Shared Resources: Bioinformatics

September 11, 2014
By: Karen E. Butler, Director of Communications, DCI

Pictured from back, left to right: Wei Chen, Ph.D., Biostatistics Shared Resource; Yuan Wu, Ph.D., Affiliated Bioinformatics Faculty; Pankaj Agarwal, Biostatistics Shared Resource; Salvatore Mungal, Biostatistics Shared Resource; Kouros Owzar, Ph.D., Biostatistics Shared Resource; Alex Sibley, Biostatistics Shared Resource; and Zhiguo Li, Ph.D., Affiliated Bioinformatics Faculty. Pictured front, left to right Dr. Raluca Gordan, Ph.D., Affiliated Bioinformatics Faculty; and Jichun Xie, Ph.D., Affiliated Bioinformatics Faculty Missing Dr. Cliburn Chan, Ph.D.; Affiliated Bioinformatics Faculty, Chen Jiang, Ph.D, Alliance for Clinical Trials in Oncology; and Flora Mulkey, Alliance for Clinical Trials in Oncology.

Bioinformatics is an interdisciplinary field in which scientists develop methods and software tools for storing, retrieving, organizing and analyzing biological data. Informatics integrates computer science, statistics, mathematics and engineering to study and process biological data.

The Duke Cancer Institute Bioinformatics Shared Resource, led by Kouros Owzar, Ph.D., professor of Biostatistics and Bioinformatics and director of DCI Informatics, supports the bioinformatics research needs of DCI investigators, including requirements for complex genomic data management, data integration, computing and statistical analysis. The Bioinformatics Shared Resource provides a high-quality, service-oriented, coordinated and cost efficient bioinformatics infrastructure for DCI researchers.

“The Bioinformatics Shared Resource provides research support to DCI investigators for the design, management and analysis of genomics data from genomic assays, including microarrays, GWAS, RNA-Seq, DNA-seq and proteomics,” said Owzar. “Our emphasis is on adherence to sound statistical principles and to the conduct of reproducible analysis. Lack of appropriate and adequate statistical methodology and computational tools should not limit the scope of science discovery and rigor.”

Kouros Owzar, PhDThe Duke Cancer Institute’s Bioinformatics Shared Resource provides processed biological data to DCI programs and individual laboratories, coordinates institutional efforts in bioinformatics, helps drive the development of the biotechnology and pharmaceutical sectors within Duke, and creates synergy between scientific and clinical groups. The importance of the Bioinformatics Shared Resource within DCI and at Duke has been amplified with the explosion of genomic, proteomic, metabolomic, and other high-throughput data types; these data carry vast potential utility for clinical and translational research, especially when combined with clinical, imaging, and other scientific data.

“The Bioinformatics shared resource provides researchers at Duke with an invaluable tool for analyzing complex datasets,” said Janet Horton, M.D., a faculty user whose ongoing project evaluates gene expression profiling after radiation. “Expertise available through this resource extends from analysis of the more common gene expression profiling tools to newer DNA/RNA sequencing platforms. In addition, strong collaborative relationships with other shared resources facilitate smooth processing and optimal data management. Finally, the statistical rigor applied to the testing of each hypothesis ensures conclusions that can be repeated and reproduced by others.

Bioinformatics services include consultation and bioinformatics programming to assist with study design and analysis, high-performance computing (HPC) leveraging CPUs and GPUs, data storage, and a strong commitment to training and education of clinical, translational, and basic science investigators. Services also include state-of-the-art hardware and software to support a full range of research involving “-omics” with a particular emphasis on open development and open source solutions.

“I am part of a research group focusing on chronic lymphocytic leukemia, and we are working with Dr. Owzar and the other statisticians,” said Daphne R. Friedman, M.D., a hematologist with Duke University Hospital and Durham VA Medical Centers. “Our research is translational, and we needed statistical and bioinformatics assistance that was rigorous and in many ways complex. We have found the DCI bioinformatics shared resource to be excellent. Bioinformatics researchers have been able address several challenging concerns in a timely fashion. It has really been a great experience.”

In an effort to lay a foundation for long-term scientific collaborations between DCI investigators and shared resource personnel, currently, DCI members are not charged for Bioinformatics Shared Resource services. These long-term collaborations are expected to lead to grant and federal and industry contract applications in which shared resource staff and faculty are included as co-investigators. The expertise of the shared resource is complemented by five affiliated faculty members, with expertise in applied and theoretical statistics, and computational biology, for the Department of Biostatistics and Bioinformatics.

“Those interested in collaborating can contact us by email to set up a face-to-face meeting, said Owzar. “We work very closely with our colleagues in the Biostatistics Shared Resource and the Information System Shared Resource, led by Terry Hyslop and Jeff Allred respectively. On the administrative side, we interact extensively with Leigh Burgess, the DCI’s chief research operations officer.”

While the shared resource has for the most part focused on genomics research, future plans include expanding its support to analysis of integrated data from electronic health records and cancer imaging platforms.

Duke Cancer Institute members also have, free of charge, access to Bioinformatics Shared Resource’s in-house computational hardware, including CPU cycles, GPUs, and local storage. These resources are available to DCI investigators 365 days a year, 24 hours a day. Bioinformatics Shared Resource is located at Hock Plaza in Durham. For more information on Duke Cancer Institute Bioinformatics Shared Resource, including types of services, integration with other Duke resources, technologies, software, assays and platforms, equipment, hardware, data storage options and more, visit Bioinformatics Shared Resource. To schedule a meeting with the bioinformatics shared resource team, email Kouros Owzar.

Circle photo (top): emacs23: The top third represents code for an R package developed by the Bioinformatics Shared Resource team. The center illustration is an example of Python code for deriving the statistical equations that are the basis of the package. The code on the bottom is LaTeX for the draft of an article about the package, which the Bioinformatics Shared Resource will submit to a journal for publication.