Legacy of the Penn Genome Frontiers Institute at the University of Pennsylvania (2001-2014)
Overview
The Penn Genome Frontiers Institute (PGFI), previously known as the Penn Genomics Institute, was established in 2001 as a Provostial institute to promote genomics at the University of Pennsylvania. PGFI has provided access to genomics technologies, assisted in the recruitment of an expanded genomics-related faculty, supported the research and service capabilities of bioinformatics and computational biology at the Penn Center for Bioinformatics (PCBI), expanded departmental and school-wide genomics cores and research, and funded interdisciplinary seed grants to facilitate genomics research. Education and outreach programs were also a vital component of PGFI. These programs kept the academic community current with genomics developments. They also helped the public understand areas of genomics that will affect personal health, the environment and other societal issues. PGFI closed June 30, 2014 after successfully fostering an environment where Penn researchers routinely produce world-class genomics research.
Drs. Eberwine and Kim are co-Directing a new research center, Penn Program for Single Cell Biology (PPSCB). Please see the PPSCB website for details.
PGFI’s Mission
- To lead the development of new quantitative genomic technologies, particularly in the area of in vivo genomics
- To promote genome-scale interdisciplinary research
- To foster integrated genomics education and training
- To assist the incorporation of genomic technologies in biomedical research
Leadership & Organization
David Roos, E. Otis Kendall Professor of Biology, was the founding director in 2001. From 2006 to 2014, Jim Eberwine and Junhyong Kim served as co-Directors of the Penn Genome Frontiers Institute. Dr. Eberwine is Elmer Holmes Bobst Professor of Pharmacology (Penn Medicine), a NIH Pioneer Award recipient who has also received a McKnight Foundation Technology Innovations Award, NIH MERIT Award and Ellison Foundation Senior Scholar Award. Dr. Eberwine, along with Dr. Kim, is a EUREKA grant awardee. Dr. Kim is Edmund J. and Louise W. Kahn Professor of Biology (School of Arts and Sciences) and has received many honors for his scholarship, including a Guggenheim Fellowship, Ellison Foundation Senior Scholar Award and the Sloan Foundation Young Investigator Award. Together, with the assistance of Associate Directors Tom Curran, Deputy Scientific Director of The Children’s Hospital of Philadelphia Research Institute, and John Hogenesch, Professor of Pharmacology, Drs. Eberwine and Kim implemented a scientific vision that leveraged Penn’s unique strengths toward the creation of a world-renowned genomics environment.
PGFI was located on the third floor of the Carolyn Lynch Laboratories on the southwest side of the Penn campus. PGFI space housed its administrative offices, conference space, High-Throughput Sequencing, Cell-Based Screening and Educational Facilities, and laboratory and office space for four of its members. PGFI provided administrative and facilities support for the on-site members. The remaining PGFI members resided throughout the campus within their home departments.
PGFI membership was open to Penn faculty, as well as to faculty in other Philadelphia-area research institutions. Membership reached 182 faculty members from five different schools across Penn (Medicine, Arts & Sciences, Engineering, Vet, Dental) and from five non-Penn institutions (Children’s Hospital of Philadelphia, Wistar, Monell Chemical Senses Center, Thomas Jefferson University, Drexel University).
PGFI Program Highlights – brief summary
Scientific
- Made cutting-edge technologies available to its members by sponsoring research facilities and contributing to existing facilities
- PGFI’s High-Throughput Sequencing Research Facility (established Sept. 2010): 5 next-generation sequencers—1 ABI SOLiD4, 1 ABI SOLiD 5500xl, 2 Illumina HiSeq2000s (upgraded to the HiSeq2500 system in 2013), 1 MiSeq (transferred to the Perelman School of Medicine Next Gen Sequencing Core)
- PGFI’s High-Performance Computing Facility: PGFI’s HPC facility contained over 1000 compute cores, connected to an array of high-performance network storage with over 800 terabytes capacity; When this capacity struggled to keep up with the newest sequencers, successful NIH funding was pursued (and awarded in 2013, $2 million in direct costs) to overhaul the HPC cluster to ensure the availability of state-of-the-art computational instrumentation (transferred to Perelman School of Medicine Academic Computing)
- Contributions of equipment, funding, and/or space to other facilities in various Penn locations (e.g., Cell-Based Screening Facility, Microarrays and Proteomics Facilities)
- Funded risky, innovative projects with promise for high impact
- Translational and Personalized Genomics Centers Initiative: PGFI facilitated large-scale projects targeting translational and personalized genomics, which is an area where genomics has tremendous potential to affect challenging biomedical problems in the near future; PGFI funded two projects at $1 million each over 3 years, and five additional projects at a seed-grant level ($200k over 3 years)
- Pilot funding for technology development and cross-disciplinary collaborative projects ($30 - $120 k awards; 29 PIs in 5 different Schools)
- Fostered the genomics community: PGFI led or was involved with 23 faculty recruitment efforts to bring new genomics expertise to Penn, hosted a monthly research seminar series, and organized informal networking events
Education and Outreach
- Provided Professional Development Workshops in the PGFI Educational Facility: wet bench training for faculty, postdoctoral researchers and graduate students in basic and advanced genomics techniques with each workshop lasting 5 days (over 290 individuals trained)
- Hosted a Genomics Techniques Workshop for reporters in the New York to Philadelphia Corridor
- Ran an Undergraduate Interdisciplinary Research Program: summer-long genomics and general scientific training program for Penn undergraduates (26 students) that integrated postdocs in genomics as formal mentors
- Acknowledged undergraduate student accomplishments in genomics with awards (10 recipients) and helped recruit promising graduate students (four-year stipend supplements for 9 PhD students)
- Organized lecture-discussion programs for the general public on relevant genomics topics like personalized medicine, stem-cells, and genomic-implications for particular diseases in partnership with The Franklin Institute (over 850 attendees)
- Sponsored a symposium on Genomics Technologies in 2007 that was attended by 200 people
- Sponsored a symposium on Single Cell Analyses in 2014 that was attended by 500 people
- Developed a genomics curriculum and training for high school educators, which was funded in part by a grant from the Arthur Vining Davis Foundation that was co-written with PGFI Associate Director for Programs, Dr. Kristin Field
- PGFI’s High-Throughput Sequencing Research Facility (established Sept. 2010): 5 next-generation sequencers—1 ABI SOLiD4, 1 ABI SOLiD 5500xl, 2 Illumina HiSeq2000s (upgraded to the HiSeq2500 system in 2013), 1 MiSeq (transferred to the Perelman School of Medicine Next Gen Sequencing Core)
- PGFI’s High-Performance Computing Facility: PGFI’s HPC facility contained over 1000 compute cores, connected to an array of high-performance network storage with over 800 terabytes capacity; When this capacity struggled to keep up with the newest sequencers, successful NIH funding was pursued (and awarded in 2013, $2 million in direct costs) to overhaul the HPC cluster to ensure the availability of state-of-the-art computational instrumentation (transferred to Perelman School of Medicine Academic Computing)
- Contributions of equipment, funding, and/or space to other facilities in various Penn locations (e.g., Cell-Based Screening Facility, Microarrays and Proteomics Facilities)
- Translational and Personalized Genomics Centers Initiative: PGFI facilitated large-scale projects targeting translational and personalized genomics, which is an area where genomics has tremendous potential to affect challenging biomedical problems in the near future; PGFI funded two projects at $1 million each over 3 years, and five additional projects at a seed-grant level ($200k over 3 years)
- Pilot funding for technology development and cross-disciplinary collaborative projects ($30 - $120 k awards; 29 PIs in 5 different Schools)