Accelerating Research to Accurately Track Patients’ Diets

2/5 Pratt School of Engineering

Duke Engineering’s new translation accelerator in the Christensen Family Center for Innovation moved a DNA-based dietary test idea further toward making a clinical impact

a bunch of different fruits and vegetables
Accelerating Research to Accurately Track Patients’ Diets

Do you remember what you had for breakfast this morning? How about Monday? How about everything you’ve eaten over the past week?

Asking patients to fill out dietary surveys has proven time and again to be an incredibly unreliable method for obtaining this data. People are forgetful in the best of times and even more so when suffering from a life-threatening disease.

Despite being an added burden on already distressed patients, food surveys are still the standard way for clinicians to understand a patient’s eating habits. And while their accuracy may not usually be the difference between life and death, sometimes it can be.

Asking patients to keep food diaries is a notoriously inaccurate way of knowing what they’re eating. PhD student Ammara Aqeel is working on a DNA-based test that could provide a better alternative.

“For people undergoing bone marrow transplants, one of the most important aspects of their recovery is making sure they are well nourished,” said Ammara Aqeel, a fourth-year PhD candidate at Duke. “Similarly, chemotherapy treatments often lead to appetite loss, but to be able to address it, doctors need to know how much a patient is eating to begin with. And patients are often too sick to do surveys or diaries.”

Aqeel thinks there might be a viable solution. Working in the laboratory of Lawrence David, associate professor of molecular genetics and microbiology at Duke, has made her well-versed in the DNA amplification and sequencing techniques that help researchers study the human microbiome by analyzing stool samples. But rather than targeting the genetic sequences of the bacteria living in our guts, the David Lab is asking what could be revealed by targeting the genetic sequences of all of the plants and animals a person might have consumed instead.

When I chose to pursue a PhD, I wanted to go to a school that wasn’t just at the cutting edge of research, but also featured all of the resources needed to explore the policy and business side of how research interfaces with the world. Duke not only offers all of that, but actively encourages students to pursue these interests without the limitations you often find in academia.

Ammara Aqeel Duke Molecular Genetics and Microbiology PhD Student

The David Lab is examining more than 1000 samples from across the world to get a sense of what species can be found within a wide variety of diets. The results of this research can be used to calculate summary metrics, such as how much food a person has eaten or the variety of food sources, which could be useful in clinical settings.

Aqeel was interested in seeing if this approach could serve as the basis of a new startup venture, but she wasn’t sure what to do next.

That’s why she was so eager to participate in the Christensen Family Center for Innovation’s first translation accelerator cohort. Led by Ibrahim Mohedas, an executive-in-residence at Duke Engineering, the 10-week program leads researchers through an exploration of key areas to get their innovation to the next step, like conducting market research, working on storytelling, and finding partners and funding sources to work with.

Ammara Aqueel running DNA tests in her laboratory at Duke

Mohedas joined Duke Engineering in the fall of 2023 and formed an accelerator cohort that focused entirely on members of the Precision Microbiome Engineering Research Center (PreMiEr) PreMiEr is a five-year, $26 million National Science Foundation center focused on understanding and engineering the microbiomes in our homes, workspaces and other built environments.

“It has been terrific working with the PreMiEr researchers in this first cohort,” Mohedas said. “Fostering a healthy microbiome within built environments is the long-term goal of PremiEr, which can have tremendous impacts on human health in the long-term. This sort of high-impact research is precisely what the accelerator was built to support.”

Fostering a healthy microbiome within built environments is the long-term goal of PremiEr, which can have tremendous impacts on human health in the long-term. This sort of high-impact research is precisely what the accelerator was built to support.

Ibrahim Mohedas Executive-in-Residence at Duke Engineering

Going into the accelerator, Aqeel had the data to show how tracking food consumption through DNA sampling in bone marrow transplant patients was viable, but she hadn’t fully thought through what a successful product might look like. How would the results be presented to users? What would the actual tests look like? Would clinicians run their own tests through premade kits or send their samples off to a centralized location for analysis? What other methods in the field are up and coming that could also address these problems?

“The accelerator experience gave me structure,” Aqeel said. “Every week covered a different topic, and while we didn’t have enough time to finish every single component, it got me started on all of them.”

One of the most rewarding parts for Aqeel, she said, was having to conduct interviews with potential stakeholders. While she normally doesn’t reach out to clinicians during her PhD work, the accelerator required her to talk to a dozen experts in her intended field of use.

With broad new perspectives in hand, the David Lab is conducting more experiments to strengthen the case for what this diet-tracking platform is capable of. Aqeel says that the additional data will make the invention ready to be disclosed to Duke’s Office of Translation and Commercialization, filed for a patent and started down the road of entrepreneurship.

“When I chose to pursue a PhD, I wanted to go to a school that wasn’t just at the cutting edge of research, but also featured all of the resources needed to explore the policy and business side of how research interfaces with the world,” Aqeel said. “Duke not only offers all of that, but actively encourages students to pursue these interests without the limitations you often find in academia.”

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