Perelman School of Medicine at the University of Pennsylvania

Genomic and Electronic Health Record Data Workshop

Presented by the Perelman School of Medicine (PSOM) I/T Council, IBI, Penn Genetics, PCPM, and Cancer Center

 Attendees

View Presentation Materials and Videos

For access, contact
Suzanne Carlin.


 When

Wednesday, January 9, 2019
8:00 AM- 4:00 PM


 Where

Gaulton Auditorium
Biomedical Research Building II/III (BRB)
421 Curie Blvd.
Philadelphia, PA 19104


 Contact

For more information, please contact:
Suzanne Carlin

 Program Agenda

8:00 AM Registration and Breakfast
8:45 AM Jonathan A. Epstein, MD
Executive Vice Dean and Chief Scientific Officer
Opening Remarks
9:00 AM Jonathan Epstein, Kevin Mahoney, David Roth MD, Dan Rader MD, Bob Vonderheide MD
Discussion: Strategic Research Priorities from a Leadership Perspective
9:30 AM Scott M. Damrauer, MD
Assistant Professor of Surgery
Keynote: Vision for Penn’s Genomics Data Warehouse
9:45 AM Scott Damrauer, MD (Moderator)
Peter E. Gabriel, MD
Li-San Wang, PhD
Marylyn Ritchie, PhD

Panel: Promoting Collaboration and Synergy among researchers
10:30 AM Coffee Break and Cores Booths
11:00 AM Katherine L. Nathanson, MD
Professor of Medicine, Professor of Genetics
Group feedback session: Feedback and thoughts on the 9:30AM “Vision” keynote
11:30 AM Marylyn Ritchie, Jim Beinlich
Presentation: Concierge Service for Access to External Datasets (dbGap, UKBiobank, TCGA, Emerge, etc.)
Noon Lunch
1:00 PM Kash Patel, Jim Beinlich, Andre Jenkins, Paul Sweatlock
Panel: High Performance Computing, DAC, LPC, storage, ISAAC – Know your resources
1:30 PM Christine Vanzandbergen & Danielle Mowery 
Presentation: Genomics data and the EMR
2:00 PM Jeff Pennington
Associate Vice-President & Chief Research Informatics Officer (CRIO)
Deanne Taylor. PhD
Scientific Director, Department of Biomedical and Health Informatics 
Presentation: Internal and external facets of large-scale informatics: Arcus and Gabriella Miller Kids First Data Resources 
2:30 PM William Nieczpiel, Albert Chi
CHOP Enterprise Analytics
CHOP Data Warehouse/Analytics Strategy
3:00 PM Lauren Steinfeld
Penn Medicine Chief Privacy Officer and Senior Advisor on Privacy
Presentation: Security and Privacy – balancing the need to protect data with access to rich research and patient data
3:45 PM Li-San Wang
Associate Professor of Pathology and Laboratory Medicine
Closing Remarks

Session Details

Discussion: Strategic Research Priorities from a Leadership Perspective

Penn Medicine senior leaders will share their high-level views on research priorities from a strategic perspective for the organization. This will help set the stage for the more granular discussions throughout the day.

Keynote: Vision for Penn Medicine’s Genomic Data Warehouse

A workgroup consisting of research, bioinformatics, and information technology staff has been working to gather, identify and summarize the organizations collective need for genomic data now and into the immediate future.  The Genomics Data Warehouse Group would like to share the collective vision that has resulted from this effort.  A session to follow later in the agenda will focus on getting some immediate feedback from attendees on the vision. 

Panel: Promoting Collaboration and Synergy among researchers

Penn has a tremendous faculty, lab staff, and bio-informaticians. The ability to easily connect with these resources opens opportunity to identify synergies among the data needs for research, allows staff to collaborate on data sets, and can reduce the effort and time to get access to the right data the first time. Simple things like creating online forums and communities can also help. This session will allow participants to share ideas and identify opportunities to build tools to support real synergistic collaboration. 

Cores Booths (during breaks)

Spend some time during breaks to visit information booths from some interesting Cores and learn more about what each one does and how you might leverage each:

Group feedback session: Feedback and thoughts on the 9:30AM “Vision” keynote

This interactive session is an opportunity for attendees to share their thoughts and ideas on the session presented earlier in the morning.

Presentation: Concierge Service for Access to External Datasets (dbGap, UKBiobank, TCGA, Emerge, etc.)

There are a number of rich external datasets available to researchers to complement the data available from Penn Medicine patients. Access to these datasets is usually left to the individual researcher to apply for access, learn how to navigate, and in some cases manage the downloading, storage, and updating of the dataset. Penn Medicine is piloting concierge services for external data set access, whether we can provide a local copy for research access that we will centrally manage or facilitate gaining access and helping with training and orientation for using the dataset. We will discuss our progress to data and solicit feedback from faculty as to how to best enhance this service.

Panel: High Performance Computing, DAC, LPC, storage – Know your resources

There is a lot of activity around High Performance Computing, the Data Analytics Center (DAC), the new IS Advisory Center (ISAAC), and other important I/T resources that will be shared in this panel session.  The focus will be on sharing information to help you know the resources available to faculty and how to get to those resources when you need them.

Presentation: Genomics Data into the EMR

As genomic data becomes more available and the EMR provides capability to house this data, we will need to make basic decision to guide what we do and do not do with this capability:

  • What data will we store in the EMR?
  • What will clinicians do with genomic data?
  • What will be the process for governing genomic data use in the EMR?

This session will introduce these topics and be a chance to get feedback from faculty.

Presentation: Internal and external facets of large-scale informatics: Arcus and Gabriella Miller Kids First Data Resource

Important questions about the interaction of biology and clinical phenotype can be addressed by integrated research and patient data. Both community-wide data sharing platforms, such as NIH’s Gabriella Miller Kids First and intra-institutional efforts such as CHOP’s Arcus initiative share core principles of curation, standardization, integration at key dimensions, accessibility, and education. CHOP research informatics leaders will share information about the origin, strategy, and progress of these complementary programs.

Presentation: CHOP Data Warehouse/Analytics Strategy

The need for operational data in healthcare has grown dramatically specifically in areas of supporting clinical decisions and quality improvement.  Additionally, the ability to link disparate data sources has shown tremendous value in supporting these initiatives.  CHOP leaders from the Center for Healthcare Quality and Analytics will share information about the operational strategy for analytics and the journey of the CHOP data warehouse. 

Presentation:  Security and Privacy – balancing the need to protect data with access to rich research and patient data

Everyone struggles with the balance between access to rich data for research and protecting the security and privacy of that data. Medical Records can be worth up to $1,000 on the black market. Penn Medicine’s Office of Privacy, Audit, and Compliance works very closely with all of us that handle data for research and clinical care to help protect our patients’ data. This session will highlight some of the recent high profile breaches throughout the country as well as recent threats and methods used by criminals to obtain protected health information. We will review what individual researchers can do to make it easier to get the data you need safely and securely using real use cases.