Genetic Testing Companies Are Facing a Racial Bias Problem in Disease Risk Tests
Earlier this year, California-based Ambry Genetics announced that it was discontinuing a test meant to estimate a person's risk of developing prostate or breast cancer. The test looks for variations in a person's DNA that are known to be associated with these cancers.
Known as a polygenic risk score, this type of test adds up the effects of variants in many genes — often in the dozens or hundreds — and calculates a person's risk of developing a particular health condition compared to other people. In this way, polygenic risk scores are different from traditional genetic tests that look for mutations in single genes, such as BRCA1 and BRCA2, which raise the risk of breast cancer.
Traditional genetic tests look for mutations that are relatively rare in the general population but have a large impact on a person's disease risk, like BRCA1 and BRCA2. By contrast, polygenic risk scores scan for more common genetic variants that, on their own, have a small effect on risk. Added together, however, they can raise a person's risk for developing disease.
These scores could become a part of routine healthcare in the next few years. Researchers are developing polygenic risk scores for cancer, heart, disease, diabetes and even depression. Before they can be rolled out widely, they'll have to overcome a key limitation: racial bias.
"The issue with these polygenic risk scores is that the scientific studies which they're based on have primarily been done in individuals of European ancestry," says Sara Riordan, president of the National Society of Genetics Counselors. These scores are calculated by comparing the genetic data of people with and without a particular disease. To make these scores accurate, researchers need genetic data from tens or hundreds of thousands of people.
Myriad's old test would have shown that a Black woman had twice as high of a risk for breast cancer compared to the average woman even if she was at low or average risk.
A 2018 analysis found that 78% of participants included in such large genetic studies, known as genome-wide association studies, were of European descent. That's a problem, because certain disease-associated genetic variants don't appear equally across different racial and ethnic groups. For example, a particular variant in the TTR gene, known as V1221, occurs more frequently in people of African descent. In recent years, the variant has been found in 3 to 4 percent of individuals of African ancestry in the United States. Mutations in this gene can cause protein to build up in the heart, leading to a higher risk of heart failure. A polygenic risk score for heart disease based on genetic data from mostly white people likely wouldn't give accurate risk information to African Americans.
Accuracy in genetic testing matters because such polygenic risk scores could help patients and their doctors make better decisions about their healthcare.
For instance, if a polygenic risk score determines that a woman is at higher-than-average risk of breast cancer, her doctor might recommend more frequent mammograms — X-rays that take a picture of the breast. Or, if a risk score reveals that a patient is more predisposed to heart attack, a doctor might prescribe preventive statins, a type of cholesterol-lowering drug.
"Let's be clear, these are not diagnostic tools," says Alicia Martin, a population and statistical geneticist at the Broad Institute of MIT and Harvard. "We can't use a polygenic score to say you will or will not get breast cancer or have a heart attack."
But combining a patient's polygenic risk score with other factors that affect disease risk — like age, weight, medication use or smoking status — may provide a better sense of how likely they are to develop a specific health condition than considering any one risk factor one its own. The accuracy of polygenic risk scores becomes even more important when considering that these scores may be used to guide medication prescription or help patients make decisions about preventive surgery, such as a mastectomy.
In a study published in September, researchers used results from large genetics studies of people with European ancestry and data from the UK Biobank to calculate polygenic risk scores for breast and prostate cancer for people with African, East Asian, European and South Asian ancestry. They found that they could identify individuals at higher risk of breast and prostate cancer when they scaled the risk scores within each group, but the authors say this is only a temporary solution. Recruiting more diverse participants for genetics studies will lead to better cancer detection and prevent, they conclude.
Recent efforts to do just that are expected to make these scores more accurate in the future. Until then, some genetics companies are struggling to overcome the European bias in their tests.
Acknowledging the limitations of its polygenic risk score, Ambry Genetics said in April that it would stop offering the test until it could be recalibrated. The company launched the test, known as AmbryScore, in 2018.
"After careful consideration, we have decided to discontinue AmbryScore to help reduce disparities in access to genetic testing and to stay aligned with current guidelines," the company said in an email to customers. "Due to limited data across ethnic populations, most polygenic risk scores, including AmbryScore, have not been validated for use in patients of diverse backgrounds." (The company did not make a spokesperson available for an interview for this story.)
In September 2020, the National Comprehensive Cancer Network updated its guidelines to advise against the use of polygenic risk scores in routine patient care because of "significant limitations in interpretation." The nonprofit, which represents 31 major cancer cancers across the United States, said such scores could continue to be used experimentally in clinical trials, however.
Holly Pederson, director of Medical Breast Services at the Cleveland Clinic, says the realization that polygenic risk scores may not be accurate for all races and ethnicities is relatively recent. Pederson worked with Salt Lake City-based Myriad Genetics, a leading provider of genetic tests, to improve the accuracy of its polygenic risk score for breast cancer.
The company announced in August that it had recalibrated the test, called RiskScore, for women of all ancestries. Previously, Myriad did not offer its polygenic risk score to women who self-reported any ancestry other than sole European or Ashkenazi ancestry.
"Black women, while they have a similar rate of breast cancer to white women, if not lower, had twice as high of a polygenic risk score because the development and validation of the model was done in white populations," Pederson said of the old test. In other words, Myriad's old test would have shown that a Black woman had twice as high of a risk for breast cancer compared to the average woman even if she was at low or average risk.
To develop and validate the new score, Pederson and other researchers assessed data from more than 275,000 women, including more than 31,000 African American women and nearly 50,000 women of East Asian descent. They looked at 56 different genetic variants associated with ancestry and 93 associated with breast cancer. Interestingly, they found that at least 95% of the breast cancer variants were similar amongst the different ancestries.
The company says the resulting test is now more accurate for all women across the board, but Pederson cautions that it's still slightly less accurate for Black women.
"It's not only the lack of data from Black women that leads to inaccuracies and a lack of validation in these types of risk models, it's also the pure genomic diversity of Africa," she says, noting that Africa is the most genetically diverse continent on the planet. "We just need more data, not only in American Black women but in African women to really further characterize that continent."
Martin says it's problematic that such scores are most accurate for white people because they could further exacerbate health disparities in traditionally underserved groups, such as Black Americans. "If we were to set up really representative massive genetic studies, we would do a much better job at predicting genetic risk for everybody," she says.
Earlier this year, the National Institutes of Health awarded $38 million to researchers to improve the accuracy of polygenic risk scores in diverse populations. Researchers will create new genome datasets and pool information from existing ones in an effort to diversify the data that polygenic scores rely on. They plan to make these datasets available to other scientists to use.
"By having adequate representation, we can ensure that the results of a genetic test are widely applicable," Riordan says.
Story by Big Think
We live in strange times, when the technology we depend on the most is also that which we fear the most. We celebrate cutting-edge achievements even as we recoil in fear at how they could be used to hurt us. From genetic engineering and AI to nuclear technology and nanobots, the list of awe-inspiring, fast-developing technologies is long.
However, this fear of the machine is not as new as it may seem. Technology has a longstanding alliance with power and the state. The dark side of human history can be told as a series of wars whose victors are often those with the most advanced technology. (There are exceptions, of course.) Science, and its technological offspring, follows the money.
This fear of the machine seems to be misplaced. The machine has no intent: only its maker does. The fear of the machine is, in essence, the fear we have of each other — of what we are capable of doing to one another.
How AI changes things
Sure, you would reply, but AI changes everything. With artificial intelligence, the machine itself will develop some sort of autonomy, however ill-defined. It will have a will of its own. And this will, if it reflects anything that seems human, will not be benevolent. With AI, the claim goes, the machine will somehow know what it must do to get rid of us. It will threaten us as a species.
Well, this fear is also not new. Mary Shelley wrote Frankenstein in 1818 to warn us of what science could do if it served the wrong calling. In the case of her novel, Dr. Frankenstein’s call was to win the battle against death — to reverse the course of nature. Granted, any cure of an illness interferes with the normal workings of nature, yet we are justly proud of having developed cures for our ailments, prolonging life and increasing its quality. Science can achieve nothing more noble. What messes things up is when the pursuit of good is confused with that of power. In this distorted scale, the more powerful the better. The ultimate goal is to be as powerful as gods — masters of time, of life and death.
Should countries create a World Mind Organization that controls the technologies that develop AI?
Back to AI, there is no doubt the technology will help us tremendously. We will have better medical diagnostics, better traffic control, better bridge designs, and better pedagogical animations to teach in the classroom and virtually. But we will also have better winnings in the stock market, better war strategies, and better soldiers and remote ways of killing. This grants real power to those who control the best technologies. It increases the take of the winners of wars — those fought with weapons, and those fought with money.
A story as old as civilization
The question is how to move forward. This is where things get interesting and complicated. We hear over and over again that there is an urgent need for safeguards, for controls and legislation to deal with the AI revolution. Great. But if these machines are essentially functioning in a semi-black box of self-teaching neural nets, how exactly are we going to make safeguards that are sure to remain effective? How are we to ensure that the AI, with its unlimited ability to gather data, will not come up with new ways to bypass our safeguards, the same way that people break into safes?
The second question is that of global control. As I wrote before, overseeing new technology is complex. Should countries create a World Mind Organization that controls the technologies that develop AI? If so, how do we organize this planet-wide governing board? Who should be a part of its governing structure? What mechanisms will ensure that governments and private companies do not secretly break the rules, especially when to do so would put the most advanced weapons in the hands of the rule breakers? They will need those, after all, if other actors break the rules as well.
As before, the countries with the best scientists and engineers will have a great advantage. A new international détente will emerge in the molds of the nuclear détente of the Cold War. Again, we will fear destructive technology falling into the wrong hands. This can happen easily. AI machines will not need to be built at an industrial scale, as nuclear capabilities were, and AI-based terrorism will be a force to reckon with.
So here we are, afraid of our own technology all over again.
What is missing from this picture? It continues to illustrate the same destructive pattern of greed and power that has defined so much of our civilization. The failure it shows is moral, and only we can change it. We define civilization by the accumulation of wealth, and this worldview is killing us. The project of civilization we invented has become self-cannibalizing. As long as we do not see this, and we keep on following the same route we have trodden for the past 10,000 years, it will be very hard to legislate the technology to come and to ensure such legislation is followed. Unless, of course, AI helps us become better humans, perhaps by teaching us how stupid we have been for so long. This sounds far-fetched, given who this AI will be serving. But one can always hope.
Interview with Jamie Metzl: We need a global OS upgrade
In this Q&A, leading technology and healthcare futurist Jamie Metzl discusses a range of topics and trend lines that will unfold over the next several decades: whether a version of Moore's Law applies to genetic technologies, the ethics of genetic engineering, the dangers of gene hacking, the end of sex, and much more.
Metzl is a member of the WHO expert advisory committee on human genome editing and the bestselling author of Hacking Darwin.
The conversation was lightly edited by Leaps.org for style and length.
In Hacking Darwin, you describe how we may modify the human body with CRISPR technologies, initially to obtain unsurpassed sports performance and then to enhance other human characteristics. What would such power over human biology mean for the future of our civilization?
After nearly four billion years of evolution, our one species suddenly has the increasing ability to read, write, and hack the code of life. This will have massive implications across the board, including in human health and reproduction, plant and animal agriculture, energy and advanced materials, and data storage and computing, just to name a few. My book Hacking Darwin: Genetic Engineering and the Future of Humanity primarly explored how we are currently deploying and will increasingly use our capabilities to transform human life in novel ways. My next book, The Great Biohack: Recasting Life in an Age of Revolutionary Technology, coming out in May 2024, will examine the broader implications for all of life on Earth.
We humans will, over time, use these technologies on ourselves to solve problems and eventually to enhance our capabilities. We need to be extremely conservative, cautious, and careful in doing so, but doing so will almost certainly be part of our future as a species.
In electronics, Moore's law is an established theory that computing power doubles every 18 months. Is there any parallel to be drawn with genetic technologies?
The increase in speed and decrease in costs of genome sequencing have progressed far faster than Moore’s law. It took thirteen years and cost about a billion dollars to sequence the first human genome. Today it takes just a few hours and can cost as little as a hundred dollars to do a far better job. In 2012, Jennifer Doudna and Emmanuel Charpentier published the basic science paper outlining the CRISPR-cas9 genome editing tool that would eventually win them the Nobel prize. Only six years later, the first CRISPR babies were born in China. If it feels like technology is moving ever-faster, that’s because it is.
Let's turn to the topic of aging. Do you think that the field of genetics will advance fast enough to eventually increase maximal lifespan for a child born this year? How about for a person who is currently age 50?
The science of aging is definitely real, but that doesn’t mean we will live forever. Aging is a biological process subject to human manipulation. Decades of animal research shows that. This does not mean we will live forever, but it does me we will be able to do more to expand our healthspans, the period of our lives where we are able to live most vigorously.
The first thing we need to do is make sure everyone on earth has access to the resources necessary to live up to their potential. I live in New York City, and I can take a ten minute subway ride to a neighborhood where the average lifespan is over a decade shorter than in mine. This is true within societies and between countries as well. Secondly, we all can live more like people in the Blue Zones, parts of the world where people live longer, on average, than the rest of us. They get regular exercise, eat healthy foods, have strong social connections, etc. Finally, we will all benefit, over time, from more scientific interventions to extend our healthspan. This may include small molecule drugs like metformin, rapamycin, and NAD+ boosters, blood serum infusions, and many other things.
Science fiction has depicted a future where we will never get sick again, stay young longer or become immortal. Assuming that any of this is remotely possible, should we be afraid of such changes, even if they seem positive in some regards, because we can’t understand the full implications at this point?
Not all of these promises will be realized in full, but we will use these technologies to help us live healthier, longer lives. We will never become immortal becasue nothing lasts forever. We will always get sick, even if the balance of diseases we face shifts over time, as it has always done. It is healthy, and absolutely necessary, that we feel both hope and fear about this future. If we only feel hope, we will blind ourselves to the very real potential downsides. If we only feel fear, we will deny ourselves the very meaningful benefits these technologies have the potential to provide.
A fascinating chapter in Hacking Darwin is entitled The End of Sex. And you see that as a good thing?
We humans will always be a sexually reproducing species, it’s just that we’ll reproduce increasingly less through the physical act of sex. We’re already seeing this with IVF. As the benefits of technology assisted reproduction increase relative to reproduction through the act of sex, many people will come to see assisted reproduction as a better way to reduce risk and, over time, possibly increase benefits. We’ll still have sex for all the other wonderful reasons we have it today, just less for reproduction. There will always be a critical place in our world for Italian romantics!
What are dangers of genetic hackers, perhaps especially if everyone’s DNA is eventually transcribed for medical purposes and available on the internet and in the cloud?
The sky is really the limit for how we can use gentic technologies to do things we may want, and the sky is also the limit for potential harms. It’s quite easy to imagine scenarios in which malevolent actors create synthetic pathogens designed to wreak havoc, or where people steal and abuse other people’s genetic information. It wouldn’t even need to be malevolent actors. Even well-intentioned researchers making unintended mistakes could cause real harm, as we may have seen with COVID-19 if, as appears likely to me, the pandemic stems for a research related incident]. That’s why we need strong governance and regulatory systems to optimize benefits and minimize potential harms. I was honored to have served on the World Health Organization Expert Advisory Committee on Human Genome Editing, were we developed a proposed framework for how this might best be achieved.
You foresee the equivalent of a genetic arms race between the world's most powerful countries. In what sense are genetic technologies similar to weapons?
Genetic technologies could be used to create incredibly powerful bioweapons or to build gene drives with the potential to crash entire ecosystems. That’s why thoughtful regulation is in order. Because the benefits of mastering and deploying these technologies are so great, there’s also a real danger of a genetics arms race. This could be extremely dangerous and will need to be prevented.
In your book, you express concern that states lacking Western conceptions of human rights are especially prone to misusing the science of genetics. Does this same concern apply to private companies? How much can we trust them to control and wield these technologies?
This is a conversation about science and technology but it’s really a conversation about values. If we don’t agree on what core values should be promoted, it will be nearly impossible to agree on what actions do and do not make sense. We need norms, laws, and values frameworks that apply to everyone, including governments, corporations, researchers, healthcare providers, DiY bio hobbyists, and everyone else.
We have co-evolved with our technology for a very long time. Many of our deepest beliefs have formed in that context and will continue to do so. But as we take for ourselves the powers we have attributed to our various gods, many of these beliefs will be challenged. We can not and must not jettison our beliefs in the face of technology, and must instead make sure our most cherished values guide the application of our most powerful technologies.
A conversation on international norms is in full swing in the field of AI, prompted by the release of ChatGPT4 earlier this year. Are there ways in which it’s inefficient, shortsighted or otherwise problematic for these discussions on gene technologies, AI and other advances to be occurring in silos? In addition to more specific guidelines, is there something to be gained from developing a universal set of norms and values that applies more broadly to all innovation?
AI is yet another technology where the potential to do great good is tied to the potential to inflict signifcant harm. It makes no sense that we tend to treat each technology on its own rather than looking at the entire category of challenges. For sure, we need to very rapidly ramp up our efforts with regard to AI norm-setting, regulations, and governance at all levels. But just doing that will be kind of like generating a flu vaccine for each individual flu strain. Far better to build a universal flu vaccine addressing common elements of all flu viruses of concern.
That’s why we also need to be far more deliberate in both building a global operating systems based around the mutual responsibilities of our global interdependence and, under that umbrella, a broader system for helping us govern and regulate revolutionary technologies. Such a process might begin with a large international conference, the equivalent of Rio 1992 for climate change, but then quickly work to establish and share best practices, help build parallel institutions in all countries so people and governamts can talk with each other, and do everything possible to maximize benefits and minimize risks at all levels in an ongoing and dynamic way.
At what point might genetic enhancements lead to a reclassfication of modified humans as another species?
We’ll still all be fellow humans for a very, very long time. We already have lots of variation between us. That is the essence of biology. Will some humans, at some point in the future, leave Earth and spend generations elsewhere? I believe so. In those new environments, humans will evolve, over time, differently than those if us who remain on this planet? This may sound like science fiction, but the sci-fi future is coming at us faster than most people realize.
Is the concept of human being changing?
Yes. It always has and always will.
Another big question raised in your book: what limits should we impose on the freedom to manipulate genetics?
Different societies will come to different conclusion on this critical question. I am sympathetic to the argument that people should have lots of say over their own bodies, which why I support abortion rights even though I recognize that an abortion can be a violent procedure. But it would be insane and self-defeating to say that individuals have an unlimited right to manipulate their own or their future children’s heritable genetics. The future of human life is all of our concern and must be regulated, albeit wisely.
In some cases, such as when we have the ability to prevent a deadly genetic disroder, it might be highly ethical to manipulate other human beings. In other circumstances, the genetic engineering of humans might be highly unethical. The key point is to avoid asking this question in a binary manner. We need to weigh the costs and benefits of each type of intervention. We need societal and global infrastrucutres to do that well. We don’t yet have those but we need them badly.
Can you tell us more about your next book?
The Great Biohack: Recasting Lifee in an Age of Revolutionary Technology, will come out in May 2024. It explores what the intersecting AI, genetics, and biotechnology revolutions will mean for the future of life on earth, including our healthcare, agriculture, industry, computing, and everything else. We are at a transitional moment for life on earth, equivalent to the dawn of agriculture, electricity, and industrialization. The key differentiator between better and worse outcomes is what we do today, at this early stage of this new transformation. The book describes what’s happening, what’s at stake, and what we each and all can and, frankly, must do to build the type of future we’d like to inhabit.
You’ve been a leader of international efforts calling for a full investigation into COVID-19 origins and are the founder of the global movement OneShared.World. What problem are you trying to solve through OneShared.World?
The biggest challenge we face today is the mismatch between the nature of our biggest problems, global and common, and the absence of a sufficient framework for addressing that entire category of challenges. The totally avoidable COVID-19 pandemic is one example of the extremet costs of the status quo. OneShared.World is our effort to fight for an upgrade in our world’s global operating system, based around the mutual responsibilities of interdependence. We’ve had global OS upgrades before after the Thirty Years War and after World War II, but wouldn’t it be better to make the necessary changes now to prevent a crisis of that level stemming from a nuclear war, ecosystem collapse, or deadlier synthetic biology pandemic rather than waiting until after? Revolutionary science is a global issue that must be wisely managed at every level if it is to be wisely managed at all.
How do we ensure that revolutionary technologies benefit humanity instead of undermining it?
That is the essential question. It’s why I’ve written Hacking Darwin, am writing The Great Biohack, and doing the rest of my work. If we want scietific revolutions to help, rather than hurt, us, we must all play a role building that future. This isn’t just a conversation about science, it’s about how we can draw on our most cherished values to guide the optimal development of science and technology for the common good. That must be everyone’s business.
Portions of this interview were first published in Grassia (Italy) and Zen Portugal.
Jamie Metzl is one of the world’s leading technology and healthcare futurists and author of the bestselling book, Hacking Darwin: Genetic Engineering and the Future of Humanity, which has been translated into 15 languages. In 2019, he was appointed to the World Health Organization expert advisory committee on human genome editing. Jamie is a faculty member of Singularity University and NextMed Health, a Senior Fellow of the Atlantic Council, and Founder and Chair of the global social movement, OneShared.World.
Called “the original COVID-19 whistleblower,” his pioneering role advocating for a full investigation into the origins of the COVID-19 pandemic has been featured in 60 Minutes, the New York Times, and most major media across the globe, and he was the lead witness in the first congressional hearings on this topic. Jamie previously served in the U.S. National Security Council, State Department, and Senate Foreign Relations Committee and with the United Nations in Cambodia. Jamie appears regularly on national and international media and his syndicated columns and other writing in science, technology, and global affairs are featured in publications around the world.
Jamie sits on advisory boards for multiple biotechnology and other companies and is Special Strategist to the WisdomTree BioRevolution Exchange Traded Fund. In addition to Hacking Darwin, he is author of a history of the Cambodian genocide, the historical novel The Depths of the Sea, and the genetics sci-fi thrillers Genesis Code and Eternal Sonata. His next book, The Great Biohack: Recasting Life in an age of Revolutionary Technology, will be published by Hachette in May 2024. Jamie holds a Ph.D. from Oxford, a law degree from Harvard, and an undergraduate degree from Brown and is an avid ironman triathlete and ultramarathon runner.