Informatics Tools for Cancer Research and Care: Bridging the Gap Between Innovation and Implementation

Our ability to collect, analyze, and integrate diverse data at multiple scales has resulted in critical advances in our understanding of cancer initiation and progression and our ability to apply this knowledge to improve cancer outcomes. These research advances have revealed the tremendous complexity and heterogeneity of cancer that underlie challenges in developing effective treatments. The advances in our understanding of the mechanisms underlying cancer have been paralleled by an explosion in computational research. Artificial intelligence methods, cloud computing, and high-performance computing are all changing our ability to work with data in new ways and at remarkable scales.

Connecting advances in computer science to critical questions in cancer research requires implementing these methods in tools that are accessible to researchers and connecting the technology advances to pressing research needs. These goals form the basis of the National Cancer Institute (NCI’s) Informatics Technology for Cancer Research (ITCR) program, an initiative to foster the development of informatics tools that span the cancer research continuum. Since 2013, ITCR has funded the development, instantiation, and extension of nearly 100 cancer informatics tools and resources that support diverse domains such as cancer genomics, intracellular networks, histology image analysis, medical image analysis, electronic health record information retrieval, and radiation therapy, among others. The central pillar of the ITCR program is connecting tool development closely to driving needs and questions in cancer research, and the program places a particular emphasis on funding user-friendly and open-access tools that will have a broad impact on that research. Indeed, some of the most widely used tools in cancer research are supported through the ITCR program. All of the tools funded through ITCR are open source and are freely available to researchers in academic and not-for-profit organizations.

In addition to developing technology, NCI is also committed to supporting activities that maximize the integration, adoption, and dissemination of these tools, including a requirement for ITCR investigators to set aside funds annually for collaborative projects that enhance the integration and/or adoption of their technology. The ITCR “Connectivity Map,” created and maintained by the Network Data Exchange (NDEx) team,¹ depicts the current and planned connections between the tools. ITCR also provides funding opportunities (competitive revisions) for NCI research grants to incorporate ITCR into their research programs. The program will soon add an ITCR Education Resource that will develop and deploy diverse cancer informatics training to a broad community to increase individual knowledge and skill development and enhance uptake and impact of informatics tools supported through ITCR. Fundamental to the mission, ITCR has supported and promoted scholarly dissemination of original research related to or arising from its project portfolio.

The goal of this Special Series of JCO Clinical Can-cer Informatics is to continue to raise awareness of the cutting-edge cancer informatics research and resources supported through the ITCR program, a topic likely to be of particular interest to the readership of the journal. It builds on the success of a Special Issue of Cancer Research published in 2017² that featured articles from ITCR as well as other NCI informatics initiatives.

Participation in this Special Series was initiated in May 2019 by inviting all current and former principal investigators of ITCR-funded projects to submit original research related to their projects. The 29 accepted for publication are those appearing in this Special Series. All are open access so they can reach the broadest possible audience. This collection of 29 articles represents the breadth of science and scale of cancer research supported through ITCR. It includes tools that support cancer research at molecular,^3-6 cellular,⁷ tissue,^8-10 organ,^11-15 individual,^16-19 and population^20-23 levels. The tools described also support a range of cancer informatics and data science functions, including data integration,^13,24-29 data curation,³⁰ deep learning,⁹ information retrieval,^20,31,32 natural language processing,²² and statistical analysis.^5,6

A catalog of all available ITCR tools can be found on the ITCR website³³ and includes links to each tool’s website, grant information, and in many cases, links to the code repository as well as a short video overview of the tool. We encourage you to visit the site and try these tools on your own data. Collaboration with the development teams is highly encouraged to ensure that these tools continue to evolve with the needs of cancer researchers.

AUTHOR CONTRIBUTIONS

Conception and design: All authors

Collection and assembly of data: Jeremy L. Warner

Data analysis and interpretation: Jeremy L. Warner

Manuscript writing: All authors

Final approval of manuscript: All authors

Accountable for all aspects of the work: All authors

AUTHORS' DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST

The following represents disclosure information provided by authors of this manuscript. All relationships are considered compensated unless otherwise noted. Relationships are self-held unless noted. I = Immediate Family Member, Inst = My Institution. Relationships may not relate to the subject matter of this manuscript. For more information about ASCO's conflict of interest policy, please refer to www.asco.org/rwc or ascopubs.org/cci/author-center.

Open Payments is a public database containing information reported by companies about payments made to US-licensed physicians (Open Payments).

Jeremy L. Warner

Stock and Other Ownership Interests: HemOnc.org

Consulting or Advisory Role: Westat, IBM

Travel, Accommodations, Expenses: IBM

No other potential conflicts of interest were reported.