Genetic Testing Companies Are Facing a Racial Bias Problem in Disease Risk Tests
The large genetic studies underlying certain disease risk tests have primarily been done in populations of European ancestry, limiting their accuracy.
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.
Will religious people reject organ transplants from pigs?
Scientists are getting better at transplanting pig organs into humans. But religious followers of prohibitions on consuming pork may reject these organs, even if their bodies could accept them.
The first successful recipient of a human heart transplant lived 18 days. The first artificial heart recipient lived just over 100.
Their brief post-transplant lives paved the way toward vastly greater successes. Former Vice President Dick Cheney relied on an artificial heart for nearly two years before receiving a human heart transplant. It still beats in his chest more than a decade later.
Organ transplantation recently reached its next phase with David Bennett. He survived for two months after becoming the first recipient of a pig’s heart genetically modified to function in a human body in February. Known as a xenotransplant, the procedure could pave the way for greatly expanding the use of transplanted vital organs to extend human lives.
Clinical trials would have to be held in the U.S. before xenotransplants become widespread; Bennett’s surgery was authorized under a special Food and Drug Administration program that addresses patients with life-threatening medical conditions.
German researchers plan to perform eight pig-to-human heart transplants as part of a clinical trial beginning in 2024. According to an email sent to Leaps.org by three scholars working on the German project, these procedures will focus on one of the reasons David Bennett did not survive longer: A porcine infection from his new heart.
The transplant team will conduct more sensitive testing of the donor organs, “which in all likelihood will be able to detect even low levels of virus in the xenograft,” note the scientists, Katharina Ebner, Jochen Ostheimer and Jochen Sautermeister. They are confident that the risk of infection with a porcine virus in the future will be significantly lower.
Moreover, hearts are not the only genetically modified organs that are being xenotransplanted. A team of surgeons at the University of Alabama at Birmingham successfully transplanted genetically modified pig kidneys into a brain-dead human recipient in September. The kidneys functioned normally for more than three days before the experiment ended. The UAB team is now moving forward with clinical trials focusing on transplanting pig kidneys into human patients.
Some experts believe the momentum for xenotransplantation is building, particularly given the recent successes. “I think there is a strong likelihood this will go mainstream,” says Brendan Parent of NYU Langone Health.
Douglas Anderson, a surgeon who is part of that kidney xenotransplant team, observes that, “organ shortages have been the major issue facing transplantation since its inception” and that xenotransplantation is a potential solution to that quandary. “It can’t be understated the number of people waiting for a kidney on dialysis, which has a significant mortality rate,” he says. According to the advocacy group Donate Life America, more than 100,000 people in the U.S. alone are waiting for a donated organ, and 85 percent of them need a kidney.
Other experts believe the momentum for xenotransplantation is building, particularly given the recent successes. “I think there is a strong likelihood this will go mainstream,” says Brendan Parent, director of transplant ethics and policy at NYU Langone Health, a New York City-based hospital system. Like the UAB team, surgeons at NYU Langone have had success coaxing modified pig kidneys to work in deceased humans.
“There is a genuinely good chance that within a generation, (xenotransplantation) might become very common in reasonably wealthy countries,” says Michael Reiss, professor of science education at University College in London. In addition to his academic position, Reiss sits on the Nuffield Council on Bioethics, a nonprofit that is one of Britain’s most prominent watchdogs regarding medical and scientific issues. Reiss is also an Anglican priest and has studied xenotransplantation from both a scientific and religious point of view.
Moreover, genetic modifications could one day lead to organs being specifically optimized for their recipients. That could ensure issues like donor rejection and the calculated risk of artificially suppressing recipient immune systems become concerns of the past.
Major bioethical, religious concerns
Despite the promise of xenotransplantation, numerous bioethical issues swirl around the procedure. They could be magnified if xenotransplantation evolves from one-off experiments to a routine medical procedure.
One of the biggest is the millennia-long prohibitions Islam and Judaism have had regarding the consumption of pork. Will followers of these religions assume such rules extend to those taboo materials being inserted into a human body?
“Initially, one’s instinctual reaction is that, oh, crumbs! – how are Jews and Muslims going to react to that?” Reiss says. But in a world where science and secularism are accepted on an everyday basis, he notes it is not a significant issue. Reiss points out that valves from pig hearts have been used in human patients for decades without any issues. He adds that both Islam and Judaism waive religious dietary restrictions if a human life is at risk.
“While nobody's saying an individual patient is to be forced to have these, the very high proportion of people who identify as Jews or Muslims when given this option are content with it,” he says.
Concurring with Reiss is Michael Gusamano, professor of health policy at Lehigh University and director of its Center for Ethics. He is currently performing research on the ethics of xenotransplantation for the National Institutes of Health.
“Leaders from all major religions have commented on this and have indicated that this is not inconsistent with religious doctrine,” Gusamano says in written remarks to Leaps.org. “Having said that, it is plausible to believe that some people will assume that this is inconsistent with the teaching of their religion and may object to…receiving a xenotransplant as part of routine medical care.”
A history of clashes
Despite those assurances, science has long clashed with theology. Although Galileo proved the planets revolved around the sun, the Catholic Church found him guilty of heresy and rewarded his discovery with house arrest for the last decade of his life. A revolt occurred in mid-19th century India after native-born soldiers believed the ammunition supplied by their British occupiers had been lubricated with pork and beef tallow. Given they had to use their mouths to tear open ammunition pouches, this violated both the tenets of Islam and Hinduism. And one of the conspiracy theories hatched as a result of COVID-19 was that the vaccines developed to fight the disease were the “mark of the beast” – a sign of impending Armageddon under evangelical Christian theology.
The German xenotransplant research team has encountered such potential concerns when the procedure is regarded through a religious lens. “The pastors in our research suspected that many recipients might feel disgust and revulsion,” they write. “Even beyond these special religious reservations, cultural scripts about pigs as inferior living beings are also generally widespread and effective in the western world, so that here too possible disgust reactions cannot be ruled out.”
The German researchers add that “Jewish and Muslim hospital pastoral workers believe possible considerable problems in this respect, which must be dealt with psychosocially, religiously, and pastorally prior to a possible transplantation in order to strengthen the acceptance of the received organ by the patients and their relatives.”
Parent, the director at NYU Langone, shares a concern that xenotransplantation could move “too fast,” although much of his worry is focused on zoonotic disease transmission – pig viruses jumping into humans as a result of such procedures.
Another ethical issue
Moreover, the way pigs and other animals are raised for transplants could pose future ethical dilemmas.
Reiss notes that pigs raised for medical procedures have to be grown and kept in what are known as a designated pathogen-free facility, or DPF. Such facilities are kept painstakingly antiseptic so as to minimize the risk of zoonotic transmissions. But given pigs are fond of outdoor activities such as wallowing in mud and sleeping on hay, they lead “stunningly boring lives” that they probably do not enjoy, Reiss observes.
Ethical concerns with using pigs may push transplantation medicine into its next logical phase: Growing functional organs for transplant in a laboratory setting.
“There’s no doubt that these research pigs have gotten much better veterinary care, et cetera, (compared to farmed pigs). But it’s not a great life,” Reiss says. “And although it hasn’t so far dominated the discussion, I think as the years go by, rather as we’ve seen with the use of apes and now monkeys in medical research, more and more theologians will get uncomfortable about us just assuming we can do this with…pigs.”
The German research team raises the same concerns, but has taken a fairly sanguine view on the topic. “The impairments of the species-typical behavior will certainly provoke criticism and perhaps also public protest. But the number of animals affected is very small in relation to slaughter cattle,” the German researchers note. “Moreover, the conditions there and also in several animal experiments are far worse.”
Observers say that may push transplantation medicine into its next logical phase: Growing functional organs for transplant in a laboratory setting. Anderson, the UAB transplant surgeon, believes such an accomplishment remains decades away.
But other experts believe there is a moral imperative that xenotransplantation remain a temporary solution. “I think we have a duty to go in that direction,” Parent says. “We have to go that way, with the xenotransplantation process (as) a steppingstone and research path that will be useful for bioengineered organs.”
The Friday Five: Scientists treated this girl's disease before she was born
In this week's Friday Five, scientists treated this girl's rare diseases in utero. Plus, how to lift weights in half the time, electric shocks help people regain the ability to walk, meditation is found to work as well as medication, and much more.
The Friday Five covers five stories in research that you may have missed this week. There are plenty of controversies and troubling ethical issues in science – and we get into many of them in our online magazine – but this news roundup focuses on scientific creativity and progress to give you a therapeutic dose of inspiration headed into the weekend.
Here are the promising studies covered in this week's Friday Five:
- Kids treated for diseases before they're born
- How to lift weights in half the time
- Electric shocks help people regain the ability to walk
- Meditation just as good as medication?
- These foods could pump up your motivation