When Beatrice Rienhoff was born in 2003 following an uneventful, full-term pregnancy, she was breathing well and had good color and muscle tone. She was on the small side, and there were some other subtle clues that something might be amiss. Her fingers and toes, especially on the right side of her body, were bent. And although no one took any measurements at the time, her hands and feet seemed longer than usual.
Three months later, Bea still hadn’t gained much weight. She was under 10 pounds and struggling with gross motor skills. At 17 months, she couldn’t stand on her own, nor could she crawl or roll over. At less than 17 pounds, she had fallen even farther on the growth chart. She was born with other distinctive features, too: an abnormally large distance between her eyes, a port-wine birthmark on her face, and a cleft in her uvula, the little flap of tissue that dangles at the back of the throat.
For her father, Hugh Rienhoff, a clinical geneticist by training and biotechnology entrepreneur in practice, some of those characteristics rang a bell. His daughter’s features share some similarities with genetic syndromes known as Marfan and Loeys-Dietz. In both of those conditions, the connective tissue that holds cells and organs together is compromised, which can produce life-threatening heart complications, among other problems. But Bea didn’t carry any of the mutations known to cause either of those disorders.
Rienhoff set off on a quest for a genetic diagnosis, with secondhand equipment cobbled together via eBay and concerns about his daughter’s potential heart problems weighing heavily on his mind. Almost 10 years later, after enlisting the help of the genome technology company Illumina, an analysis of genomic DNA extracted from Bea’s blood cells along with those of her two older, unaffected siblings and her parents provided the answer, which Rienhoff reported in the American Journal of Medical Genetics last year along with pertinent details of Bea’s life and condition up to age 9.
Bea carries a de novo mutation, one that neither of her parents or siblings — or anyone else, for that matter — is known to carry, in a single gene called TGFB3, for transforming growth factor beta. TGFB3 belongs to a family of growth factors with key roles in normal development and in diseases, not coincidentally including Marfan and Loeys-Dietz syndromes. Bea is the first person known to carry a mutation in the portion of the TGFB3 gene that codes for protein, and her features suggest that the gene is important for the development of the palate and for normal muscle growth. While Marfan and Loeys-Dietz have both been tied to an increase in TGF-beta signaling, the evidence suggests Bea, rather fortunately perhaps, has just the opposite.
Not So Rare
Bea’s story is but one relatively early and high-profile example of a rising trend in the rare disease arena made possible by recent advances and falling costs in next-generation genome sequencing technology. In part because diseases like Bea’s are rare, Rienhoff found it rather difficult in those earlier days to attract and sustain interest from people in the right positions to help him along the way. Without his clinical genetics background and determination, he might not have succeeded. While challenges still remain for families affected by rare diseases — insurance doesn’t always pay, and there is no one go-to place to find help — more and more rare disease sequencing programs have popped up around the world. Times have definitely changed.
“I don’t think you need to be a millionaire or computer wizard or geneticist like I was to initiate this kind of stuff now,” Rienhoff says. “I think there’s enough publicity about these cases that doctors and researchers are sensitive to this data, and the technology is much more accessible than it was four years ago. We are just going to see more of it and more of these unusual cases, and the heartbreak will be that there’s [often] nothing you can do. You get a diagnosis, but there’s nothing you can do but watch your daughter melt away or whatever it happens to be. Fortunately, for me, that’s not the case at all.”
That’s not to say that finding a convincing disease variant in exome data is a breeze. A person can vary at millions of sites in the genome. Once all of those variants are identified for any one individual, they must be filtered through and narrowed to a smaller number of potential suspects, based on comparisons against the general population. The genomic data of family members help, too, as does knowledge about the condition together with the scientific literature on individual genes and gene pathways.
Bea’s molecular diagnosis hasn’t led to any new treatment regimen or a clearer prognosis given the uniqueness of her condition and relative health either. So far, her management plan primarily involves braces she wears on her legs and exercises that would have been recommended with or without her genetic sequence. She does now take care of a pet mouse every day that carries her same mutation, given to her by researchers who are using similar mice as models to explore the biology associated with her condition in greater detail. Her father, too, continues to look for other people with changes in the same gene, and especially one just like Bea’s. The ultimate dream, Rienhoff says, is to find an 80-year-old with Bea’s TGFB3 mutation who has done just fine.
When Sequence Saves Lives
There have been other notable examples of the power of genome sequencing when applied to difficult rare disease cases, and some of them have produced lifesaving results. In 2011, Nicholas Volker became the “first child saved by DNA sequencing.” After hundreds of surgeries to address his mysterious and significant gut problems, doctors at the Medical College of Wisconsin sequenced Volker’s DNA, to uncover evidence that convinced them to try an umbilical cord blood transplant, a risky procedure, but one that resolved his symptoms and that otherwise wouldn’t have been warranted. That same year, the news broke that researchers at Baylor College of Medicine had sequenced Alexis and Noah Beery, to uncover a mutation that suggested a new approach to their treatment, too.
While doctors had already diagnosed the twins with the movement disorder known as dopa-responsive dystonia, Alexis had developed a new and unexplained symptom: a cough so severe at times that she nearly couldn’t breathe. The DNA data suggested that the twins, who were already taking a precursor of dopamine for the dystonia, might benefit from a serotonin boost, too.
As the twins’ mother, Retta Beery, told Nature at the time, “We honestly didn’t know if Alexis was going to make it through this. Sequencing has brought her back to life.”
While each of these cases is incredibly unique by definition, there is good reason for researchers to focus their attention on ways to get to the bottom of rare diseases, especially now that the costs associated with exome sequencing — in which all of the protein-coding regions of the genome are spelled out — have dropped. There are an estimated 7,000 rare, single-gene disorders, defined as conditions affecting fewer than 200,000 people in the United States or fewer than 2,000 in Europe. When you add all of those incidences of rare disease together, you discover that millions of people around the world are affected, even if you don’t consider their families.
“When you talk about rare diseases in general, people will often roll their eyes and think, ‘It’s rare. How many people are affected?” says Howard Jacob, the geneticist who sequenced Nicholas Volker and who is also a member of Genome magazine’s scientific advisory board. “For any particular disease, that’s right. But the estimate is that 0.4 percent of live births have a rare disease. Of those surviving, there are 20 million Americans running around with a rare disease. Cumulatively, rare disease is not rare.”
As the leader of a project called Finding of Rare Disease Genes (FORGE) in Canada, Kym Boycott is one of the top experts in the world in the application of exome sequencing to solve rare disorders. The Canadian project involves a network of doctors and scientists all across the country looking to identify patients with rare childhood conditions and refer them when appropriate for sequencing and analysis.
In June, the team published their first summary results in an American Journal of Human Genetics commentary. While the Canadian team set out hoping to explain 50 disorders, in reality they did much better. Of 264 rare disorders submitted by geneticists, the FORGE team has already managed to solve 146 of them — more than half. And, in the process, they identified 67 novel genes that had never been associated with any rare disease before. In the simplest cases, Boycott says they can come up with an answer in a matter of hours. In others that are more complicated, it can take weeks, months, or even years.
Still, the pace of progress is remarkable and hard to keep up with, Boycott says. She recalls in graduate school that entire labs would sometimes spend years to understand a single gene. Now, her team can be working on several genes in a single day. Overall, she estimates that the research community is uncovering about 200 new rare disease genes a year, and some unexpected patterns have emerged.
“We are seeing that in a significant subset, the same gene can be mutated in a different way, causing different disease,” Boycott says. “It’s almost like we are seeing rare disease in a subset of the genome, and that subset may be smaller than had been appreciated. We’ve always said there were 7,000 rare diseases, and there may be more rare disease phenotypes, but the number of genes is probably less than 5,000. We are making progress because next-gen sequencing is increasing the number of genes we understand, and the ceiling on the top number of [rare disease] genes has come down.”
That kind of overlap in biological pathways responsible for rare diseases could be very fortuitous when it comes to potential therapies because it suggests a single drug might be used to treat multiple conditions. “With only one or two patients, it’s hard to get resources,” Boycott explains. “But if there are approaches to tackle more than one disease, you’ve got some good legs.”
Changing the Game
Based on the early success in Nic Volker’s case, the Medical College of Wisconsin has launched a Genomics Medicine Clinic, as have other prominent medical centers around the country. While Jacob was surprised at the level of skepticism he met at first, there has clearly been a shift toward the use of genome sequencing to solve tough medical cases.
“I always believed at some point that [genome sequencing] would be a game changer,” Jacob says. “The difference in the Nic Volker case was that it went from a belief to a known. That changed my perspective because the reality is it does work. Now we have to do it better, faster, smarter, and enable more people to use it.”
The National Institutes of Health has expanded its Undiagnosed Diseases Program, with the goal to provide answers — based on DNA and other evidence — for patients whose conditions have eluded diagnosis for years. The nonprofit Rare Genomics Institute helps those with undiagnosed genetic diseases connect to doctors and researchers who might help them. When funding is an issue, they even offer assistance with online crowdfunding. In February, Global Genes announced a new partnership with SWAN USA (Syndromes Without A Name) to allow undiagnosed rare disease patients with limited financial resources to obtain a free clinical genomic sequencing test. Sequencing costs have dropped considerably, but exome sequencing can still run thousands of dollars and is often not covered by insurance.
Jacob is quick to note that genome sequencing won’t be the answer in every case. But, he says, genetic programs around the country used to come to a diagnosis for only 5 or 10 percent of their patients. Now, that number has jumped to an average closer to 25 percent. His group initially obtained a definitive diagnosis in 27 percent of its sequencing cases, seven out of the first 26 patients, all of whom made their way to the Genomics Medicine Clinic only after exhausting all other avenues. And it gets better over time, the Wisconsin group has found. Since they published their initial results last year, the number of cases they’ve been able to solve jumped from 27 percent to 39 percent, based on the same DNA sequence data combined with newly reported scientific discoveries.
“The medical literature is now showing that things we thought were important really are, and we’ve come back and made a diagnosis,” Jacob says. “In other words, the search for the answer can continue because we’ve digitalized the DNA and have the ability to keep searching. Collectively, that’s better medicine.”
Answers Without Cures
Better medicine doesn’t mean there is likely to be a cure, but in the most exceptional cases, nor should anyone expect otherwise.
“In most of medicine, we don’t make cures; we come up with better strategies,” Jacob says. “All we are doing is bringing the same thing to rare disease. If the end point is parents have a diagnosis, that’s gigantic from a healthcare delivery perspective. Parents can stop looking from place to place, test to test. On the physician side, we can stop being aggressive about some treatments and feel more comfortable about the treatments we are using. Even if there is no cure, it means better care because everyone knows what they are dealing with.”
Boycott says that the genetic diagnosis has made a dramatic difference in the way their patients are managed about 1 to 3 percent of the time. But the impact they’ve been able to have is surely greater than those figures let on.
“In all cases it makes a difference because families find themselves in an area of uncertainty without a diagnosis,” she says. “They participate because they want a diagnosis; they want a name to it. Most go into it knowing it probably won’t change things. For many rare diseases, I’m not sure how much of it is changeable. These are children born with differences we probably can’t impact with some sort of magic pill.”
Examples like Nic Volker and the Beery twins notwithstanding, Rienhoff is right to point out that there will still be plenty of heartbreak. He views genomics as the first step in understanding what a genetic condition is and what it isn’t. Is it a mitochondrial disease? In Bea’s case, no. Will it affect intelligence? Again, thankfully, no.
“We don’t know long-term answers, but having some certainty about the molecular pathology, we can take some comfort,” Rienhoff says. “We can look at related conditions and extrapolate to Bea’s clinical fate. There’s no question that having some kind of diagnosis is better than none. It hasn’t eliminated uncertainty about the future; it has eliminated uncertainty about what is going on, what is the root of this. But what is the fruit of this going forward? That remains a mystery.”
Despite that lingering uncertainty, Rienhoff is the first to recognize how lucky they have been. Bea has an echocardiogram every year, and there has been no evidence that her young heart is compromised by the genetic mutation she carries. His daughter, now 11 years old, is a well-adjusted, happy kid, not to mention that she earned an orange belt in karate last year.
“When you see her she has a little bit of an awkward gait,” Rienhoff says. “You can see that her fingers on the right side are a little bent, but she’s not very self-conscious of it, and she deals with life mostly with the view that she’s just like every other kid. Every kid has challenges, and these are her challenges. There’s no suggestion she feels she needs to hide it from other kids in school or that she’s at a significant disadvantage or angry at the world. Mostly, she does her thing, recognizing there are things she can’t do well, and she basically avoids those things. She plays on her strengths.”