Genomic Data Has a Diversity Problem, But Global Efforts Are Underway to Fix It
Genomics has begun its golden age. Just 20 years ago, sequencing a single genome cost nearly $3 billion and took over a decade. Today, the same feat can be achieved for a few hundred dollars and the better part of a day . Suddenly, the prospect of sequencing not just individuals, but whole populations, has become feasible.
The genetic differences between humans may seem meager, only around 0.1 percent of the genome on average, but this variation can have profound effects on an individual's risk of disease, responsiveness to medication, and even the dosage level that would work best.
Already, initiatives like the U.K.'s 100,000 Genomes Project - now expanding to 1 million genomes - and other similarly massive sequencing projects in Iceland and the U.S., have begun collecting population-scale data in order to capture and study this variation.
The resulting data sets are immensely valuable to researchers and drug developers working to design new 'precision' medicines and diagnostics, and to gain insights that may benefit patients. Yet, because the majority of this data comes from developed countries with well-established scientific and medical infrastructure, the data collected so far is heavily biased towards Western populations with largely European ancestry.
This presents a startling and fast-emerging problem: groups that are under-represented in these datasets are likely to benefit less from the new wave of therapeutics, diagnostics, and insights, simply because they were tailored for the genetic profiles of people with European ancestry.
We may indeed be approaching a golden age of genomics-enabled precision medicine. But if the data bias persists then there is a risk, as with most golden ages throughout history, that the benefits will not be equally accessible to all, and existing inequalities will only be exacerbated.
To remedy the situation, a number of initiatives have sprung up to sequence genomes of under-represented groups, adding them to the datasets and ensuring that they too will benefit from the rapidly unfolding genomic revolution.
Global Gene Corp
The idea behind Global Gene Corp was born eight years ago in Harvard when Sumit Jamuar, co-founder and CEO, met up with his two other co-founders, both experienced geneticists, for a coffee.
"They were discussing the limitless applications of understanding your genetic code," said Jamuar, a business executive from New Delhi.
"And so, being a technology enthusiast type, I was excited and I turned to them and said hey, this is incredible! Could you sequence me and give me some insights? And they actually just turned around and said no, because it's not going to be useful for you - there's not enough reference for what a good Sumit looks like."
What started as a curiosity-driven conversation on the power of genomics ended with a commitment to tackle one of the field's biggest roadblocks - its lack of global representation.
Jamuar set out to begin with India, which has about 20 percent of the world's population, including over 4000 different ethnicities, but contributes less than 2 percent of genomic data, he told Leaps.org.
Eight years later, Global Gene Corp's sequencing initiative is well underway, and is the largest in the history of the Indian subcontinent. The program is being carried out in collaboration with biotech giant Regeneron, with support from the Indian government, local communities, and the Indian healthcare ecosystem. In August 2020, Global Gene Corp's work was recognized through the $1 million 2020 Roddenberry award for organizations that advance the vision of 'Star Trek' creator Gene Roddenberry to better humanity.
This problem has already begun to manifest itself in, for example, much higher levels of genetic misdiagnosis among non-Europeans tested for their risk of certain diseases, such as hypertrophic cardiomyopathy - an inherited disease of the heart muscle.
Global Gene Corp also focuses on developing and implementing AI and machine learning tools to make sense of the deluge of genomic data. These tools are increasingly used by both industry and academia to guide future research by identifying particularly promising or clinically interesting genetic variants. But if the underlying data is skewed European, then the effectiveness of the computational analysis - along with the future advances and avenues of research that emerge from it - will be skewed towards Europeans too.
This problem has already begun to manifest itself in, for example, much higher levels of genetic misdiagnosis among non-Europeans tested for their risk of certain diseases, such as hypertrophic cardiomyopathy - an inherited disease of the heart muscle. Most of the genetic variants used in these tests were identified as being causal for the disease from studies of European genomes. However, many of these variants differ both in their distribution and clinical significance across populations, leading to many patients of non-European ancestry receiving false-positive test results - as their benign genetic variants were misclassified as pathogenic. Had even a small number of genomes from other ethnicities been included in the initial studies, these misdiagnoses could have been avoided.
"Unless we have a data set which is unbiased and representative, we're never going to achieve the success that we want," Jamuar says.
"When Siri was first launched, she could hardly recognize an accent which was not of a certain type, so if I was trying to speak to Siri, I would have to repeat myself multiple times and try to mimic an accent which wasn't my accent so that she could understand it.
"But over time the voice recognition technology improved tremendously because the training data was expanded to include people of very diverse backgrounds and their accents, so the algorithms were trained to be able to pick that up and it dramatically improved the technology. That's the way we have to think about it - without that good-quality diverse data, we will never be able to achieve the full potential of the computational tools."
While mapping India's rich genetic diversity has been the organization's primary focus so far, they plan, in time, to expand their work to other under-represented groups in Asia, the Middle East, Africa, and Latin America.
"As other like-minded people and partners join the mission, it just accelerates the achievement of what we have set out to do, which is to map out and organize the world's genomic diversity so that we can enable high-quality life and longevity benefits for everyone, everywhere," Jamuar says.
Empowering African Genomics
Africa is the birthplace of our species, and today still retains an inordinate amount of total human genetic diversity. Groups that left Africa and went on to populate the rest of the world, some 50 to 100,000 years ago, were likely small in number and only took a fraction of the total genetic diversity with them. This ancient bottleneck means that no other group in the world can match the level of genetic diversity seen in modern African populations.
Despite Africa's central importance in understanding the history and extent of human genetic diversity, the genomics of African populations remains wildly understudied. Addressing this disparity has become a central focus of the H3Africa Consortium, an initiative formally launched in 2012 with support from the African Academy of Sciences, the U.S. National Institutes of Health, and the UK's Wellcome Trust. Today, H3Africa supports over 50 projects across the continent, on an array of different research areas in genetics relevant to the health and heredity of Africans.
"Africa is the cradle of Humankind. So what that really means is that the populations that are currently living in Africa are among some of the oldest populations on the globe, and we know that the longer populations have had to go through evolutionary phases, the more variation there is in the genomes of people who live presently," says Zane Lombard, a principal investigator at H3Africa and Associate Professor of Human Genetics at the University of the Witwatersrand in Johannesburg, South Africa.
"So for that reason, African populations carry a huge amount of genetic variation and diversity, which is pretty much uncaptured. There's still a lot to learn as far as novel variation is concerned by looking at and studying African genomes."
A recent landmark H3Africa study, led by Lombard and published in Nature in October, sequenced the genomes of over 400 African individuals from 50 ethno-linguistic groups - many of which had never been sampled before.
Despite the relatively modest number of individuals sequenced in the study, over three million previously undescribed genetic variants were found, and complex patterns of ancestral migration were uncovered.
"In some of these ethno-linguistic groups they don't have a word for DNA, so we've had to really think about how to make sure that we communicate the purposes of different studies to participants so that you have true informed consent," says Lombard.
"The objective," she explained, "was to try and fill some of the gaps for many of these populations for which we didn't have any whole genome sequences or any genetic variation data...because if we're thinking about the future of precision medicine, if the patient is a member of a specific group where we don't know a lot about the genomic variation that exists in that group, it makes it really difficult to start thinking about clinical interpretation of their data."
From H3Africa's conception, the consortium's goal has not only been to better represent Africa's staggering genetic diversity in genomic data sets, but also to build Africa's domestic genomics capabilities and empower a new generation of African researchers. By doing so, the hope is that Africans will be able to set their own genomics agenda, and leapfrog to new and better ways of doing the work.
"The training that has happened on the continent and the number of new scientists, new students, and fellows that have come through the process and are now enabled to start their own research groups, to grow their own research in their countries, to be a spokesperson for genomics research in their countries, and to build that political will to do these larger types of sequencing initiatives - that is really a significant outcome from H3Africa as well. Over and above all the science that's coming out," Lombard says.
"What has been created through H3Africa is just this locus of researchers and scientists and bioethicists who have the same goal at heart - to work towards adjusting the data bias and making sure that all global populations are represented in genomics."
Meet Dr. Renee Wegrzyn, the first Director of President Biden's new health agency, ARPA-H
In today’s podcast episode, I talk with Renee Wegrzyn, appointed by President Biden as the first director of a health agency created last year, the Advanced Research Projects Agency for Health, or ARPA-H. It’s inspired by DARPA, the agency that develops innovations for the Defense department and has been credited with hatching world-changing technologies such as ARPANET, which became the internet.
Time will tell if ARPA-H will lead to similar achievements in the realm of health. That’s what President Biden and Congress expect in return for funding ARPA-H at 2.5 billion dollars over three years.
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How will the agency figure out which projects to take on, especially with so many patient advocates for different diseases demanding moonshot funding for rapid progress?
I talked with Dr. Wegrzyn about the opportunities and challenges, what lessons ARPA-H is borrowing from Operation Warp Speed, how she decided on the first ARPA-H project that was announced recently, why a separate agency was needed instead of reforming HHS and the National Institutes of Health to be better at innovation, and how ARPA-H will make progress on disease prevention in addition to treatments for cancer, Alzheimer’s and diabetes, among many other health priorities.
Dr. Wegrzyn’s resume leaves no doubt of her suitability for this role. She was a program manager at DARPA where she focused on applying gene editing and synthetic biology to the goal of improving biosecurity. For her work there, she received the Superior Public Service Medal and, in case that wasn’t enough ARPA experience, she also worked at another ARPA that leads advanced projects in intelligence, called I-ARPA. Before that, she ran technical teams in the private sector working on gene therapies and disease diagnostics, among other areas. She has been a vice president of business development at Gingko Bioworks and headed innovation at Concentric by Gingko. Her training and education includes a PhD and undergraduate degree in applied biology from the Georgia Institute of Technology and she did her postdoc as an Alexander von Humboldt Fellow in Heidelberg, Germany.
Dr. Wegrzyn told me that she’s “in the hot seat.” The pressure is on for ARPA-H especially after the need and potential for health innovation was spot lit by the pandemic and the unprecedented speed of vaccine development. We'll soon find out if ARPA-H can produce gamechangers in health that are equivalent to DARPA’s creation of the internet.
Show links:
ARPA-H - https://arpa-h.gov/
Dr. Wegrzyn profile - https://arpa-h.gov/people/renee-wegrzyn/
Dr. Wegrzyn Twitter - https://twitter.com/rwegrzyn?lang=en
President Biden Announces Dr. Wegrzyn's appointment - https://www.whitehouse.gov/briefing-room/statement...
Leaps.org coverage of ARPA-H - https://leaps.org/arpa/
ARPA-H program for joints to heal themselves - https://arpa-h.gov/news/nitro/ -
ARPA-H virtual talent search - https://arpa-h.gov/news/aco-talent-search/
Dr. Renee Wegrzyn was appointed director of ARPA-H last October.
Tiny, tough “water bears” may help bring new vaccines and medicines to sub-Saharan Africa
Microscopic tardigrades, widely considered to be some of the toughest animals on earth, can survive for decades without oxygen or water and are thought to have lived through a crash-landing on the moon. Also known as water bears, they survive by fully dehydrating and later rehydrating themselves – a feat only a few animals can accomplish. Now scientists are harnessing tardigrades’ talents to make medicines that can be dried and stored at ambient temperatures and later rehydrated for use—instead of being kept refrigerated or frozen.
Many biologics—pharmaceutical products made by using living cells or synthesized from biological sources—require refrigeration, which isn’t always available in many remote locales or places with unreliable electricity. These products include mRNA and other vaccines, monoclonal antibodies and immuno-therapies for cancer, rheumatoid arthritis and other conditions. Cooling is also needed for medicines for blood clotting disorders like hemophilia and for trauma patients.
Formulating biologics to withstand drying and hot temperatures has been the holy grail for pharmaceutical researchers for decades. It’s a hard feat to manage. “Biologic pharmaceuticals are highly efficacious, but many are inherently unstable,” says Thomas Boothby, assistant professor of molecular biology at University of Wyoming. Therefore, during storage and shipping, they must be refrigerated at 2 to 8 degrees Celsius (35 to 46 degrees Fahrenheit). Some must be frozen, typically at -20 degrees Celsius, but sometimes as low -90 degrees Celsius as was the case with the Pfizer Covid vaccine.
For Covid, fewer than 73 percent of the global population received even one dose. The need for refrigerated or frozen handling was partially to blame.
The costly cold chain
The logistics network that ensures those temperature requirements are met from production to administration is called the cold chain. This cold chain network is often unreliable or entirely lacking in remote, rural areas in developing nations that have malfunctioning electrical grids. “Almost all routine vaccines require a cold chain,” says Christopher Fox, senior vice president of formulations at the Access to Advanced Health Institute. But when the power goes out, so does refrigeration, putting refrigerated or frozen medical products at risk. Consequently, the mRNA vaccines developed for Covid-19 and other conditions, as well as more traditional vaccines for cholera, tetanus and other diseases, often can’t be delivered to the most remote parts of the world.
To understand the scope of the challenge, consider this: In the U.S., more than 984 million doses of Covid-19 vaccine have been distributed so far. Each one needed refrigeration that, even in the U.S., proved challenging. Now extrapolate to all vaccines and the entire world. For Covid, fewer than 73 percent of the global population received even one dose. The need for refrigerated or frozen handling was partially to blame.
Globally, the cold chain packaging market is valued at over $15 billion and is expected to exceed $60 billion by 2033.
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Freeze-drying, also called lyophilization, which is common for many vaccines, isn’t always an option. Many freeze-dried vaccines still need refrigeration, and even medicines approved for storage at ambient temperatures break down in the heat of sub-Saharan Africa. “Even in a freeze-dried state, biologics often will undergo partial rehydration and dehydration, which can be extremely damaging,” Boothby explains.
The cold chain is also very expensive to maintain. The global pharmaceutical cold chain packaging market is valued at more than $15 billion, and is expected to exceed $60 billion by 2033, according to a report by Future Market Insights. This cost is only expected to grow. According to the consulting company Accenture, the number of medicines that require the cold chain are expected to grow by 48 percent, compared to only 21 percent for non-cold-chain therapies.
Tardigrades to the rescue
Tardigrades are only about a millimeter long – with four legs and claws, and they lumber around like bears, thus their nickname – but could provide a big solution. “Tardigrades are unique in the animal kingdom, in that they’re able to survive a vast array of environmental insults,” says Boothby, the Wyoming professor. “They can be dried out, frozen, heated past the boiling point of water and irradiated at levels that are thousands of times more than you or I could survive.” So, his team is gradually unlocking tardigrades’ survival secrets and applying them to biologic pharmaceuticals to make them withstand both extreme heat and desiccation without losing efficacy.
Boothby’s team is focusing on blood clotting factor VIII, which, as the name implies, causes blood to clot. Currently, Boothby is concentrating on the so-called cytoplasmic abundant heat soluble (CAHS) protein family, which is found only in tardigrades, protecting them when they dry out. “We showed we can desiccate a biologic (blood clotting factor VIII, a key clotting component) in the presence of tardigrade proteins,” he says—without losing any of its effectiveness.
The researchers mixed the tardigrade protein with the blood clotting factor and then dried and rehydrated that substance six times without damaging the latter. This suggests that biologics protected with tardigrade proteins can withstand real-world fluctuations in humidity.
Furthermore, Boothby’s team found that when the blood clotting factor was dried and stabilized with tardigrade proteins, it retained its efficacy at temperatures as high as 95 degrees Celsius. That’s over 200 degrees Fahrenheit, much hotter than the 58 degrees Celsius that the World Meteorological Organization lists as the hottest recorded air temperature on earth. In contrast, without the protein, the blood clotting factor degraded significantly. The team published their findings in the journal Nature in March.
Although tardigrades rarely live more than 2.5 years, they have survived in a desiccated state for up to two decades, according to Animal Diversity Web. This suggests that tardigrades’ CAHS protein can protect biologic pharmaceuticals nearly indefinitely without refrigeration or freezing, which makes it significantly easier to deliver them in locations where refrigeration is unreliable or doesn’t exist.
The tricks of the tardigrades
Besides the CAHS proteins, tardigrades rely on a type of sugar called trehalose and some other protectants. So, rather than drying up, their cells solidify into rigid, glass-like structures. As that happens, viscosity between cells increases, thereby slowing their biological functions so much that they all but stop.
Now Boothby is combining CAHS D, one of the proteins in the CAHS family, with trehalose. He found that CAHS D and trehalose each protected proteins through repeated drying and rehydrating cycles. They also work synergistically, which means that together they might stabilize biologics under a variety of dry storage conditions.
“We’re finding the protective effect is not just additive but actually is synergistic,” he says. “We’re keen to see if something like that also holds true with different protein combinations.” If so, combinations could possibly protect against a variety of conditions.
Commercialization outlook
Before any stabilization technology for biologics can be commercialized, it first must be approved by the appropriate regulators. In the U.S., that’s the U.S. Food and Drug Administration. Developing a new formulation would require clinical testing and vast numbers of participants. So existing vaccines and biologics likely won’t be re-formulated for dry storage. “Many were developed decades ago,” says Fox. “They‘re not going to be reformulated into thermo-stable vaccines overnight,” if ever, he predicts.
Extending stability outside the cold chain, even for a few days, can have profound health, environmental and economic benefits.
Instead, this technology is most likely to be used for the new products and formulations that are just being created. New and improved vaccines will be the first to benefit. Good candidates include the plethora of mRNA vaccines, as well as biologic pharmaceuticals for neglected diseases that affect parts of the world where reliable cold chain is difficult to maintain, Boothby says. Some examples include new, more effective vaccines for malaria and for pathogenic Escherichia coli, which causes diarrhea.
Tallying up the benefits
Extending stability outside the cold chain, even for a few days, can have profound health, environmental and economic benefits. For instance, MenAfriVac, a meningitis vaccine (without tardigrade proteins) developed for sub-Saharan Africa, can be stored at up to 40 degrees Celsius for four days before administration. “If you have a few days where you don’t need to maintain the cold chain, it’s easier to transport vaccines to remote areas,” Fox says, where refrigeration does not exist or is not reliable.
Better health is an obvious benefit. MenAfriVac reduced suspected meningitis cases by 57 percent in the overall population and more than 99 percent among vaccinated individuals.
Lower healthcare costs are another benefit. One study done in Togo found that the cold chain-related costs increased the per dose vaccine price up to 11-fold. The ability to ship the vaccines using the usual cold chain, but transporting them at ambient temperatures for the final few days cut the cost in half.
There are environmental benefits, too, such as reducing fuel consumption and greenhouse gas emissions. Cold chain transports consume 20 percent more fuel than non-cold chain shipping, due to refrigeration equipment, according to the International Trade Administration.
A study by researchers at Johns Hopkins University compared the greenhouse gas emissions of the new, oral Vaxart COVID-19 vaccine (which doesn’t require refrigeration) with four intramuscular vaccines (which require refrigeration or freezing). While the Vaxart vaccine is still in clinical trials, the study found that “up to 82.25 million kilograms of CO2 could be averted by using oral vaccines in the U.S. alone.” That is akin to taking 17,700 vehicles out of service for one year.
Although tardigrades’ protective proteins won’t be a component of biologic pharmaceutics for several years, scientists are proving that this approach is viable. They are hopeful that a day will come when vaccines and biologics can be delivered anywhere in the world without needing refrigerators or freezers en route.