2017-2018 Bass Connections Projects

During the 2017-2018 academic year, CAGPM partnered with the Duke Center for Genomic and Computational Biology (GCB) and Bass Connections for two Bass Connections project teams: Enabling Precision Health & Medicine and the Blue Devil Resistome.

Enabling Precision Health and Medicine

The Enabling Precision Health and Medicine Bass Connection project spanned two semesters and immersed students in a team-based experiential learning environment to research and design a clinical test to meet the real-world needs of patients in the Duke Health System. The team was split into two subteams: Family Health History and Burkholderia.

Family Health History

Collecting medical history about family members is standard practice for almost every type of physician. Family health history is more valuable than many people realize. We share our genes with all of our blood relatives, and we share our environment with our immediate family. Both genes and environment can contribute to our health risks.

The Family Health History Bass Connections team focused on expanding the utility and usefulness of the MeTree™ application. MeTree™ is a patient-facing web-based family health history-driven risk assessment application. The app is integrated into clinical practices and provides clinical decision support to patients and their primary care providers about risk levels and recommendations for risk management for 30 different conditions.

Our goals were to expand the MeTree™ platform to use with different patient populations and medical specialties in the U.S. and abroad. It is currently serving as a demonstration of a new technology called "SMART-FHIR," which permits third-party applications to integrate with electronic medical records. This interface will be the first of its kind, but additional work needs to be done to support the expansion of this application. We explored the perception of patients and providers around family history and risk management, shared decision-making, and engagement in health care for the population as a whole or subgroups like minorities or those with low education/low literacy. We also explored privacy issues and patient behavior around sharing family history information. Students considered how often people share health information and how these behaviors could be used to improve family health collection.

Family Health History Wrap-up


Infectious disease is a major contributor to mortality in critically ill patients, particularly those who are immunosuppressed. The immediate post-transplant population is acutely at risk for infection, given the heavy doses of induction immunosuppression needed to maintain the graft. Lung transplant patients are particularly at risk for infection, as the transplanted organ is continuously exposed to microorganisms in the environment. Many of the pathogens that afflict lung transplant patients are highly resistant organisms, although resistance patterns are difficult to predict and require time-consuming confirmation by culture and anti-microbial drug testing. Additionally, many of these organisms are fastidious and cannot be cultured or tested for by standard means. As a tertiary care institution, we currently send many patient samples to outside laboratories to test for specific organisms. This delays diagnosis and adds significant complexity to the care of critically ill patients when hours matter.

The goals of the Burkholderia Bass Connections team were to identify genetic markers that can accurately distinguish pathogenic from benign bacteria in Burkholderia and develop a rapid and robust diagnostic assay around these markers. Our long-term goal is to provide assay results to physicians int he Duke Health System so they can tailor antimicrobial therapy for critically ill transplant patients.

Students worked to develop and optimize a PCR protocol to genotype strains from patients and conducted bioinformatics analyses of sequence data from Burkholderia strains.

Blue Devil Resistome

CAGPM partnered with GCB, the Department of Civil & Environmental Engineering, and the Department of Molecular Genetics & Microbiology to form the Blue Devil Resistome Bass Connections project team. The course ran from summer 2017 through spring 2018, and students collaborated to map and analyze microbiological samples from Duke campus.

To gain a better understanding of antibiotic resistance in our environment, how different types of antibiotic resistance spread and how to interfere with such spread, students mapped the distribution of antibiotic-resistance genes across the Duke campus. The project was highly multidisciplinary, engaging researchers and undergraduate and graduate students with backgrounds in biology, engineering, genomics, computational sciences, bioinformatics, global health and policy. The project provided a concrete context for participating students to conduct research that has direct societal impact, with global implications.

The project allowed researchers to develop a better understanding of the potential risks associated with hospitals and healthcare centers, which may be generally relevant to similar facilities elsewhere. It also allowed us to evaluate intervention strategies that can curtail the spread of antibiotic resistance, again applicable beyond Duke. Scientifically, the work generated a valuable resource for future multidisciplinary research on environmental microbes and infectious diseases.