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Northwestern University Feinberg School of Medicine
Research

Staff Q&A: Jennifer Pacheco, NUgene Informatics Lead

Jennifer Pacheco

Where are you originally from?

I was born in Connecticut and raised in a small town in southern Indiana.

What is your educational background?

I love learning, so my education is varied, yet it all comes together. I have a bachelor’s degree in computer science, with a minor in psychology, a post-baccalaureate certificate in biology, a graduate certificate in bioinformatics, and now it’s all coming together as I’m working on my master’s degree in biomedical informatics.

Please tell us about your professional background prior to your current position.

My first job after obtaining my bachelor’s degree was as a data mining technology consultant based in Chicago, which was fun—I worked with the latest technology at the time and traveled around the world. After almost five years as a consultant, I settled down and moved to Boston to work as a scientific systems analyst at a pharmaceutical company for a few years. Then I came to Northwestern.

Why did you choose to work at Northwestern?

I was looking at graduate degree programs at Northwestern University and also looking for a simple information technology job at the University to provide some income while I went to graduate school. I came upon the job description for my current position, and when I realized it basically described my dream job, I applied right away. I’ve been here for nine years now.

What is your role at NUgene?

My main role within NUgene is to work with scientists at Feinberg and elsewhere to extract phenotypic information from the electronic health record (EHR). I spend most of my time working on the eMERGE (electronic MEdical Records and GEnomics) project, a national consortium of 10 sites with DNA biorepositories linked to EHR data; NUgene is one of those biorepositories. The goal of eMERGE is to use these EHR-linked biorepository data to conduct large high-throughput genetic research studies, and to ultimately return genetic test results to patients.

How do you help scientists at the medical school?

I help researchers select the appropriate subjects and phenotype data for their genetic research studies. First, I help researchers apply for grants to conduct their research by providing them with a concrete idea of the feasibility of their study using NUgene to help them get funded. Then, I collaborate with them to define and iteratively refine an EHR algorithm for selecting the right subjects, so that I can select case and/or control subjects for their study with the high specificity that is needed to conduct genetic research. Lastly, I mine the EHR and the self-reported health, social, and family history data gathered from NUgene participants in a questionnaire when they enroll; this is the data researchers need from those subjects for their study. Most of the data I gather comes from the Northwestern Medicine Enterprise Data Warehouse (NMEDW), which I query directly to mine EHRs for all the information researchers need. Sometimes, the data that researchers need is not easily extracted from the EHR, so I will work with NMEDW team to find it, or if the data is buried in the narrative (such as in the text of a procedurereport), I will work with my colleagues, William Thompson, PhD and Siddhartha Jonnalagadda, PhD, who are experts in natural language processing, to extract data from the text.

What is your favorite part of the job?

I learn so much from the researchers with whom we work. I love learning about their research and the diseases they study. It is motivating to be a part of research that helps patients in one way or another. It is also great to be a part of the eMERGE network, where we are developing best practices in EHR-based phenotyping and the delivery of personalized medicine.

What exciting projects are you working on?

All of the phenotypes I work on with researchers are exciting! It is wonderful to learn something new; I recently learned that infectious disease is a type of phenotype that has a genetic component. Currently I am working on a study of influenza host-pathogen interactions, or fluomics, led by Ellie Sang Sukerman, MD, and a study of the genetic host factors of caMRSA (community associated Methicillin-resistant Staphylococcus aureus), led by my eMERGE colleague who is a medical informaticsexpert here, Abel Kho, MD. The other really exciting project I’m working on is the eMERGE PGx (pharmacogenomics) project led here by my boss, the director of NUgene and co-principal investigator (PI) of eMERGE, Maureen Smith, MS, and Rex Chisholm, PhD, vice  dean of scientific affairs and graduate education, NorthwesternUniversity associate vice president for research, co-PI of eMERGE and PI of NUgene. This project is pilot testing the return of genetic results for clinical care—in particular, the individual variation in response to different drugs. This means a patient and his or her doctor can know, before even prescribing a drug, whether or not the drug might be the right one for the patient, what the right dose will probably be, and/or whether or not the patient might have an adverse reaction to the drug. This is exciting because it is a the future of so-called personalized medicine, and it’s happening here now!

Connect with Jennifer on LinkedIn.