation, and our own gastrointestinal tracts, has a natural ability to produce catalase, one of the enzymes needed for honey production. The product is still currently under development.
Whether this project results in a real-world jar of honey we'll be able to buy at the grocery store remains to be seen, but imagine how happy the bees—and vegans—would be if it did.
A few days before Christmas 2015, Paige Alexandria, a 28-year-old counselor at the Austin Women's Health Center in Texas, found out she was pregnant.
Alexandria had missed the cutoff for a medication abortion by three days.
"It was an unplanned pregnancy, and instantaneously I knew I needed an abortion," Alexandria recalls. Already a mother of two children, one with special needs, a third child was not something Alexandria and her husband felt prepared to take on. "Mentally, I knew my limit. I wasn't prepared for a third and I didn't want one," she says.
At an ultrasound appointment one week later, scans showed she was a little over eight weeks pregnant. Alexandria opted to have an abortion as soon as possible, and preferably with medication. "I really wanted to avoid a surgical abortion," she says. "It sounded a lot more invasive, and I'm already uncomfortable with pap smears and pelvic exams, so I initially went in wanting to do the pill."
But at the time, medication guidelines stipulated that one of the pills, called Mifepristone, could only be prescribed to end a pregnancy at eight weeks gestation or earlier – Alexandria had missed the cutoff by three days. If she wanted to end the pregnancy, she would need to undergo a surgical abortion, otherwise known as a vacuum aspiration abortion.
With a vacuum aspiration abortion, doctors dilate the cervix and manually aspirate out the contents of the uterus. Medication abortion, on the other hand, consists of the patient taking two pills – Mifepristone, which blocks the hormones that help the pregnancy develop, and Misoprostol, which empties the uterus over a period of days, identical to a miscarriage.
Alexandria was upset about the change of plans but resolute in her decision to end the pregnancy. "The fact that I didn't really have a choice in how my procedure was performed has made the experience just a little more sensitive for me," she says. She scheduled the earliest available appointment for a surgical abortion.
Paige Alexandria would have chosen to terminate her pregnancy with medication if the regulations were less stringent.
(Photo courtesy of Alexandria)
Like Alexandria, many people looking to terminate a pregnancy opt to do so with medication. According to research from the Guttmacher Institute, medication abortions accounted for nearly 40 percent of all abortions in the year 2017 – a marked increase from 2001, when medication abortions only accounted for roughly five percent of terminations. Taken 24-48 hours apart, Mifepristone and Misoprostol have a 95-99 percent success rate in terminating pregnancies up to 63 days – or nine weeks – of gestation, according to the American College of Obstetrics and Gynecology (ACOG).
But even though the World Health Organization (WHO) considers medical abortion to be highly safe and effective, the medication is still carefully guarded in the United States: Mifepristone is only available for terminating pregnancies up to 10 weeks gestation, per the FDA, even though limited research suggests that both are safe and effective at terminating pregnancies between 12 and 20 weeks.
Additionally, a separate set of regulations known as a Risk Evaluation and Mitigation Strategy (REMS) means that patients can only take Mifepristone under specific circumstances. Mifepristone must be distributed in person by a healthcare provider – usually interpreted in most states as a doctor or nurse practitioner – who has registered with the drug's manufacturer. The medication cannot be distributed through a pharmacy, so doctors who wish to provide the drug must stock the medication in-office, and both the provider and the patient must sign a form that warns them of the "risk of serious complications associated with Mifepristone," according to the FDA.
"REMS is a set of restrictions that the FDA puts on the distribution of drugs it considers dangerous or risky in some way," says Dr. Elizabeth Raymond, an OB-GYN and senior medical associate at Gynuity Health Projects. Although not always called REMS, these restrictions have been imposed on Mifepristone since the medication was approved by the FDA in 2000, Raymond says.
Raymond is part of a growing number of physicians and researchers who want to eliminate the REMS requirements for Mifepristone, also known by its brand name Mifeprex. In 2017, Raymond and several other physicians authored a paper in the New England Journal of Medicine (NEJM) arguing that Mifepristone is extremely safe and needlessly over-regulated.
"When the FDA first approved [Mifepristone] and imposed these requirements, they might have made sense 19 years ago when there was limited information about the use of this treatment in the United States," says Dr. Daniel Grossman, director at Advancing New Standards in Reproductive Health at UCSF and co-author of the 2017 report in the NEJM. "Now, after 19 years, it's clear that this medication is very safe, and safer than a lot of others available in a pharmacy."
Since 2000, Mifepristone has been implicated in 19 deaths, making its mortality rate 0.00063 percent.
According to their research, over three million people have taken Mifepristone since it was approved in 2000. Since then, Mifepristone has been implicated in 19 deaths, making its mortality rate 0.00063 percent. Even then, the risk is inflated, Grossman says.
"The requirement is that practitioners need to report any deaths that occur after taking these medications, and so you'll see deaths included in that figure which are homicides or suicides or something unrelated to taking Mifepristone," says Grossman. In contrast, Acetaminophen – better known as Tylenol – was associated with 458 overdose deaths between 1990 and 1998, as well as 56,000 emergency room visits and 26,000 hospitalizations. Sildenafil, better known as Viagra, was linked to 762 deaths in the first twenty months after it was approved by the FDA. Yet neither Tylenol nor Viagra have been burdened with the same REMS restrictions as Mifepristone.
"It's clearly about more than just the safety of the medication at this point," says Grossman. "It's more about stigma related to abortion and politics."
For people who want a medication abortion, the REMS requirements mean they often need to take off work to schedule a doctor's appointment, arrange for transportation and childcare, and then arrange an additional doctor's appointment days afterward to take the second dose of medication. While surgical abortion procedures are quicker (usually a one-day outpatient procedure, depending on gestation), many people prefer having the abortion in the comfort of their home or surrounded by family instead.
Paige Alexandria, who counsels people seeking abortions at her job, says that survivors of sexual violence often prefer medical abortions to surgical ones. "A lot of time survivors have a trauma associated with medical instruments or having pelvic exams, and so they're more comfortable taking a pill," she says.
But REMS also creates a barrier for healthcare providers, Grossman says. Stocking the medication in-office is "a hassle" and "expensive," while others are reluctant to register their name with the drug manufacturer, fearing harassment or violence from anti-choice protestors. As a result, the number of practitioners willing to provide medical abortions nationwide is severely limited. According to Grossman's own research published in the journal Obstetrics and Gynecology, 28 percent of OBGYNs admitted they would administer medication abortions if it were possible to write a prescription for Mifepristone rather than stock it in-office.
Amazingly, the restrictions on Mifepristone have loosened since it first came on the market. In 2016, the FDA updated the guidelines on Mifepristone to allow its use until 10 weeks gestation, up from eight weeks. But doctors say the REMS restrictions should be eliminated completely so that people can obtain abortions as early as possible.
"REMS restrictions inhibit people from being able to get a timely abortion," says Raymond, who stresses that abortion is generally more comfortable, more affordable, and safer for women the earlier it's done. "Abortion is very safe no matter when you get it, but it's also easier because there's less risk for bleeding, infections, or other complications," Raymond says. Abortions that occur earlier than eight weeks of gestation have a complication rate of less than one percent, while an abortion done at 12 or 13 weeks has a three to six percent chance of complications.
And even for people who want a medication abortion early on in their pregnancy, REMS restrictions make it so that they may not have time to obtain it before the 10-week period lapses, Raymond says.
"If you're seven weeks pregnant but it takes you three weeks to figure out travel and childcare arrangements to go into the doctor and take this medication, now you're at the cutoff date," she says. "Even if you manage to get an abortion at nine weeks, that's still a later gestational age, and so the risks are increased."
In 2016, at a little over nine weeks gestation, Alexandria completed her abortion by having a D&E. But because she didn't have anyone to drive her home after the procedure, she wasn't able to have sedation throughout, something she describes as "traumatic."
"I had the abortion completely aware and coherent, and paired with the fact that I hadn't even wanted a surgical abortion in the first place made it harder to deal with," Alexandria says.
"When you're just a day or two past eight weeks and you want an abortion – why is medication not immediately available?"
Today, Alexandria shares her story publicly to advocate for abortion care. Although she doesn't regret her surgical abortion and acknowledges that not everyone experiences surgical abortion the same way she did, she does wish that she could have gone a different route.
"If I had to do it over, I would still try to do the pill, because [the surgical abortion] was such a terrifying experience," she says. "When you're just a day or two past eight weeks and you want an abortion – why is medication not immediately available? It just doesn't make sense."