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Winners Announced for the 2015 DCEG Informatics Tool Challenge

Nine winners have been announced for the 2015 DCEG Informatics Tool Challenge. The competitive funding challenge, inaugurated in 2014, was conceived by DCEG Director Stephen J. Chanock, M.D. “We were pleased to receive so many compelling submissions for this years’ challenge,” said Dr. Chanock. “The winning ideas include expansions on last year’s successful submissions, as well as novel approaches to improve, enhance, or streamline epidemiological methods, data collection, analysis, and the critical component of managing the scientific process. I expect the entire Division to benefit from these remarkable innovations.”

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Proposals were evaluated for their innovative use of current technologies to address a specific research need, the ability for the project to be completed within one year of initiation, and the cost, which was not to exceed $20,000.

NCI’s Center for Biomedical Informatics and Information Technology (CBIIT) is providing technical support for four of the projects, NIH’s Center for Information Technology (CIT) is collaborating on one project researchers from the International Agency for Research on Cancer are collaborators on another, and contractors are providing support for two others. Researchers from DCEG and the NCI Division of Cancer Control and Population Sciences (DCCPS) and the Division of Cancer Prevention (DCP) are working together on one of the projects.

Out of 13 proposals that were submitted, the nine described below were selected for funding.

The DCEG Review Navigator

Amy Berrington de González, Annelie Landgren, Jenna Nober, Geoffrey Tobias, Alyssa Voss (DCEG)

This web-based tool will guide DCEG investigators on the reviews necessary when submitting requests for scientific study proposals, research conducted with non-DCEG funds, support service contracts, and workshops/meetings. After users answer a series of questions about the project, the Navigator generates a customized review roadmap for the proposal and a checklist or routing document with links to the applicable review committee materials.

Web-based Code and Template Repository

Elizabeth Cahoon, Lienard Chang, Wayne Liu, Dayton McMillan (DCEG)

This repository will facilitate the reuse of code, improving the efficiency and quality assurance of programming tasks performed by DCEG fellows and investigators, and enhancing integration among working groups. By re-using code, programmers will be able to reduce redundancy by taking advantage of assets that have already been created in some form by others.

SOCAssign: Companion Software to Aid Expert Coders in Manual Review of Standardized Occupation Codes Assigned by SOCcer, a Computerized Coding Algorithm

Melissa Friesen (DCEG); Sue Pan, Carl McCabe (CBIIT); Daniel Russ, Calvin Johnson (NIH/CIT)

To facilitate the incorporation of occupational risk factors into large-scale epidemiological studies, DCEG recently developed the SOCcer algorithm (http://soccer.nci.nih.gov), which automatically assigns standardized occupation classification codes based on job descriptions. Manual review of some SOCcer-assigned codes remains necessary, however, and the SOCAssign companion tool will aid coders in selecting appropriate occupation codes during this manual review. SOCAssign will be made freely available for download to users of the SOCcer website.

Automating and Securing Remote Data Transfer on a Smartphone-based Time and Activity Log Application for Characterizing Temporal and Geospatial Variability in Exposure-related Activities

Sarah Locke, Jonathan Hofmann, Michael Alavanja, Laura Beane Freeman, Melissa Friesen (DCEG); James McClain (DCCPS); Heather Bowles (DCP)

Researchers from DCEG’s Occupational and Environmental Epidemiology Branch, DCCPS, and DCP will enhance the data transfer and security capabilities of the “Life in a Day” smartphone application for collecting exposure-related information reported by participants in epidemiological studies. DCCPS and DCP researchers developed “Life in a Day” to collect information on daily risk factor-related activity, but the original application required users to manually email data files to investigators following study completion. The enhanced version will automatically authenticate and transfer data from the mobile user to an NCI exchange portal over a secure network connection.

The Polyphenol Enriched Resource for Coffee (PERC) Software Application and Database

Erikka Loftfield, Neal D. Freedman, Rashmi Sinha, Joshua Sampson (DCEG); Joe Rothwell, Augustin Scalbert (International Agency for Research on Cancer); Adam Risch, Adam Vaughn (IMS)

The PERC software application and complementary database will help researchers quantify bioactive compounds in coffee and better understand the mechanisms by which coffee compounds may alter risk of cancer and other chronic diseases. Researchers with data on coffee brew method and caffeine type will be able to use the software to investigate coffee-related hypotheses. They will also be able to assess the production and preparation variables that affect the chemical composition of a cup of coffee in future large population studies.

A General Purpose Web Tool for Evaluating Absolute Risk

Paige Maas, Nilanjan Chatterjee (DCEG); Sue Pan, Carl McCabe (CBIIT)

Evaluation of absolute risk is critical for assessing the impact of etiologic findings for translational research. This web tool, which uses a general-purpose R program developed by Dr. Maas, gives researchers the ability to create absolute risk models for any disease outcome, calibrated to any particular population and based on any desired set of risk factors.

LDlink 2.0: SNPclip, SNPchip, and Expanded LDlink Options

Mitchell Machiela (DCEG)

DCEG recently launched LDlink, a tool to simplify the task of finding correlated alleles of SNPs in high linkage disequilibrium. LDlink was a winning proposal in last year’s Informatics Tool Challenge, and LDlink 2.0 will expand user options and add new functionality with the SNPclip module for variant LD thinning that references publically available data from the 1000 Genomes Project and the SNPchip module for finding commercial array genotyping platforms.

Moles, Dysplastic Nevi and Melanoma: A Recognition Tool

Geoffrey Tobias, Mary Fraser, Margaret Tucker (DCEG)

This web tool will be developed to help educate patients, non-dermatology healthcare workers, and the general public on how to recognize dysplastic nevi (DN), important risk markers and precursor lesions for melanomas, and melanomas arising from DN. The tool will include photographs of lesions from protocol patients that illustrate phases in the spectrum of the natural history of normal nevi and DN.

A Web Tool for Conducting Pathway Analysis Using Summary Data from GWAS

Han Zhang, Jianxin Shi, Nilanjan Chatterjee, Kai Yu (DCEG); Bill Wheeler (IMS); Sue Pan, Carl McCabe (CBIIT)

This easy-to-use web tool will allow a wider range of researchers to explore various disease-pathway associations using summary results from genome-wide association studies (GWAS). The tool will not require R programming experience or the large computing resources that are necessary with current pathway analysis software. Instead, an investigator will be able to take advantage of the computing resources at the NCI and evaluate an association between a candidate pathway and a disease outcome using the web tool’s simple inputs.