New Genomics Institute and New Cancer Genomics Program

President Judith Rodin and Provost Robert Barchi announced yesterday the establishment of a new Genomics Institute that will spearhead future development in this critical new area. Professor of Biology David Roos has been named Director of the Institute. This initiative comes at a time when many Penn schools and departments have made genomics research a priority, including the departments of Biology and Genetics, and the new Cancer Genomics Program of The Abramson Family Cancer Research Institute [AFCRI] at the Cancer Center. The financial investment in genomics initiatives across the University is expected to exceed $75 million over the next five years.

"The establishment of this important new institute demonstrates once again that the University is committed to playing a key role in the development of new fields of knowledge for the 21st century," said President Rodin. "Penn's historic emphasis on interdisciplinary study and research will enable us to take full advantage of the exciting new possibilities we expect to emerge from the field of genomics."

The new field of genomics involves the large-scale analysis of complex biological systems- -the simultaneous consideration of the entire genome and its manifestations, rather than studying biology one gene at a time. Genomics-scale approaches take particular advantage of novel engineering technologies for data production, and of computational strategies for data integration and analysis. The new discipline of bioinformatics operates at the interface between biology and computer science-dedicated to the development, integration, and analysis of rich datasets.

"Genomics and proteomics represent a fundamental revolution in the way we will approach the biological sciences in the next decade," said Provost Barchi. "With Penn's strengths in the biomedical sciences and in computer and information sciences, we are uniquely situated to play a leading role in this revolution. We intend to take full advantage of our strengths and create new opportunities for breakthrough research in these dynamic new sciences."

The Genomics Institute

The new Penn Genomics Institute has four primary goals:

  • To establish intellectual leadership in studying genomes as a whole and undertake large-scale analysis of gene products.
  • To provide a focus for the genomics community, fostering interdisciplinary projects integrating biology, medicine, engineering and computer science. The Genomics Institute will also link academics and industry, as appropriate.
  • To advance the educational mission of the University, defining a new discipline at the interface between biomedical research, engineering, and computer science.
  • To facilitate access to technology, ensuring rapid dissemination of genomics approaches (including bioinformatics) throughout biomedical research.

Institute Leadership

The Genomics Institute will benefit from the world-renowned leadership and experience of its director, David S. Roos. Dr. Roos is Professor of Biology in SAS. Dr. Roos is also affiliated with the Department of Microbiology in the School of Medicine, the Department of Pathobiology in the School of Veterinary Medicine, and graduate programs in Biology, Biotechnology, Cell and Molecular Biology, Computational Biology/Genomics, and Parasitology. Dr. Roos received his undergraduate degree in biology from Harvard College in 1979, a Ph.D. in Virology from The Rockefeller University in 1984, and joined the Penn faculty in 1989 after post-doctoral training at Stanford University.

The Roos Laboratory is well known for developing new technologies for experimental investigation; most recently, these studies have led to the identification of novel drug targets and elucidation of drug resistance mechanisms, the discovery of a novel organelle in malaria parasites, and the implementation of computational tools that expedite drug discovery through genome database mining. Dr. Roos lectures widely and has received numerous awards, including a Presidential Young Investigator Award from the N.S.F., a Merit Award from the N.I.H., and a Scholar Award from Burroughs Wellcome Fund. He also serves as a consultant for organizations such as the NIH, the World Health Organization (Geneva), and the International Centre for Genetic Engineering and Biotechnology (Delhi).

"Recent years have seen the rapid integration of biomedical research, to the extent where it is no longer possible to distinguish between such previously disparate disciplines as anatomy, biochemistry, botany, cell biology, genetics, microbiology, pathology, pharmacology, physiology, and zoology," said Dr. Roos. "As this integrative expansion encompasses engineering technologies developed in computer science, materials, and

robotics, it is now becoming possible to examine entire systems: for example, all the genes in a genome, all the proteins in a cell or all the metabolic processes in a tissue. This is an incredibly exciting time to be a biologist, particularly at Penn, which has a strong history of fostering interdisciplinary research."

Richard Spielman will serve as Associate Director of the Genomics Institute. Dr. Spielman is the Butterworth Professor of Genetics in the School of Medicine, and an expert on mapping and identification of genes for human diseases. He organized the consortium of labs that carried out "genome scans" for juvenile diabetes, and his lab has mapped genes for diabetes and other endocrine diseases. His work with Dr. Warren Ewens, Professor of Biology, has produced a statistical test (the TDT) that has become a standard approach to analysis of candidate gene studies in human genetics.

The proposal for a University-wide Genomics Institute grew out of discussions of a task force (Almanac January 18, 2000) comprised of Penn faculty including representatives from Medicine, SEAS, SAS and Veterinary Medicine. The Genomics Institute will advance its mission through a combination of intellectual, educational and service activities, including:

  • Coordinating and facilitating faculty recruitment and program development in genomics, proteomics, bioinformatics, and the ethical issues related to these new areas of inquiry.
  • Sponsoring lectures and seminars in the field, interdisciplinary pilot projects, and courses at the undergraduate, doctoral, and post-doctoral levels. The Computational Biology training program at Penn is one of the oldest and largest anywhere; this program will be expanded to incorporate a novel Bioinformatics Fellows program.
  • Providing service facilities to the University community and promoting the implementation of genomics-related technologies.

Cancer Genomics Program of the AFCRI

"The development of the Cancer Genomics Program is a critical next step for understanding the genetic basis of cancer development," said Dr. Craig Thompson, scientific director of the AFCRI. "In order to keep the AFCRI at the forefront of cancer research as whole genome sequences become available, the institute has recently established a new program in Cancer Genomics which will be led by Dr. Barbara Weber, professor of medicine." This program is an integral component of the Penn Genomics Institute and will interact closely with other programs in the AFCRI, the Cancer Center and across the University.

The Cancer Genomics program will study genetic changes that occur during the transition from normal to malignant to metastatic cells. Research will focus on breast, colon and prostate cancer and melanoma, using new technologies and methodologies amenable to the study of all cancers. Such approaches include DNA-based SNP and sequence analysis, RNA-based transcriptional profiling, and proteomics analysis.

One unique aspect of this component include the collaboration with the Cancer Genetics Project at the Sanger Center. The collaboration with the Sanger group will allow access to tumor-derived DNA sequence and epigenetic data that will provide focus to the Cancer Genomics studies.

Dr.Weber, Director of the Cancer Program at AFCRI, and other Penn investigators, will conduct research in three key programatic areas:

  • Genomics--SNP, DNA sequence and transcriptional profiling of multiple tumor models as well as array-based CGH and array-based genome wide methylation scanning.
  • Computational Biology--a dry lab to provide complex data analysis and data mining. Independent research would be focused methodology and software development for analysis of data coming from the projects described above.
  • Translational Research--projects will be focused on evaluating data from the larger genomic screens in the context of risk markers, early markers of malignant transformation, markers of treatment response and selection and therapeutic and prevention targets.


The University has developed substantial new resources for the Life Sciences in recent years, including construction of 173,000 square feet of additional research space in the Biomedical Research Buildings II-III, with additional plans to develop a new Life Sciences Building. Phase One of the Life Sciences Building will include 13,000 square feet of space specifically dedicated to the support of the Genomics Institute. In addition, recent and planned renovations of Blockley Hall provide 12,000 square feet of dry-lab space for research in the rapidly developing field of bioinformatics.With this new building, the University's total commitment for biomedical research facilities will total over one million square feet.

Penn has made commitments of nearly $38 million for the expansion of genomics research facilities, development of various support facilities, and recruitment of new faculty in this burgeoning area. In addition to existing grant support for genomics research, Penn anticipates significant external funding support through grants and fundraising initiatives that will bring the total amount of investment in this new genomics initiative to over $75 million.

Almanac, Vol. 47, No. 21, February 6, 2001

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