By Scott Harris
“Would you like to take part in the Penn Medicine BioBank?” This question now greets any and every adult patient at Penn Medicine when they check in for an appointment, electronically through the MyChart by myPennMedicine web portal or at clinics across the region. Those who say “yes” go on to be part of a remarkably powerful living laboratory. The Penn Medicine BioBank helps clinicians and scientists improve, formulate, and address key research topics, from genetics to chemotherapy to COVID-19.
The Penn Medicine BioBank recently surpassed 250,000 patient participants, and it continues to grow.
The idea behind the BioBank is relatively, perhaps deceptively, simple: a program that facilitates the preservation of the medical data and specimens—including blood, urine, and other bodily fluid and tissue samples—that are collected as part of routine patient care, then makes them available for research purposes. The result is a rich repository of material and information with nearly countless scientific applications.
“Every clinical interaction gets captured in our electronic health record,” said Penn Medicine BioBank Co-Director Marylyn Ritchie, PhD, who is also vice president for Research Informatics for the University of Pennsylvania Health System and director of the Institute for Biomedical Informatics at the Perelman School of Medicine at the University of Pennsylvania. “We don't recruit people with specific diseases; some have diseases, some are healthy. This creates opportunities to ask a lot of different research questions.”
Power in Numbers
The Penn Medicine BioBank mainly operates through PennChart, Penn Medicine’s electronic health record system. Every adult patient visiting one of Penn Medicine’s six hospitals or dozens of other clinical sites is eligible to enroll, a process that is now easier than ever thanks to streamlined patient consent processes in MyChart by myPennMedicine, the system’s digital patient portal. Along with physical biospecimens, the BioBank holds a wealth of imaging, survey, and medication data—just about any piece of information captured by the electronic health record.
With 250,000+ patients enrolled in the Penn Medicine BioBank, the information these patients have provided for research includes:
- 70,000+ patients’ blood and tissue samples
- 44,000 clinical genomic sequences
- 47 million clinical visits documented
- 10 million diagnoses
- 6.3 million medication orders
- 3.6 million procedures
Researchers can use this data and these samples to ask all sorts of questions across all types of diseases and medical specialties.
How the BioBank Opens New Research Possibilities and Connects Discovery to Patient Care
Marylyn Ritchie, PhD, and Daniel Rader, MD, are co-directors of the Penn Medicine BioBank.
One of the most promising uses of the Penn Medicine BioBank is genetic research.
“Typically with genetic research, you enroll a bunch of people with diabetes, for example, and a bunch of control participants without diabetes, and then you look across their genome to examine the differences between the two,” explained Penn Medicine BioBank Co-Director Daniel Rader, MD, who serves as chair of the Department of Genetics and chief of the Division of Translational Medicine and Human Genetics in the Perelman School of Medicine. “What the Penn Medicine BioBank allows you to do is flip that on its head. You now have access to genomic data for many thousands of people, so you can ask the question in reverse. An investigator who's worked on gene X for the last 30 years may have done work in mouse models or cells, but they can now say, ‘I want to know all the people in the BioBank who have mutations in gene X.’”
When the COVID-19 pandemic threw a wrench into many research operations, the Penn Medicine BioBank, with its pre-existing collection of specimens and data, facilitated important research in the era of social distancing. “Early in the pandemic, we were able to pull bio-specimens for virology and immunology that we needed at a time when you couldn't recruit people for studies,” Ritchie said. “We already had the specimens, so there was some really nice research and great papers from the BioBank.”
A biobank’s specimens and data are a powerful resource for all sorts of research questions, not just those prompted by a pandemic emergency. They can help identify rare genetic mutations that are connected to disease symptoms, for example, or combinations of relatively common variants that connect with a risk of diabetes.
A single-institution biobank like Penn’s is also a crucial starting point for finding opportunities to improve patient care in systematic ways. One example is in pharmacogenomics, or the prescribing of drugs based on knowledge of patients’ different susceptibility to their effects, or tendency to have side effects, depending on their genes. “We were seeing a lot of patients carrying DNA variations that would change their response to a given drug,” Ritchie said.
A team led by Sony Tuteja, PharmD, a research assistant professor of Medicine, used the BioBank to estimate how many patients had genetic variants that would impact the types of drugs they should receive. As a result, they were able to home in on two classes of chemotherapy drugs that caused major side effects for a subset of patients with a particular genetic variant. They went on to create a pathway for all patients to get timely genetic testing before they receive these drugs. Physicians then have the insight they need to prescribe the right dose of chemotherapy for each patient based on their DNA.
One of the Largest, Most Diverse Single-Institution Bio Banks
As one of just a handful of single-institution biobanks in the nation, the Penn Medicine BioBank is unusual. What puts it in a class by itself, however, is the racial, socioeconomic, and medical diversity of its participant population. For example, a total of 17% of Penn Medicine BioBank participants—over 40,000 patients—are Black, higher than any other biobank of its kind, leaders said. Broadly speaking, Black patients have been historically underrepresented in clinical research trials. Greater inclusivity in trials—across not just ancestry or ethnicity but also socioeconomic status and other factors—is widely recognized as a critical tool in reducing health disparities and developing treatments and approaches that are more effective for more people.
“We have the lowest-income neighborhoods all the way to some of the most affluent neighborhoods in the United States,” Ritchie said. “We have urban, we have suburban, we have rural [populations]. We have patients in settings from primary care through neurosurgery, dermatology, cardiology, and beyond. Our age spectrum goes from age 18 up through over 100 years of age.”
Large study populations are important in clinical research because they yield more information and more reliable results. Larger numbers mean greater statistical power, which translates to more certainty that a correlation between a genetic variant and a symptom, for example, are the result of a true relationship between them and not just chance. They also make rare connections possible to find. As Penn Medicine BioBank leaders and their colleagues worked in recent years to scale up the BioBank to its current size, one key challenge loomed over the others: a new, universal, online model for soliciting and securing patient consent. This project took on new urgency during the COVID-19 pandemic.
Previously, staff were only enrolling patients in the Penn Medicine BioBank through face-to-face interaction. “When COVID-19 happened, that’s really what motivated us to scale at the rate that we did, although we had been discussing it before the pandemic,” Ritchie said. “People can now do it at home through their patient portal, and front desk staff all over the region can pull in that information and have patients sign when they check in. That has enabled us to scale in a really big way.” Setting up this streamlined electronic consent process was a collaborative process led and piloted at the Abramson Cancer Center by Katherine Nathanson, MD, the Pearl Basser Professor for BRCA-Related Research and deputy director of Penn Medicine’s Abramson Cancer Center, along with Ritchie and Rader, as well as Michael Feldman, MD, PhD, now at Indiana University School of Medicine.
Ritchie and Rader envision Penn Medicine BioBank participants ultimately topping 1 million. That BioBank evolution—and the scientific breakthroughs it facilitates—continues with each passing day.
“We get new specimens every day,” Ritchie said. “Every clinical interaction gets captured in the EHR. This infrastructure is organic in that way, and that to me is what makes it a living laboratory. The data will live on for years to come and continue to grow.”