When the Smithsonian National Museum of Natural History opened its genomics exhibit in 2013, the field was just celebrating the 10th anniversary of the completed Human Genome Project. Sequencing that first genome cost over $500 million. The genomes since cost $10,000.
In 2022, as the museum prepares to wrap up the landmark exhibit, much has changed. Gene names such as BRCA1 and HER2 have entered the public consciousness. Sequencing DNA has become faster, cheaper, and smaller-scale. Portable sequencers that were not even being sold commercially in 2013 have since been used to trace the evolution of the Ebola virus as it wreaked havoc in West Africa. The development of CRISPR-Cas9 landed a Nobel Prize. The cost of genome sequencing is rapidly approaching $100.
“What seemed cutting edge maybe in 2013, now in 2022, were just things that were somewhat more routine,” said Carla Easter, who helped organize the exhibit while at the National Human Genome Research Institute, which partnered with the Smithonian to launch the project.
“Nobody knew what CRISPR was ten years ago,” added Easter, now at the Smithsonian. “But now, people will mention it and they’ll know what that is. They may not know — understand the science behind it, but at least they’ve heard the word.”
Before the exhibit closes its doors later this year, STAT spoke with curators, educators, and leading scientists involved in its creation about how genomics has changed in the past decade.
“The field of genomics has gone way beyond genomics experts, people who would call themselves genomicists, and it’s applied everywhere,” said Lawrence Brody, who leads the NHGRI Division of Genomics and Society. “We’ve done these analyses of the NIH budget, and there’s way more genomics being done outside of our institute than there is inside our institute, because it’s such a powerful tool. And that’s a great thing.”
Most of those improvements have been with sequencing, he said. “We’re now talking about what genetic variation might be. If you study people who have a disease, [and] find a genetic variant that seems to be common in those people, you don’t really know anything until you ask yourself, ‘How common is that variant in people who don’t have the disease?’ And you need to look at large numbers of people to understand that.” This also means involving people who are not normally represented in research, a task the NIH-funded All of Us program has taken up.
Another change he sees is the newfound ability to broadly study the entire genome, rather than only specific genes, and to analyze how various parts of the genome are being turned on or off in individual cells.
Even though all cells but sperm and egg share the same genome, they do not all make the same proteins. A decade or two ago, studying these differences involved an arduous process, and scientists could only study a few specific genes at a time. But Brody said that has changed thanks to advances in RNA sequencing, which allow “you to ask questions about all the genes completely, objectively, and agnostically. And to me, that’s really the power and has always been the power of genetics — is to ask the question and have the organism tell you what’s important, as opposed to guess and saying ‘It must be this gene or it must be that gene.’”
Now, he said, the field needs to understand how diseases are caused by a combination of genes and environmental exposures, manipulate the genome to treat diseases, and survey life on the planet because, as a geneticist, “it’s really important for me to know the variations out there.”
“We often say ‘Oh, in ten years, we’ll be doing this,’ and if you look back at those predictions, we’re wrong a lot,” said Brody. “But we will get there.”
To Stephen Palumbi, a professor of marine sciences at Stanford who studies corals, the biggest change in genomics is the speed and cost of sequencing.
“The same questions are there, the same approaches are there,” said Palumbi. “But it’s like you took a garden hose that you were — plenty of water flow and everything — and you turned it into a firehose of information. That deluge of data that you can get right now is incredible. So the whole field, not just natural history or oceans, but the whole field of genomics, has become more and more and more tuned to being a high-flow data-rich, incredible science of what’s now called bioinformatics. Bioinformatics at the time, a decade ago, was really important. It’s probably increased in importance 50-fold because the data sets have increased 100-fold, and being able to actually pull information out of these data sets has become one of the most interesting, challenging, and rewarding parts of how genomes are used.”
“The human genome is the most traveled, well-mapped genome in the known universe, no big surprise. But I study organisms that are not humans and have genomes anyway. And so we’re always sort of scrambling a little bit behind that technology, but adopting it and adapting it,” he said.
He pointed to work he is doing to study corals living on reefs in an archipelago in Palau that look strikingly similar, but have turned out to be genetically different. Being able to deeply mine the genomes of those corals offers valuable clues about their genetic capacity to adapt to environmental change.
“So genomics gives me a map to their current patterns of adaptation that I would not get in any other way,” he said. “When this exhibit opened, I couldn’t have done what I just told you because it would have been prohibitively expensive. And the people who can do the bioinformatics really weren’t there. And the genetic, genomic resources that I need to do this work weren’t there. But they’re there now. So that’s where the whole field has changed so much. In that period of time, 2011 till now, the entire landscape, seascape, forestscape changed.”
He said the field’s advances — like enabling handheld sequencing — will make it even easier to reveal DNA in the environment, whether that is samples pulled from a kelp forest or fungus living in the soil of wetlands. Those insights are more critical than ever, as they can offer insights on monitoring pathogens and endangered species.
“What I don’t want to see in 50 years in a genome exhibit, is a whole lot of genomes of extinct species that we’ve lost because of climate change.”
Harvard professor and genetics pioneer George Church was involved in the Human Genome Project from its earliest days, having joined the effort in 1984, years before the National Institutes of Health got involved. He saw the project pique the interest first of lawmakers, and then the public at large. “Some projects that are highly technical, whether they’re expensive or not, are unpopular or ignored,” said Church. “But this one actually captured Congress’s interest, around 1987 was really when they started paying attention. …They liked this and they committed to $3 billion, which was quite a lot in 1987. And then they proceeded to get excited in all kinds of science and they ended up doubling the NIH budget, which is almost unprecedented and hasn’t happened since then.”
And despite the celebration of the sequencing of the human genome, Church said, the work is far from over.
“[It] had been sort of declared done in 2001, and then was re-declared done in 2004. And it’s actually still not done in my opinion. This year marks the first year that we’ve finished one genome, one human genome, but in a way that really isn’t generally applicable — we did it to a haploid cell.” Haploid cells have only a single set of chromosomes, in contrast to the typical human cell which is diploid and has two. “So if you want to diagnose a patient, you have to be able to do a diploid genome. And no one’s ever completed a diploid genome yet, although we are on our way,” Church said.
Church said genomics has already made an impact in medical care. It played a role in the development of the Covid-19 vaccines, and can give prospective parents insight about when they carry a recessive gene for certain diseases. It also enabled the development of the first first gene therapy to be approved by the Food and Drug Administration. Even when the exhibit was being developed a decade ago, he said, the idea of “gene therapy wasn’t that popular. In fact, it just barely was recovering from its 2001 setback, or 1999 to 2001 setbacks, plural.”
In the future, Church would like to see a “bioweather map” that uses genomics to keep tabs on and track the evolution of viruses and bacteria, akin to a weather forecast. “‘What flu just flew in the town? And what is happening at the daycare? Should you take your kid?’” he asked.
But for all his big ideas about genomics, Church also has his sticking points. Among them: “One of my pet peeves is when people say, ‘Oh, you know that humans share fill in your favorite number with fill in your favorite organism. So it’d be like 46% related to plants or bananas,” he said. “I mean, it’s a completely meaningless statistic.”
(It is a battle he did not win with the Smithsonian exhibit, which tells viewers that the human genome is 41% similar to a banana’s.)
For Joann Boughman, a senior vice chancellor at the University System of Maryland, advances in genomics have changed how people perceive genetic diseases. “From the historical perspective, if you will, in human genetics, we have understood and have always looked at variability as an essential theme,” said Boughman. “It wasn’t until the human genome started and people started understanding about the variations at the DNA level that they made the connection between genes and ultimate phenotype, what we look like. And it has been really fascinating to see how these two worlds, as you will, collide and hopefully come together.”
During the pandemic, Boughman served as the point person for the Maryland university system’s Covid response, which included a community of over 200,000 students, staff, and faculty. “And I realize I’m working with an educated population, but all kinds of people really understood when we started talking about viral variants, they understood what had changed was the DNA in the virus, that there had been a mutation. These were not absolutely foreign concepts to people, and they, with very little explanation, would understand why one vaccine might fight this virus, but not a mutated form of that virus,” Boughman said.
This is part of a growing awareness she had seen unfolding long before the pandemic hit. “The fact that the double strand of DNA is not a foreign concept, even to relatively small children, really makes our conversation different. And that’s been an incredible thing to watch over the last 40 years.” Today, “if people see an image of DNA, they’ll recognize it.”
Boughman said that shift struck her recently when she saw a commercial for a treatment for a rare genetic disease. “It hit me right between the eyes that they actually have an ad on TV and named a genetic syndrome and talked about that drug that was helping these children. But 20 years ago, the idea of putting on television a picture of a child who has physical abnormalities and labeling them as having a genetic disease or a genetic syndrome just would have been devastating. But now that we are getting to the point where we understand enough about the genetics that we can start to intervene and treat, it becomes a very different perspective than somebody who is simply doomed. They labeled it genetic and they labeled it as a syndrome, and then they talked about hope that they had. And that simply was not the case 20 or 30 years ago, at all.”
As a geneticist and professor at the University of Pennsylvania, Sarah Tishkoff originally got involved in the exhibit to share her expertise on what genetics and genomics can tell us about the evolutionary history of humans. Given her research, she is keenly aware of how much the field has changed in the past few decades.
She is also aware of how far the field still needs to go — specifically when it comes to securing better representation in genomics research, which is overwhelmingly centered on white and European populations. “What we don’t really have are good reference genomes,” she said. “So there are populations or people in different parts of the world that might have insertions or deletions in their genome or things that aren’t even in that reference.”
But if the Smithsonian were to open the exhibit again in 50 years, she said, we will have unraveled far more mysteries — and the public will be far more familiar with the science.
“I think at that point, most people are going to have their genome sequenced,” she said. That would give scientists a far deeper trove of data to understand structural variation — large-scale differences across the DNA of individuals, including duplications of certain genes — and, in turn, knowledge of how humans have adapted to different environments and develop different levels of risk for disease. She added that by that time, “we’re going to know more about what the genome variation actually does,” similar to her findings that multiple different gene mutations can cause lactose tolerance.
She is also hopeful that we will have wide-ranging insights into ancient DNA and the origins of human history, including a far more complete picture. Right now, she noted, we are limited by the fact that ancient DNA is often poorly preserved. “Someday, somebody is going to get ancient DNA from a fossil in Africa that’s 50,000 years old or 100,000 or 200,000. That’s going to really help shed light on human history in that region, which is where we all evolved,” Tishkoff said. “I’m hoping that we’re going to know a lot more examples of how people adapted to different environments.”
In addition to his day job at the E.O. Wilson Biodiversity Foundation, Dennis Liu serves on the board of the American Chestnut Foundation, which has funded efforts to introduce a gene into American chestnut trees that can help them resist a group of diseases known as blight. To Liu, there are clear benefits that advances in genomics can bring to conservation efforts like this one.
But as the field ages, he also sees a downside to the growing distance from the Human Genome Project.
When the initiative launched, Liu said, “there was a sense of a moonshot at the time. And I think that kind of new excitement isn’t necessarily here. I haven’t done a survey or a poll, but I imagine that these things are now kind of all lumped together with big pharma and the pharmaceutical industry and sort of high-tech medicine. And I would imagine that a lot of people still would wonder, ‘Oh, I don’t know, what does this do for me?’ I do think they’d hope, of course, that this kind of information is going to help cancer treatments, for example, and those sorts of things.”
For example: To the field, the increase in sequencing speeds is a huge advance. ”But I don’t think that means much of anything to the general public,” Liu said. Instead of feeling that genomics completed with the sequencing of the genome, he hopes we will continue to wonder about genomics. It is not like “‘Oh, the genome, we did that, it’s over.’ It’s like, ‘No, it’s both that this work has continued and it continues to matter,’” said Liu, who was then with the Howard Hughes Medical Institute, “‘And you should know something about it even if you’re not a professional scientist.”
Eric Green has served as the director of the NHGRI since 2009. The biggest difference he sees in genomics then, and genomics now? “At the time I started as director, when this exhibition was being created, there was a lot of clarity around what had been accomplished and a lot of growing knowledge about how the human genome works. But the idea of actually using genomic information for the practice of medicine was pretty hypothetical.”
When he stepped into his role, he wanted to close that gap and “figure out how to use genomic information to improve the practice of medicine. …And the biggest difference between then and now is then it was hypothetical and, while it is certainly not pervasive in medicine, there are a number of just very clear areas where now genomics is mainstream.” Green highlighted the use of genomics to diagnose rare diseases. “They were like the very first home runs in those areas,” he said. “But now it’s just routine practice.” Another notable change, he added, is the proliferation of DNA genealogy tests from companies such as 23andMe and Ancestry.
Looking ahead, Green said he is a “realist” about the role of genomics in medicine.
“The implementation of some aspects of genomic medicine are no longer scientifically difficult. They’re sociological, because of the societal challenges associated with health care,” said Green, who trained as a physician-scientist. “What I would say going forward is that, I’m actually quite optimistic we’re going to figure out a lot of these really valuable uses of genomics. But I can’t claim to be as optimistic about the effective use of those tools in health care, because we all appreciate that health care is really complicated.”
It is a hurdle he had not considered early on in research, he said. “Science drives some things, but it’s not the only thing.”