Student Spotlight: Alyna Khan

by Diane Xue | Apr 13, 2023 | Interviews

Alyna Khan is a PhD Candidate at the Institute for Public Health Genetics. In addition to being a student, she is also a research scientist at the UW Genetic Analysis Center. Alyna is lead author on “Recommendations on the use and reporting of race, ethnicity, and ancestry in genetic research: Experiences from the NHLBI TOPMed program” published in Cell Genomics this past year. We have invited her to hear about her experiences as a a student and scientist and where she sees her place in the interdisciplinary field of public health genetics.

Diane: IPHG is a unique program, spanning various fields. This program attracts trainees who have interests across genetic epidemiology and the Ethical, Legal, and Social implications of genetics in practice. What were the steps that led you to this interdisciplinary program?

Alyna: I’ve always kind of been interested in so many different topics and subjects. In college, I studied Classics and Poetry and Evolutionary Biology. I feel like I’ve always been pulled to being involved in multiple different fields and learn different perspectives and how they influence each other. So when I learned about this program, it seemed to be such a great fit for me. I didn’t actually take genetics in college, but I learned a lot about genetics through my evolutionary biology classes. Especially in my comparative biology class, I got to learn about different types of organisms, how they’re unique, but also how they’re connected through genetics. I saw classics the same way. It helped me learn about societies’ ideals and institutions, systems, and philosophies.

When I think of public health, I think of so many broad things — not just epidemiology, disease and community health, but also understanding systems: System and policies, systems of justice and law, systems of language, and culture and so on. Public health to me is this big umbrella field where I’m allowed to kind of throw all these things that I’m really fascinated by into one field and also allows me to explore genetics.

After college, I didn’t have a straightforward path, but exposure to genetics was one of the several threads that ran through my work experiences. I started off working at an autism clinic, then moved to a start-up toy company. Directly before coming to UW, I worked at a company that sequenced cancer tumors,  analyzing genetic sequences of somatic tumors. And now I’m at the UW Genetic Analysis Center!

Diane: How would you articulate your main research interest now and long-term goals?

Alyna: My main research interests now are around the use of race, ethnicity, and ancestry in genome-wide association studies and polygenic risk scores. The main interest I have is really to get a better understanding of how and why – what the motivations are for using race, ethnicity, and ancestry variables in genetic studies. I’m interested in this because there’s a lot of meaning that can come out of the practice of incorporating those variables into genetics, whether that’s meaning assigned to how those variables are defined, the meaning assigned to the results and interpretation, and how these interpretations are taken up in public understanding.

Diane: Are there particular experiences or courses you’ve had in the program that have shaped your interests or shaped your view of what public health genetics is and where you fit in that interdisciplinary space?

Alyna: Yeah! One of the courses that I’m realizing had a pretty big impact on me was the Genetics and the Law course. I’ve always been really interested in law and in policy making, so I was really excited at the opportunity to get to take a law class, and it was really reassuring to me to see how big of a space genetics can take up in the law. It not only not only made me realize, like, ‘Oh! I have this genetics training, but I can actually work in a more legal, social space.’ I’m realizing I can work in any space with this training, and that’s really cool. I don’t have to be a geneticist who works in a lab at a University. I can apply my training anywhere, including like entertainment and television and policy. Another reason that this class was impactful for me was that Anna (Anna Mastroianni) introduced us to the Innocence Project in that class. I’d heard about it before a little bit, but we had one class where she invited somebody to come in and speak about it. That stuck with me for a while, because learning about the Innocence Project in my Ph. D. program was another specific moment where I thought ‘Oh, I’m capable of working in this space! And the Innocence Project continues to be on my radar for what I want to do after the program.

Similarly pharmacogenetics exposed me to ways in which, having this genetic knowledge, again can open doors for me to work in all sorts of fields that I previously had not thought to be connected to prior to this program.

Diane: Along those lines, are there areas where you think public health and genetics could be more integrated to have a bigger impact on improving population health?

Alyna: I would love to see our program get more involved or provide more opportunities to understand the role of genetics and infectious disease. In 2018, I read about the cholera outbreak in Yemen that was during the Civil War there, and I recall seeing news on genetic sequencing use to trace the cholera outbreak. I remember just being struck by how they were trying to leverage genetics to trace the outbreak, and understand the mutations and the changes. And I know a lot of that had has been going on with Covid, too, but I would love to learn more about how that tracing works. I would love to see our program have more dedicated courses or opportunities like lectures or seminars in that area of genetics and public health. Because we’ve been forced to live through a global pandemic, we’ve seen public health genetics grow and be more in the public mindset. Our program could be positioned to be helpful in those efforts with some additional training opportunities.

Because I’m very interested in law and policy, I do think that there is a lot of potential and great urgency for genetics to be more incorporated in those fields, especially as tech is rapidly increasing and improving and genetics information is become rapidly accessibly. This program highlights the need for policy to keep up with that change – whether that’s in insurance or surveillance or data governance. In the future, as more people have genetic data access, the ELSI (ethical, legal, and social implications) components of our program will only become more important.

Diane: Speaking of ELSI, you were recently a lead author of a paper that provided a set of recommendations for how we should or shouldn’t interpret genetic findings that specifically focuses on delineations between genetic ancestry, race, and ethnicity. This paper describes overlaps and differences between these concepts and offers guidance on when it’s appropriate to use different terms and analysis in order to not conflate these concepts. What was the motivation for writing this paper and how did you get involved?

Alyna: I’ll start with how I got involved. I had overheard my colleagues at the Genetic Analysis Center talking about race and genetics, and I popped my head out of the cubicle and I was like, ‘Hey, you know I clearly was eavesdropping, and I would love to learn more’ and they shared with me that they had started a discussion group at the Genetic Analysis Center to set aside a meeting time where people could discuss topics pertaining to race and genetics. That meeting time was when people would bring up books or articles or podcasts to discuss anything from statistical methods and analytical approaches to working with diverse populations, talking about ethnographies or sociology. There were very rich discussions that touched upon so many different aspects of genetic research from statistical genetics all the way to communication and reporting of genetic studies. I started attending those meetings, and I got involved in the project by volunteering to help draft a set of recommendations. Back at that time we thought ‘Oh, these could just be guidelines for analysts.’ And since at the GAC, we were the data coordinating center for NHLBI’s TOPMed Consortium,  we thought it might be helpful to have some guidelines created as a resource for analysts who might be thinking about some of the same questions we were thinking about. So it really just started off as kind of like an organic internal brainstorm as people who have experience working with diverse TOPMed data and being part of the coordinating center. At that time I had been working as part of the phenotype harmonization team. I was gaining experience working with phenotype data, including how we were categorizing and harmonizing race and ethnicity. We were confronted with a lot of challenges in that.

At the same time there were articles and events around that time that were perpetuating ideas of white supremacy and those white supremacist groups were using genetics as justification for their actions and their thoughts and beliefs. That was the year that the American Society of Human Genetics put out a statement denouncing the misappropriation of genetics for white supremacists and so these conversations surrounding race and genetics were happening on a national and global scale, and these recommendations formed as we dug deeper into understanding different perspectives and thinking about how they affected our work.

Diane: You mentioned the possible misappropriation of genetics by white supremacist and others who aim to discriminate on the basis of genetics. I’m guessing these people are probably not going to be the ones looking up this paper and being exposed to these recommendations. In terms of next steps, do you have thoughts about what needs to be done to make these ideas more widely disseminated or reach audiences that aren’t necessarily thinking about how to improve the fields of genetic epidemiology or statistical genetics?

Alyna: I think that’s there’s so many pieces to it. Starting with the genetics community, I think there’s pretty widespread consensus that genetics does not inform race, and vice versa. But I think there’s still a lot of opportunity to iron out the details and the rationale and learn how best to communicate that idea. I think it’ll be important to invite a lot of non-geneticists into that conversation and to be open to understanding what historians and sociologists and anthropologists, et cetera, are saying about race, and what their conceptions of race and biology and ethnicity and ancestry are. And while I’m framing this as like “we as a genetics community invite people in,” I think that exchange, even though I was portraying it as something unidirectional, I think that exchange is bi-directional. Through engaging in that kind of invitation and that kind of conversation with different fields, these ideas will flow between these fields.

There are so many ways in which I try not to talk about genetic exceptionalism. However, I think there are aspects of the genetics field that carry a different burden than other scientific fields in terms of its relationship to (genetics and) race. It’ll be really important for the genetics community to take on and act on the responsibility of decoupling that association. In order to do that, we, as genetic students and scientists and researchers, have to understand and grow professionally with that mindset and communicate with geneticists and non-scientists.

Another thing is to place importance and give credit to is small acts, right. Like for example, not using the word Caucasian in research is a small act that has a big impact.  We have a big impact on the language society uses to talk about science and identity. I’m learning about little tweaks one can make in the way that we represent data, like the standards that are set for submitting data tables and their data sets. Even those small acts like ‘Oh, I can’t just say white here. Oh, I need to say country of recruitment, country of birth.’ These are small things. And humans are so resilient; we can get used to new systems.

I just also want to say I feel very impacted by the people around me — whether it’s our PIRS (Progress in Research Seminar) program and Journal Club and PHG students as a whole. My gosh! I don’t know if I can curse on this thing, but like oh, my gosh! Like we know and discuss all these ideas. Opening up more spaces where we can have these conversations will be important. And I just feel so fortunate to be working at the GAC where the people I work with have shared a lot of these ideas or exposed me to the ways that things can be changes. So I’m very grateful for that, too.

Diane : I’m really glad to hear that. It seems like your work environment has provided a pretty inspirational experience.

Alyna: Inspirational and aspirational, yeah. I just feel very lucky to work with them and learn from them.

Diane:  It seems like the writing process of this paper was highly collaborative. What was the process of working with a large group of authors?

Alyna: There came to be this desire or potential to eventually turn the guidelines [on reporting of race, ethnicity, and ancestry in genetic research] that we were creating for the consortium into some kind of more formal commentary. While the initial motivation was creating a resource that would be really helpful for TOPMed analysts, there was also a hope that we could turn this into something that would be more broadly accessible. We started with these discussions at the GAC and then reached out to other TOPMed investigators including the executive committee and various committees. We invited anyone who was interested, which helped us build out some specific examples directly from PIs of diverse studies. Then we got an invitation to present the guidelines at ASHG 2020 (American Society for Human Genetics Annual Meeting). We presented it as a talk and got really wonderful feedback from people, one of whom was the editor-in-chief of Cell Genomics, so that sort of started the formal writing process after we got invited to write it as a perspective piece in Cell Genomics. At this point, we reached out to various investigators again. And we really wanted to emphasize that this would represent the views of the authors, not of TOPMed or NHLBI specifically.

I volunteered to do a literature review for the guidelines and took on the role of following up with people who volunteered, organizing logistics and those kinds of things. Then Sarah Nelson and Stephanie Gogarten and Matt Conomos had a lot of the driving ideas, along with other members at the GAC. But because I submitted the abstract to ASHG, when it was accepted as a talk, I was the one to present, and from there, it kind of just blossomed into me being a co-lead (with Stephanie Gogarten) and corresponding author and Sarah took on the role of senior author. In the writing process, my roles included writing, helping with the conceptualization, organization, helping with content, and editing. My area of focus was the harmonization section since that was what I had experience with at work. Logistically, it was also my role to work on setting deadlines and goals, making sure we were hitting those targets, reaching out to co-authors. But we all really did it together- Stephanie, Matt (Conomos), Sarah, and Caitlin McHugh, who’s no longer at GAC. In addition to the input and feedback from others, Sarah, Matt, Stephanie and I split the core writing, editing, conceptualizing- all those different stages, which was really great especially since that was my first time ever participating in all of those roles. I feel really lucky to have that support through this whole process. They always encouraged me any time I had doubts and imposter syndrome about presenting, or being lead author. Getting a PhD can be a very isolating process, but then I got to participate in this very collaborative efforts that felt like a supportive community. It was super cool.

Diane: That is super cool! And I think it’s also great for our students to hear that these collaborative and supportive spaces exist within our academic space. Along that line, what is your number one survival tip that you would give someone starting out in our program? Now, as a fifth-year PhD candidate, what do you wish you had known?

Alyna: I have so many, but I’ll try to pull out the common thread. Having a strong community of friends or family, or chosen family, whatever it is – have a strong community of social support. I that that would have been the number one most helpful thing to have int he PhD. Fortunately I’ve been able to build a little bit of that over time, but again with grad school, it’s so transient. You meet people and they leave, they graduate. So having something that is a constant is something I would have loved to have from the start. The other piece of advice is have one or several forms of escape. Originally for me it was snowboarding in the winter and going to the mountains. Completely disconnect from school and from the city. Lately my major sources of escape and disconnect have been playing Zelda and watching Love is Blind. It is the most ridiculous TV show I’ve ever seen.

Diane: I think these are great tips – it’s really important to remind ourselves and each other that work-life balance is a good thing, especially with balancing student and employee roles. 

Alyna: My setup is that I’m an employee at the Genetic Analysis Center, and so I’m not a full time student. I’m not a research assistant, or TA. That has helped me balance. I feel like I’m protected by employee benefits in working twenty hours a week. And so if I want to work more, I can. But if I don’t, I’m protected to work twenty hours a week, and that is like a mental relief. I think knowing that I have that protection as being part of that system of being an employee at the UW — that designation does also remind me that I have a job, and it’s a job that is separate from school. It’s not always an exact divider, especially now in my research days, where I am working with people in my job who are also helping me work on my dissertation. So that line is definitely blurred. But, symbolically, it has helped me maintain a balance between work and school.

Diane: That sounds very healthy. Finally, having lived in Seattle for the past few years, what are three things you recommend? It can be anything.

Alyna:

1. The mountains. We live out in this beautiful, beautiful, beautiful place — this is definitely the most beautiful place in the world I’ve ever lived. As students, we have the flexibility to go at off peak times and explore the beautiful nature around us. I’m a mountains person. But obviously out here, if you love water like there’s plenty of that, too.
2. Rupee Bar in Ballard. The best cocktails. My favorite place to get cocktails and Sri Lankan snack food. So even if you don’t want to drink anything, they have great vegetarian options and vegan options. A highly recommend!
3. Hmmm. Okay. Eating chocolate chip cookies. I’ve had an awesome time applying the skills I’m learning as a PhD student in terms of the depth and planning and logistics of a dissertation to finding my favorite chocolate of cookies in the city. One of the things I’ve been most surprised about living here in Seattle is how many people I’ve met who don’t know what the Metropolitan Market chocolate chip cookie is. It’s a good chocolate chip cookie if you want something rich. And you’re not allergic to nuts. If you want a regular chocolate chip cookie, the chocolate chip cookies at PCC are really good. If you want to up your game, get the dough and bake it yourself. I’ll give you one more. Hello, Robin’s Chocolate chip cookie!