August 18, 2011

New quantitative sciences center to help manage data

New quantitative sciences center to help manage data

Yu Shyr, Ph.D., professor of Biostatistics, Cancer Biology and Preventive Medicine and Biomedical Informatics, and chief of the Division of Cancer Biostatistics, has been named director of the newly formed Center for Quantitative Sciences.

Though currently housed within Vanderbilt-Ingram Cancer Center (VICC), the new center is available to assist all Vanderbilt investigators in integration of quantitative sciences across bioinformatics, biostatistics, biomathematics and computational biology.

Yu Shyr, Ph.D.

Yu Shyr, Ph.D.

Having such a centralized quantitative sciences operation will uniquely position VICC and VUMC among peer institutions.

“I am very honored to help lead this important enterprise,” Shyr said. “This center will create a multi-disciplinary resource that provides quantitative support, service and collaboration for data-intensive projects and major grant proposals for VUMC investigators. We are here to help people do better science.”

The Center for Quantitative Sciences was created in response to a shift in biomedical research toward generating high dimensional data sets, especially in the context of clinical and translational studies. For example, traditional research focuses on one or two biological features (proteins, genes, lipids, metabolites, etc.) at a time.

By contrast, cutting-edge “-omics” approaches (proteomics, genomics, lipidomics, metabolomics, etc.) generate data for thousands of biological features with each experiment. To derive real knowledge from such enormous amounts of data requires integrated capacities for data storage, management, preprocessing, analysis and interpretation.

Shyr said that VICC and the institution must have the infrastructure in place to provide such capacity. He plans to work with University as well as School of Medicine departments to recruit faculty and staff scientists from across quantitative disciplines to help analyze and manage data-intensive projects.

“If you do whole-genome sequencing, one patient’s data may require one-half a terabyte of storage space,” Shyr explained.

“As another example, single-cell ‘mass cytometry’ allows for simultaneous measurement of up to 100 parameters per cell, for each of thousands or millions of cells per experiment. Think about the storage, the input-output speed and data mining capacities required to categorize, analyze and manage such a huge amount of information. That is beyond the scope of a single person or group.”

An experienced staff of quantitative experts also will play a key role in ensuring high-throughput research conducted at Vanderbilt is reproducible by other investigators.

“We must be able to manage and analyze data so that the quantitative methods we are using are as transparent and reproducible as the methods section of the research paper,” said Shyr.

“Vanderbilt’s strong commitment to leading-edge research makes such centers imperative,” said Susan Wente, Ph.D., associate vice chancellor for Research at VUMC.

Integrating the material generated by investigators with the decision-support tools used by physicians is essential for the delivery of personalized medicine to patients, said Jennifer Pietenpol, Ph.D., director of VICC.

“The ability to manage this vast amount of data and make it accessible and useful for scientists and physicians is what sets Vanderbilt apart from other cancer centers and universities,” said Pietenpol.

The new center is a logical extension of the University’s commitment to research.

“Vanderbilt is now recognized for the growth of its human genetics, genomics, proteomics, imaging, informatics, biostatistics, epidemiology, and many other programs, and for the strength of the scientists engaged in discovery and validation of biologic signals found in complex high-dimensional information," said Frank Harrell, Ph.D., chair of the Department of Biostatistics.

“The new Center will help to coordinate many data-centric resources at Vanderbilt and to increase capabilities in the era of information explosion. It is also an opportunity for Biostatistics to further its mission of reproducible research and reliable inference from data.

“In addition to Yu Shyr's ability to build, administrate and mentor, his amazing track record in increasing the quality and quantity of cancer research can now be brought to bear on a wider range of problems,” Harrell said.

Several other Vanderbilt leaders were crucial to the development of the new center, including Nancy Brown, M.D., chair of the Department of Medicine, Mark Magnuson, M.D., director of the Center for Stem Cell Biology, Jonathan Haines, Ph.D., director of the Center for Human Genetics Research, Harold L. (Hal) Moses, M.D., director emeritus of VICC, and Scott Hiebert, Ph.D., associate director of Basic Research at VICC.

Shyr is Ingram Professor of Cancer Research.