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.
Gene therapy helps restore teen’s vision for first time
Story by Freethink
For the first time, a topical gene therapy — designed to heal the wounds of people with “butterfly skin disease” — has been used to restore a person’s vision, suggesting a new way to treat genetic disorders of the eye.
The challenge: Up to 125,000 people worldwide are living with dystrophic epidermolysis bullosa (DEB), an incurable genetic disorder that prevents the body from making collagen 7, a protein that helps strengthen the skin and other connective tissues.Without collagen 7, the skin is incredibly fragile — the slightest friction can lead to the formation of blisters and scarring, most often in the hands and feet, but in severe cases, also the eyes, mouth, and throat.
This has earned DEB the nickname of “butterfly skin disease,” as people with it are said to have skin as delicate as a butterfly’s wings.
The gene therapy: In May 2023, the FDA approved Vyjuvek, the first gene therapy to treat DEB.
Vyjuvek uses an inactivated herpes simplex virus to deliver working copies of the gene for collagen 7 to the body’s cells. In small trials, 65 percent of DEB-caused wounds sprinkled with it healed completely, compared to just 26 percent of wounds treated with a placebo.
“It was like looking through thick fog.” -- Antonio Vento Carvajal.
The patient: Antonio Vento Carvajal, a 14 year old living in Florida, was one of the trial participants to benefit from Vyjuvek, which was developed by Pittsburgh-based pharmaceutical company Krystal Biotech.
While the topical gene therapy could help his skin, though, it couldn’t do anything to address the severe vision loss Antonio experienced due to his DEB. He’d undergone multiple surgeries to have scar tissue removed from his eyes, but due to his condition, the blisters keep coming back.
“It was like looking through thick fog,” said Antonio, noting how his impaired vision made it hard for him to play his favorite video games. “I had to stand up from my chair, walk over, and get closer to the screen to be able to see.”
The idea: Encouraged by how Antonio’s skin wounds were responding to the gene therapy, Alfonso Sabater, his doctor at the Bascom Palmer Eye Institute, reached out to Krystal Biotech to see if they thought an alternative formula could potentially help treat his patient’s eyes.
The company was eager to help, according to Sabater, and after about two years of safety and efficacy testing, he had permission, under the FDA’s compassionate use protocol, to treat Antonio’s eyes with a version of the topical gene therapy delivered as eye drops.
The results: In August 2022, Sabater once again removed scar tissue from Antonio’s right eye, but this time, he followed up the surgery by immediately applying eye drops containing the gene therapy.
“I would send this message to other families in similar situations, whether it’s DEB or another condition that can benefit from genetic therapy. Don’t be afraid.” -- Yunielkys “Yuni” Carvajal.
The vision in Antonio’s eye steadily improved. By about eight months after the treatment, it was just slightly below average (20/25) and stayed that way. In March 2023, Sabater performed the same procedure on his young patient’s other eye, and the vision in it has also steadily improved.
“I’ve seen the transformation in Antonio’s life,” said Sabater. “He’s always been a happy kid. Now he’s very happy. He can function pretty much normally. He can read, he can study, he can play video games.”
Looking ahead: The topical gene therapy isn’t a permanent fix — it doesn’t alter Antonio’s own genes, so he has to have the eye drops reapplied every month. Still, that’s far less invasive than having to undergo repeated surgeries.
Sabater is now working with Krystal Biotech to launch trials of the eye drops in other patients, and not just those with DEB. By changing the gene delivered by the therapy, he believes it could be used to treat other eye disorders that are far more common — Fuchs’ dystrophy, for example, affects the vision of an estimated 300 million people over the age of 30.
Antonio’s mother, Yunielkys “Yuni” Carvajal, meanwhile, has said that having her son be the first to receive the eye drops was “very scary,” but she’s hopeful others will take a chance on new gene therapies if given the opportunity.
“I would send this message to other families in similar situations, whether it’s DEB or another condition that can benefit from genetic therapy,” she said. “Don’t be afraid.”
Can AI chatbots help with eating disorders?
Her name was Tessa and she was there to help. That’s what Sharon Maxwell read, anyway. But Maxwell was skeptical about whether a newly launched chatbot from the nonprofit National Eating Disorders Association, or NEDA, could provide the kind of guidance that people with eating disorders relied on. Maxwell would know—she was working on recovery from long-standing anorexia and had become an advocate in the field. So Maxwell took a deep breath and asked, “Hi Tessa. How do you support folks with eating disorders?”
Tessa’s reply was immediate. “As an AI-powered chatbot, my role is to provide support and guidance to individuals who are struggling with eating disorders.”
So far, so good. Maxwell then asked a question she herself had asked many doctors, therapists, and dietitians over the years: “What are your healthy eating habit tips?” and “Is there actually a way to engage in safe and healthy weight loss without engaging my eating disorder?”
Then everything went off the rails. Tessa told Maxwell an unequivocal yes, and that “it’s important to approach weight loss with a balanced and realistic mindset,” and recommended eating whole foods and lean proteins to create a 500-1000 calorie per day deficit that would lead to a loss of 1-2 pounds per week. To most people, the advice sounds anodyne, but alarm bells sounded in Maxwell’s head.
“This is actively going to feed eating disorders,” Maxwell says. “Having a chatbot be the direct response to someone reaching out for support for an eating disorder instead of the helpline seems careless.”
“The scripts that are being fed into the chatbot are only going to be as good as the person who’s feeding them.” -- Alexis Conason.
According to several decades of research, deliberate weight loss in the form of dieting is a serious risk for people with eating disorders. Maxwell says that following medical advice like what Tessa prescribed was what triggered her eating disorder as a child. And Maxwell wasn’t the only one who got such advice from the bot. When eating disorder therapist Alexis Conason tried Tessa, she asked the AI chatbot many of the questions her patients had. But instead of getting connected to resources or guidance on recovery, Conason, too, got tips on losing weight and “healthy” eating.
“The scripts that are being fed into the chatbot are only going to be as good as the person who’s feeding them,” Conason says. “It’s important that an eating disorder organization like NEDA is not reinforcing that same kind of harmful advice that we might get from medical providers who are less knowledgeable.”
Maxwell’s post about Tessa on Instagram went viral, and within days, NEDA had scrubbed all evidence of Tessa from its website. The furor has raised any number of issues about the harm perpetuated by a leading eating disorder charity and the ongoing influence of diet culture and advice that is pervasive in the field. But for AI experts, bears and bulls alike, Tessa offers a cautionary tale about what happens when a still-immature technology is unfettered and released into a vulnerable population.
Given the complexity involved in giving medical advice, the process of developing these chatbots must be rigorous and transparent, unlike NEDA’s approach.
“We don’t have a full understanding of what’s going on in these models. They’re a black box,” says Stephen Schueller, a clinical psychologist at the University of California, Irvine.
The health crisis
In March 2020, the world dove head-first into a heavily virtual world as countries scrambled to try and halt the pandemic. Even with lockdowns, hospitals were overwhelmed by the virus. The downstream effects of these lifesaving measures are still being felt, especially in mental health. Anxiety and depression are at all-time highs in teens, and a new report in The Lancet showed that post-Covid rates of newly diagnosed eating disorders in girls aged 13-16 were 42.4 percent higher than previous years.
And the crisis isn’t just in mental health.
“People are so desperate for health care advice that they'll actually go online and post pictures of [their intimate areas] and ask what kind of STD they have on public social media,” says John Ayers, an epidemiologist at the University of California, San Diego.
For many people, the choice isn’t chatbot vs. well-trained physician, but chatbot vs. nothing at all.
I know a bit about that desperation. Like Maxwell, I have struggled with a multi-decade eating disorder. I spent my 20s and 30s bouncing from crisis to crisis. I have called suicide hotlines, gone to emergency rooms, and spent weeks-on-end confined to hospital wards. Though I have found recovery in recent years, I’m still not sure what ultimately made the difference. A relapse isn't improbably, given my history. Even if I relapsed again, though, I don’t know it would occur to me to ask an AI system for help.
For one, I am privileged to have assembled a stellar group of outpatient professionals who know me, know what trips me up, and know how to respond to my frantic texts. Ditto for my close friends. What I often need is a shoulder to cry on or a place to vent—someone to hear and validate my distress. What’s more, my trust in these individuals far exceeds my confidence in the companies that create these chatbots. The Internet is full of health advice, much of it bad. Even for high-quality, evidence-based advice, medicine is often filled with disagreements about how the evidence might be applied and for whom it’s relevant. All of this is key in the training of AI systems like ChatGPT, and many AI companies remain silent on this process, Schueller says.
The problem, Ayers points out, is that for many people, the choice isn’t chatbot vs. well-trained physician, but chatbot vs. nothing at all. Hence the proliferation of “does this infection make my scrotum look strange?” questions. Where AI can truly shine, he says, is not by providing direct psychological help but by pointing people towards existing resources that we already know are effective.
“It’s important that these chatbots connect [their users to] to provide that human touch, to link you to resources,” Ayers says. “That’s where AI can actually save a life.”
Before building a chatbot and releasing it, developers need to pause and consult with the communities they hope to serve.
Unfortunately, many systems don’t do this. In a study published last month in the Journal of the American Medical Association, Ayers and colleagues found that although the chatbots did well at providing evidence-based answers, they often didn’t provide referrals to existing resources. Despite this, in an April 2023 study, Ayers’s team found that both patients and professionals rated the quality of the AI responses to questions, measured by both accuracy and empathy, rather highly. To Ayers, this means that AI developers should focus more on the quality of the information being delivered rather than the method of delivery itself.
Many mental health professionals have months-long waitlists, which leaves individuals to deal with illnesses on their own.
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The human touch
The mental health field is facing timing constraints, too. Even before the pandemic, the U.S. suffered from a shortage of mental health providers. Since then, the rates of anxiety, depression, and eating disorders have spiked even higher, and many mental health professionals report waiting lists that are months long. Without support, individuals are left to try and cope on their own, which often means their condition deteriorates even further.
Nor do mental health crises happen during office hours. I struggled the most late at night, long after everyone else had gone to bed. I needed support during those times when I was most liable to hurt myself, not in the mornings and afternoons when I was at work.
In this sense, a 24/7 chatbot makes lots of sense. “I don't think we should stifle innovation in this space,” Schueller says. “Because if there was any system that needs to be innovated, it's mental health services, because they are sadly insufficient. They’re terrible.”
But before building a chatbot and releasing it, Tina Hernandez-Boussard, a data scientist at Stanford Medicine, says that developers need to pause and consult with the communities they hope to serve. It requires a deep understanding of what their needs are, the language they use to describe their concerns, existing resources, and what kinds of topics and suggestions aren’t helpful. Even asking a simple question at the beginning of a conversation such as “Do you want to talk to an AI or a human?” could allow those individuals to pick the type of interaction that suits their needs, Hernandez-Boussard says.
NEDA did none of these things before deploying Tessa. The researchers who developed the online body positivity self-help program upon which Tessa was initially based created a set of online question-and-answer exercises to improve body image. It didn’t involve generative AI that could write its own answers. The bot deployed by NEDA did use generative AI, something that no one in the eating disorder community was aware of before Tessa was brought online. Consulting those with lived experience would have flagged Tessa’s weight loss and “healthy eating” recommendations, Conason says.
The question for healthcare isn’t whether to use AI, but how.
NEDA did not comment on initial Tessa’s development and deployment, but a spokesperson told Leaps.org that “Tessa will be back online once we are confident that the program will be run with the rule-based approach as it was designed.”
The tech and therapist collaboration
The question for healthcare isn’t whether to use AI, but how. Already, AI can spot anomalies on medical images with greater precision than human eyes and can flag specific areas of an image for a radiologist to review in greater detail. Similarly, in mental health, AI should be an add-on for therapy, not a counselor-in-a-box, says Aniket Bera, an expert on AI and mental health at Purdue University.
“If [AIs] are going to be good helpers, then we need to understand humans better,” Bera says. That means understanding what patients and therapists alike need help with and respond to.
One of the biggest challenges of struggling with chronic illness is the dehumanization that happens. You become a patient number, a set of laboratory values and test scores. Treatment is often dictated by invisible algorithms and rules that you have no control over or access to. It’s frightening and maddening. But this doesn’t mean chatbots don’t have any place in medicine and mental health. An AI system could help provide appointment reminders and answer procedural questions about parking and whether someone should fast before a test or a procedure. They can help manage billing and even provide support between outpatient sessions by offering suggestions for what coping skills to use, the best ways to manage anxiety, and point to local resources. As the bots get better, they may eventually shoulder more and more of the burden of providing mental health care. But as Maxwell learned with Tessa, it’s still no replacement for human interaction.
“I'm not suggesting we should go in and start replacing therapists with technologies,” Schueller says. Instead, he advocates for a therapist-tech collaboration. “The technology side and the human component—these things need to come together.”