Wright Center Bioinformatics Specialist earns PhD and sets sights on future policy implications for Multiple Sclerosis patients
Defending a dissertation and subsequently obtaining a PhD is an enormous accomplishment. To Amy Olex, PhD, it is just the beginning of her lifelong journey in research which is deeply personal.
Dr. Olex, senior bioinformatics specialist at the Wright Center, began her PhD journey a few years before she came to the Wright Center. She entered a PhD program at Virginia Polytechnic Institute and State University focusing on biomedical engineering. However, just as she passed her qualifying exams, her husband’s multiple sclerosis (MS) progressed rapidly, and they had to relocate with their two young children to Richmond, where they had more support from family.
Fortunately, Dr. Olex found the informatics position at the Wright Center, and the job description matched what her experiences were, where she was in life, and her passions. Since her start eight years ago, Dr. Olex has focused on providing research services, expanding her skillset, and learning sequencing. In this position, Dr. Olex provides research services for university faculty, research scientists, and students. Since 2020, in addition to providing research services to the VCU community, Dr. Olex founded and leads an international team of scientists studying the effects of COVID-19 in the immunosuppressed/compromised population as a core member of the National COVID Cohort Collaborative (N3C), which has led to policy recommendations to the CDC.
Another facet of her position is teaching. After organizing and teaching her first seminar series (Bioinformatics 101) in 2015 she realized how much she enjoyed interacting with faculty and students. Dr. Olex found joy in teaching and witnessing students get a “spark in their eye when they understood.” This experience inspired her to return to the classroom and pursue a PhD once again. Dr. Olex enjoyed the challenge of translational research, but she also loved making a difference through translational research. This led her to studying Clinical Natural Language Processing (NLP) for her dissertation through which she feels that she found a new passion and direction for her research career, “I found my niche!”
Over the years, Dr. Olex has integrated her newfound NLP skills into her work, and continues to develop NLP services within the Wright Center. This has led to multiple collaborations, including a collaboration with Drs. Deborah DiazGranados, Sally Santen, Adam Garber, and Stephanie Goldberg from the School of Medicine, and Dr. Bridget McInnes from the Computer Science department, to develop an NLP tool called TopEx. This tool enables medical educators to analyze medical students’ reflective writing blog posts from their 4th year internship program. Through mining these responses from students, they were able to identify key challenges to be addressed in the program; one of which was students having difficulty learning how to use the specialized equipment when tending to patients in specialized units,such as the ICU, which made it hard to focus on patient care. In response to these findings, additional course content and objectives were implemented during orientation and for specific rotations to help focus the students on the learning objectives. This TopEx tool has been used by numerous departments at VCU, and even in collaboration with other major research universities (see manuscript on tool here).
Dr. Olex’s research interests were formed shortly after attending a nursing informatics bootcamp at the National Institutes of Health in 2017 where she was introduced to the nursing perspective on how patient care is viewed, which was largely symptom based. She immediately connected this to multiple sclerosis, and how the illness is categorized into groups such as relapsing-remitting, primary progressive, secondary progressive, and others. This knowledge along with her personal experience with MS–knowing that there are different trajectories based on a person’s symptom timeline and how one responds to different medications–motivated Dr. Olex to pursue the utilization of NLP to aid in patient care. Her dissertation focus was based on pulling out temporal information contained within clinical notes, or more specifically, relative temporal expressions. Dr. Olex explains that when a doctor is writing a narrative in a patient’s medical notes, a phrase referring to a time period (for example ‘three weeks ago’) is a relative expression, because it depends on the date that the physician is writing the note or when a specific event happened. Previous literature on extracting temporal information have struggled with relative expressions because they could be vague or imply information not in the document. Dr. Olex’s dissertation focused on identifying relative expressions as a discrete date, such as when something happened, and durations, which are expressions relaying that something has occurred continuously over a period of time. Ultimately, the goal of this project is to build a tool that assists clinicians and care providers in extracting critical information faster from clinical notes. Dr. Olex would like for medical providers to be able to get a fuller picture of the patient’s medical history and lead to better care through medication recommendations and treatment.
Dr. Olex has MS research goals that could have possible policy implications. Since MS has affected her family, she wants to be able to utilize this research to enable better care for those impacted with the disease. “Right now, many insurance companies still try to implement step therapy,” says Dr. Olex. “You are forced to take the first tier of drugs before you can start the second tier. Physicians can not start the patient on tier three drugs unless you have done tier one, even if they think starting third tier drugs would be more beneficial for the patient.” Looking at the correlation between symptom progression timelines and the drugs patients have been on, then doing a temporal analysis to see if a patient has a certain trajectory of symptoms could aid in providing a patient with a plan for the best medication to take. If Dr. Olex can show scientifically that patients with a certain trajectory of symptoms don’t respond to a tier one drug, there might be an incentive to make policy changes around the step therapy model.
In addition to Dr. Olex’s research goals, she wants to one day become a Director of an informatics core; she is also seeking a faculty position at VCU. Her work and dedication to science and patient care are evident in the work she does at the Wright Center, and her work as a scholar shows that life experiences can be the most important inspiration for lifelong learning and life changing patient care.
If you would like to read more on Dr. Olex’s dissertation, you can find it here. To contact Dr. Olex, you can email her at alolex@vcu.edu.
Categories Education, Research, Staff