Cancer Informatics Shared Resource

University Of Wisconsin-Madison, Madison WI

Investigators

Linked publications, trials & patents

Abstract

PROJECT SUMMARY / ABSTRACT The mission of the Cancer Informatics Shared Resource (CISR) is to promote high quality, innovative cancer research by providing members of the University of Wisconsin Carbone Cancer Center (UWCCC) with cutting- edge and efficient informatics, including bioinformatics, clinical informatics, image analysis, machine learning, and computational science. CISR accomplishes this mission through a team of five highly skilled PhD staff scientists, four world-renowned informatics faculty, and the substantial computational systems and support of the University of Wisconsin Department of Biostatistics and Medical Informatics (BMI), within which CISR was established in 2003. Specific Aim 1. Provide State-of-the-art Informatics Services. CISR provides deep and broad expertise in bioinformatics and machine learning analysis of biological, clinical, and imaging data. CISR staff are well versed in the latest computational approaches for a wide variety of tasks and can efficiently implement and apply them to support UWCCC member projects. This support is provided through dedicated effort of CISR staff to members’ funded projects; involvement of CISR staff in study design, pilot studies, and grant application development; and development of standardized computational pipelines. Specific Aim 2. Develop Innovative Informatics Methodology to Support Cancer Research. CISR staff develop novel computational approaches and algorithms to allow UWCCC research to reach its full potential when existing approaches are insufficient. Support for this aim is bolstered by the effort of four faculty members with expertise in the development of novel algorithms in areas such as machine learning, electronic health record analysis, causal discovery from observational data, natural language processing, deep learning, and RNA-Seq gene expression data analysis. Faculty both collaborate with and mentor the PhD scientists in the development of novel computational approaches and their application to members’ research. During the current Cancer Center Support Grant (CCSG) cycle, support for this aim was enhanced with the growth of the staff from three to five scientists, further increasing capacity and expanding the expertise of CISR to include immunological signaling, genome annotation, transcriptional regulatory networks, and epigenetics. During this cycle, CISR supported 61 individual UWCCC members across all six scientific programs and usage doubled over the prior cycle, in terms of the average number of members served per year. With UWCCC investigators, CISR staff co-authored 34 cancer-related articles, contributed to the submission of 30 grant applications, and supported grants totaling $14M in direct costs, including five from the NCI and four from other NIH institutes. CISR has had important roles in several large-scale UWCCC projects, including the Head and Neck Cancer SPORE (P50DE026787) and a P01 for targeted radionuclide therapy (P01CA250972). CCSG funding of CISR will ensure that its team will continue to be well positioned to meet the evolving computational research needs of UWCCC investigators for cutting-edge cancer research, which is increasingly reliant on massive and heterogeneous data sets.