Fellows Feature: Alice Popejoy


Alice is a public health geneticist and computational biologist, working at the intersections of evolutionary genomics, statistical genetics, and the ethical, legal, social implications (ELSI) of genomics research. Alice received her PhD in Public Health Genetics and Certificate in Statistical Genetics from the University of Washington. She is working on comparative evolutionary genomics as a CEHG Fellow, and as a postdoctoral scholar in the Bustamante Lab, she leads the Ancestry & Diversity Working Group of the Clinical Genome Resource (ClinGen) consortium.

Can you tell us a bit about yourself, personally and professionally?

Originally from Sacramento, I was fortunate to grow up in one of the world’s most diverse and integrated cities, with the largest urban tree canopy of any city in North America. I moved to upstate New York to attend Hamilton College, where I double-majored in Biology and French, took classes in Japanese and Religious Studies, and studied abroad for a year of full immersion in Paris. After college, the financial crisis combined with my desire to influence science policy led me to Washington, DC where I worked service industry jobs to support an unpaid internship in the U.S. House of Representatives. While giving tours of the Capitol and answering constituent phone calls, I landed a two-year Public Policy Fellowship at the Association for Women in Science (AWIS), where I worked with Congressional offices, the White House, professional organizations, and research institutes to advocate for programs to support diversity and inclusion in science, technology, engineering and mathematics (STEM). At AWIS, we also conducted research on gender representation among winners of scholarly awards and prizes, relative to the pool of qualified candidates and scholars, and found that women are over-represented among prize winners for service, teaching, and mentorship, whereas they are sorely under-recognized for academic research and scholarship.

Thanks to encouragement from accomplished female scientists at AWIS, I returned to academia to pursue my early interest in genetics and the law. At the University of Washington in Seattle, I earned a PhD in Public Health Genetics and a Certificate in Statistical Genetics, conducting several studies across comparative evolutionary genomics, statistical genetics, and ethical, legal, social implications (ELSI) of research. At UW, I served as the Graduate Student Body President and sat on the Board of Regents as well as several other high-profile committees, putting my public policy skills to work advocating for the needs of graduate and professional students. In my spare time, I learned Norwegian and, before graduating, spent six months as an International Research Fellow at the University of Oslo. Upon graduation, I was recruited to the Bustamante Lab in the Department of Biomedical Data Science at Stanford and have been a postdoctoral fellow here for the last year and a half. In addition to a CEHG Fellowship, I have affiliations with the Center for Integration of Research on Genetics and Ethics (CIRGE) at the Stanford Center for Biomedical Ethics (SCBE) and Stanford Precision Health for Ethnic and Racial Equity (SPHERE).

How did you end up here? How did you first become interested in genetics and science?

I remember visiting the American Museum of Natural History in New York City as a child and seeing an exhibit on the Human Genome Project. It highlighted the fact that humans are made up of the same stuff as fruit flies and bananas, and I remember thinking that was the most important thing I’d ever learned. If we were all connected to other species, including plants, then surely this information would help people realize that we are all one big family of humans. Later, while studying genetics in high school biology, I became obsessed with the idea that there should be lawyers who knew about DNA and the importance of genetic information for society.

When asked by adults what I wanted to be when I grew up (as children often are), I explained that my future career would involve ‘a field that doesn’t exist yet, at the intersections of genetics and the law’. Nearly a decade later, I began a PhD program in Public Health Genetics and continue to operate at the intersections of genetics and society.

Can you tell us about your current research and what you hope to achieve with it? 

As an interdisciplinary researcher, I have many projects that span multiple lines of inquiry. Related to computational and evolutionary genomics, I study light receptor genes called opsins, which are well-known as color vision photoreceptors in rods and cones of the retina, and lesser known as mysterious non-visual photoreceptors expressed throughout the body, especially in the brain and central nervous system. For the CEHG Fellowship, I am expanding on this work from my dissertation to study variation in opsins within and between human populations. Most people are generally surprised to find out that there are light receptors all over the human body and that we have no idea what they do. While other scientists tend to be more skeptical that non-visual opsins have retained their light-sensing function, most non-scientists are often intuitively comfortable that this makes sense, in theory.

My other primary focus is genetics and diversity, specifically how ‘race’, ‘ethnicity’, and ‘ancestry’ are interpreted and used in clinical genomics. I currently co-Chair with Carlos Bustamante the ClinGen Ancestry and Diversity Working Group (ADWG, https://www.clinicalgenome.org/working-groups/ancestry/) and we are collecting evidence to inform the development of guidelines for the use of diversity measures in clinical genomics and research.

The most common question I get asked about this research is whether we can simply do away with the collection of measures such as ‘race’ and ‘ethnicity’, in favor of inferring genetic ancestry and using that instead. The answer is that these issues are complicated, and the variables mentioned are capturing different kinds of information. For example, complex traits with both polygenic and environmental factors are likely influenced by background genetic architecture (often modeled by ancestry), and societal determinants of health (for which race or ethnicity are often used as a proxy). While many geneticists often think of diversity in genomics as an ethical issue, it is in fact a substantial scientific problem in terms of ascertainment and measurement bias, information disparity across populations, and inappropriate assumptions about the validity of using socio-cultural factors to model genetic background.

Why is your research important? What are the possible real world applications?

My research is important because all of the questions I ask center on challenging established assumptions about the world and the ways in which we conduct scientific research. For example, bacterial rhodopsin is in widespread use as a tool to study gene expression and other cellular mechanisms, but very little is known about the endogenous function of non-visual opsins in humans. Considering that light is the most ubiquitous source of life on Earth, and we are constantly inundated with synthetic photic signals in daily life (often paired with a chronic deficit of exposure to natural light), it is bizarre that so little attention is paid to this mysterious gene family. Similarly, terms such as ‘race’, ‘ethnicity’, and ‘ancestry’ are often used interchangeably and included as variables to correct for population structure in genetic association studies. However, there are important and complex differences between these concepts that often go unexamined. A lack of diverse representation in genomics research means that we actually know very little about the full range of human genomic variation that underlies disease etiology, and yet ‘precision medicine’ initiatives are rolling out in hospitals across the nation as if we have all of this figured out. The importance of what I’m doing across all of my projects is in the questioning of baseline assumptions that are often taken for granted – a practice that I feel is sorely missing from pedagogy these days.

What happens next in the process of discovery?

In my research, the process of discovery doesn’t just end and begin with the revelation of novel analytic and experimental findings. While dissemination in the form of academic papers is the norm, and this may be sufficient for some forms of discovery, it is essential that researchers whose work impacts people and populations focus on disseminating our findings in more meaningful and far-reaching ways. For example, the ClinGen Ancestry and Diversity Working Group is now conducting a survey of clinical genomics professionals and researchers to determine how ‘race’, ‘ethnicity’, and ‘ancestry’ are perceived and utilized for the purposes of variant interpretation and clinical care. Our findings from this survey will then be used in the development of guidelines for the use of diversity measures in clinical genomics. In this way, the results of our study are not only informative, they are also being used to improve the implementation of precision medicine.

Briefly, what’s the coolest thing about your work?

One of the coolest things about my work is how many different kinds of people from various disciplines are involved. The next step in my research on light receptors will involve collaborating with a quantum physicist, for example. In the context of my work on diversity in genetics, I regularly interface with statistical and population geneticists, clinical genetics professionals, bioethicists, and public health and health disparities researchers. The multi-disciplinary teams in which I’m involved enrich and deepen the research, while naturally expanding the reach of its impact.

Were there people (or one person) in particular to whom you would attribute your professional success?

I have had several mentors over the years who taught me valuable lessons both personally and professionally, each of them having contributed to my success in various ways. One in particular, Dr. Phoebe Starfield Leboy, is most notable for without her, I probably never would have even considered pursuing a PhD. Phoebe was a biochemist at UPenn and a past-President of the Association for Women in Science (AWIS) when I started working there in 2010. She was also the PI of an NSF-ADVANCE grant to look at scholarly awards and prizes in professional and disciplinary societies. The first day we met, Phoebe asked me what I wanted to do in life and how she could help me achieve it. She took me under her wing as an apprentice of sorts, both in terms of conducting analyses on her awards data and in terms of navigating science and the strange world of academic researchers as a young woman. She was also diagnosed with ALS (Lou Gehrig’s Disease) within the first ten days of our meeting, so the two years we worked together were the last two of her life. I think she felt it important to instill in me all of her knowledge and experience about what it was like to be a woman in science, and how to successfully navigate the barriers that naturally present themselves. As her final mentee out of dozens throughout her prolific career in academia, I feel extremely fortunate to have learned from her – not only how to think, write, and operate as a successful scientist, but also how to live a good life and appreciate every day as if it might be our last.

What advice would you offer to other grad students or postdocs who are considering pursuing a similar educational and career path as you? 

For any other postdocs or graduate students considering a similar educational path, I would emphasize the need to be comfortable with the unknown and ambiguous. In science, we so often wish to nail down precisely what we are going to do and how we are going to achieve it. When working on complex issues that span genomics and the ethical, legal, social implications (ELSI), as we do in Public Health Genetics, there are often unforeseen twists and turns with research projects that reflect a need for flexibility to accommodate stakeholder concerns, in addition to other ethical, legal, and social issues.

In addition to comfort with ambiguity, I strongly encourage persistence and a personal commitment to some values-based cause that drives the research forward. Despite all of the collaborative opportunities, interdisciplinary work can sometimes be solitary in that others who are entrenched in siloed departments and institutions may not always see the value in what you are doing. The bottom line is to never give up, even if it seems like you are the only one who cares, and to treat situations of misunderstanding as opportunities for teaching others about the importance of what you do, rather than as a sign that you should abandon all hope of living at the intersections and find a box to crawl into.

What are your future plans? Where do you see yourself professionally in the next 5 or 10 years?

My future plans are to build a world-class academic research lab in Public Health Genomics, with training and research opportunities for young scholars interested in evolutionary genomics and ethical, legal, social implications (ELSI) of genomics research and technologies. In the next 5-10 years, I will ideally be on faculty at a University in Northern California, conducting cutting-edge research and training the next generation of Public Health Geneticists!

CEHG’s core values include “interdisciplinary research” and “collaboration.” Can you speak to the ways your work has embodied these values?

I feel like my research exemplifies CEHG’s core values of interdisciplinary research and collaboration, as these are two key pillars of everything that I do. In order to address the most complex and challenging questions of our time, it is essential to bring diverse stakeholders and researchers with a wide variety of expertise to the table. This diversity in perspectives not only makes our science better; it is also valuable from an ethical and social standpoint.

Tell us what you do when you aren’t working on research and why. Do you have hobbies? Special talents? Other passions besides science?

When I’m not working on research, I spend time with my family outdoors and especially enjoy hiking, skiing, rock climbing and parkour*. In addition to running, jumping, climbing, etc. that are involved in parkour, I also enjoy teaching the sport. I became a parkour instructor during graduate school in 2014 and have been committed to teaching people (especially women) ever since. Besides these athletic endeavors, I greatly enjoy a high-quality coffee shop and spending time in quiet contemplation, whether that is during yoga or sitting out in nature.

* – “Parkour is a training discipline using movement that developed from military obstacle course training. Practitioners aim to get from one point to another in a complex environment, without assistive equipment and in the fastest and most efficient way possible.” – wikipedia.com


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