Cancer Bioinformatics Q&A

Wan

Lanman

The Cancer Bioinformatics Core is a shared facility between IU Simon Cancer Center (IUSCC) and Purdue University Center for Cancer Research (PUCCR). Jun Wan, Ph.D., serves as director of the core at IUSCC. He and Nadia Atallah Lanman, Ph.D., manager of the core at PUCCR, answered questions about the facility.

Q: How would you describe the core and what it offers researchers at IU and Purdue?

A: The core was initiated in 2015 by Dr. Timothy Ratliff of PUCCR and Dr. Patrick Loehrer of IUSCC and with the generous financial support from Walther Cancer Foundation. The mission of the core is to enable investigators from both IU and PU cancer centers to perform “omics” cancer research by taking full advantage of cutting-edge technologies that have been rapidly developing during the last decade, from basic molecular studies to translational and clinical investigations. We enable researchers at both cancer centers to leverage massive amounts of data and information, which would otherwise be inaccessible, to gain insight into cancer biology. Our aim is to integrate and accelerate cancer discovery, drug discovery, and precision medicine to improve and save lives through joint bioinformatics, molecular genetics, and genomics research. 

Q: The Cancer Bioinformatics Core is unique since it’s shared between IU and Purdue. Anything else make it unique?

A: In addition to standard bioinformatics analyses, such as NGS data analysis, the core emphasizes in-depth bioinformatics support to enhance the research and strengthen the grant applications for our investigators. The core’s team at IUSCC and PUCCR uses the same standard of operating procedure (SOP) by sharing the identical pipelines and tools for NGS data analysis that fits the NIH requirement about the reproducibility. It also promotes interactions between investigators from both cancer centers and core bioinformaticians so that researchers from either IUSCC or PUCCR can contact staff at either campus. Hence, researchers may take advantage of any core personnel’s expertise specific to their own projects. Cancer Bioinformatics has been working with the Center for Computational Biology and Bioinformatics (CCBB) and other shared facilities in the IUSCC. We successfully offered in-depth collaborative level bioinformatics services for our cancer researchers on experimental designs, data collection, processing, and diverse analyses.

Q: What expertise does the core’s staff offer?

A: The staff has intensive experience in diverse omics data analyses. We can process most NGS data, such as RNA-seq, single cell RNA-seq, ChIP-seq, ATAC-seq, DNA methylation data and Whole Genome/Exome Sequencing, with potential downstream analysis, including biological functions and molecular pathways. The core is also committed to project-oriented, more advanced comprehensive bioinformatics analyses in which we would customize or even develop novel bioinformatics approaches according to special demands and experiment designs from researchers. It is devoted to data mining, learning, integrating, and visualizing large public domain datasets from projects such as TCGA, CCLE, and TARGET to complement data from our cancer researchers.

Q: What can you tell us about the translational and clinical research that’s been supported by the core?

A: In addition to fundamental research support, the core also assists with translational studies, from modeling to predict the success of treatment in individual patients to the development of drugs and treatments specific to cancer. For example, we worked with Dr. Mark Kelley and his team to integrate proteomics and transcriptome data from his Phase I clinical trial on the drug APX3330. We were able to identify in patient tumor samples from the trial effects of the drug on the target protein, APE1, validating the drug-target interaction and pharmacodynamics. We had assisted Dr. Kelley’s team on similar preclinical studies, which allowed us to translate those preclinical findings to clinical data.

In addition, the core works with the Data Science and Informatics Program on the IU Grand Challenge Precision Health Initiative. The core provides expert support on genomics analysis, integration of genomic data with clinical data to inform novel, testable hypothesis from the cancer precision medicine clinic to the laboratory bench for further innovation.

Q: What has the core accomplished to date?

A: The core has successfully assisted 107 members from IUSCC and PUCCR on 310 different projects during the past three to four years. Working with researchers at the two cancer centers, the core has co-authored 33 peer-reviewed cancer-related papers, half of which were published in high-impact factor journals, including Nature Nanotechnology, Journal of Clinical Investigation, Nature Communications, Leukemia, Journal of Thoracic Oncology, Clinical Cancer Research, PNAS, Cancer Research.

Another goal of Cancer Bioinformatics is to use our expertise to strengthen grant applications to be funded for our researchers in addition to providing them with preliminary data. So far, the core has successfully supported about 21 cancer-related external grants funded during the past three to four years.

Q: What else would you like researchers to know about the core?

A: The core’s staff is always happy to help our investigators in experiment design, data analysis and mining, bioinformatics modeling and tool development. We encourage frequent communications between the researchers and the core’s staff about results of their specific projects. A recent survey showed that 89 percent of users were satisfied with the core’s services and 87 percent rated it “excellent.”

Q: If a researcher is interested in using the core, who should they contact?

A: Researchers can contact us at junwan@iu.edu or natallah@purdue.edu.