PennOmics Contest Announcement


Penn Medicine is challenging its members to utilize PennOmics’s Cohort Explorer tool to perform creative and purposeful research of Penn Medicine patient data. Participants’ efforts will be presented in a poster competition sponsored by Abramson Cancer Center, the Institute for Translational Medicine and Therapeutics, and Precision Medicine and is open to all School of Medicine and UPHS faculty, staff and students. Participants may enter under two categories: Genomics or Clinical. The genomic category requires applicants to use the genomic features of PennOmics with or without the clinical data available in the PennOmics dataset. The clinical category requires applicants to use only the clinical data. The top submission in each category will receive $10,000 towards professional expenses.


To Participate:

  1. Obtain access to the cohort Explorer by following the steps here.
  2. Submit an application describing your general area of research. Given that PennOmics is meant to encourage exploration, we expect that you will refine your hypothesis as you study the data while developing PennOmics queries.  Email your application to with the title: Pennomics Contest Application - your name
  3. Develop your ideas in Pennomics.   The contest does not require a publishable result, but should demonstrate how you used Pennomics to advance and refine your ideas in a meaningful way. 
  4. Prepare your entry in the form of a poster. Submit an electronic copy for the contest judges to evaluate. You will be invited to display your poster in a public area when the contest winners are announced.
  5. If you are entering the contest as a group, at least one contestant must be affiliated with the Pereleman School of Medicine or UPHS. All team members must be affiliated with the University of Pennsylvania, as faculty, staff, or students.

Contest Evaluation Criteria and Judging

The goal of this contest is to promote the use of PennOmics within the University of Pennsylvania. Entries will be judged for originality, scientific merit and sophistication in the use of the PennOmics Cohort Explorer tool. A panel of scientific and IT judges will evaluate each entry. A first, second and third prize will be awarded.


  1. All submissions must use Cohort Explorer generated data to design an experiment, evaluate a hypothesis, or to develop a tool. This may result in a study design, validation of existing papers, analysis of available data, or development of a tool/procedure.
    1. While results are not required, presenters will be judged on the content of their poster and how they used the Cohort Explorer tool to support their work.
  2. All submissions must be presented in poster format with supporting queries published in the PennOmics Cohort Explorer tool.
  3. You are encouraged to build on queries that others have developed, but you must document each one that you use.
  4. Participants must submit an abstract to Renae Judy by 09/30/2015 if you wish to participate in the poster presentation. Please do this by completing the PennOmics Contest Entry form.
  5. Prize money will be disbursed to support professional and education expenses. The details of disbursement will be worked out by the ACC Financial Director according to the situation of the prize winner(s).
  6. The prize money will be allocated evenly among the group members of the winning entry.

Example Entries

Germ-line Genetic Factors Example

The gene, STXBP5, is a regulating factor of the Von Willebrand Factor (VWF) protein and as such plays some role in blood clotting. Recent work has shown STXBP5 to have a detrimental effect on the cardiovascular health of mice. To evaluate this risk in humans, the diagnosis and variant data from patients expressing variants within the STXBP5 gene were analyzed to determine a preliminary correlation between STXBP5 mutations and cardiovascular health.

Clinical Tool Development Example

Care of patients with chronic conditions is a prevalent and complex issue, and is becoming more so with an aging population. In order for health systems to properly care for their populations it is necessary to train patients and give them the tools to monitor and control their conditions. To this end our group identified two common chronic conditions: chronic heart failure and Type II diabetes. We used PennOmics to download all the diagnoses and encounters associated with patients diagnosed with these conditions. Using this list we identified common complications associated with the conditions and how frequently patients scheduled and appeared at appointments. We developed a set of training materials for both conditions that were unique to the top 10 complications identified in the data set. We then designed an app that works and integrates with MyPennMedicine and other Penn Medicine data sources to trigger the appropriate training and management tools for participating patients. The app also supports patient reported metrics such as weight, temperature, level of fatigue, etc. and reports this back to the Penn system to be used as a warning to staff or simply to track a given population.

Study Development Example

Individuals undergoing cardiac surgery may lose a significant amount of blood during their procedure which requires blood transfusions to keep the patient stable. These transfusions result in more infections, longer time spent on a ventilator, and an increased risk of mortality. Given these serious risks, our team chose to evaluate all patients who underwent cardiac surgery in the last two years. We pulled the dates of their procedure as well as all their lab tests that require blood that were performed around the time of their procedure. We also pulled blood related diagnoses from these patients such as anemia. What we present now is the result of these analyses and our plan to expand this study to determine which tests are necessary and how often in the hopes that we can decrease the occurrence of blood transfusions and anemia among a vulnerable patient population.

Frequently Asked Questions

  1.  How can I work with PennOmics?
    1. As you develop your hypothesis, run some simple queries in Cohort Explorer to see if the data you need is available. For example, if you are exploring clinical correlations around testosterone levels, what tests would you query to find those results? There are likely several other clinical or genetic criteria you will need to explore before you find what you need. Develop and refine each of your query criteria separately then combine them into a single, compound query.
  2.  Are group entries permitted?
    1. Yes, entries may either be submitted by an individual or a group.
  3. Can I supplement my entry with data from my own lab's resources?
    1. Yes, but the contest evaluation is partially based on how you use PennOmics so be sure to highlight that in your poster.
  4. How do I credit contributors of the data I use?
    1. PennOmics receives information from multiple clinical and research sources. If you use genomic data and the corresponding specimen vendor is listed as CPD, CLB, PCVI, or WLAB please be sure to thank the Center for Personalized Diagnostics, the Penn Medicine Biobank, the Penn Cardiovascular Institute (specifically Dr. Tom Coppolla and Mike Morely), or Dr. Li-San Wang from the Center for Neurodegenerative Research respectively. If you want additional information about their methods please contact Renae Judy and she will connect you with the correct person.
  5. Where can I find queries that others have developed?
    1. If a user has chosen to share their query with the PennOmics user community it will be under the “Queries Shared with Me” module on the “My Workspace” page under the “Home” tab.
  6. Is there a template for the poster?
    1. Yes, please use the template found HERE for your entry.
  7. How do I capture and share my contest queries?
    1. Save your query
    2. Share the query with the PennOmics_Contest User in the Manage Queries sub-tab