PURPOSE: Advances in next-generation sequencing technologies have led to a reduction in sequencing costs, which has increased the availability of genomic data sets to many laboratories. Increasing amounts of sequencing data require effective analysis tools to use genomic data for biologic discovery and patient management. Available packages typically require advanced programming knowledge and system administration privileges, or they are Web services that force researchers to work on outside servers. METHODS: To support the interactive exploration of genomic data sets on local machines with no programming skills required, we developed D3Oncoprint, a standalone application to visualize and dynamically explore annotated genomic mutation files. D3Oncoprint provides links to curated variants lists from CIViC, My Cancer Genome, OncoKB, and Food and Drug Administration-approved drugs to facilitate the use of genomic data for biomedical discovery and application. D3Oncoprint also includes curated gene lists from BioCarta pathways and FoundationOne cancer panels to explore commonly investigated biologic processes. RESULTS: This software provides a flexible environment to dynamically explore one or more variant mutation profiles provided as input. The focus on interactive visualization with biologic and medical annotation significantly lowers the barriers between complex genomics data and biomedical investigators. We describe how D3Oncoprint helps researchers explore their own data without the need for an extensive computational background. CONCLUSION: D3Oncoprint is free software for noncommercial use. It is available for download from the Web site of the Biometric Research Program of the Division of Cancer Treatment and Diagnosis at the National Cancer Institute ( https://brb.nci.nih.gov/d3oncoprint ). We believe that this tool provides an important means of empowering researchers to translate information from collected data sets to biologic insights and clinical development.
PURPOSE: Advances in next-generation sequencing technologies have led to a reduction in sequencing costs, which has increased the availability of genomic data sets to many laboratories. Increasing amounts of sequencing data require effective analysis tools to use genomic data for biologic discovery and patient management. Available packages typically require advanced programming knowledge and system administration privileges, or they are Web services that force researchers to work on outside servers. METHODS: To support the interactive exploration of genomic data sets on local machines with no programming skills required, we developed D3Oncoprint, a standalone application to visualize and dynamically explore annotated genomic mutation files. D3Oncoprint provides links to curated variants lists from CIViC, My Cancer Genome, OncoKB, and Food and Drug Administration-approved drugs to facilitate the use of genomic data for biomedical discovery and application. D3Oncoprint also includes curated gene lists from BioCarta pathways and FoundationOne cancer panels to explore commonly investigated biologic processes. RESULTS: This software provides a flexible environment to dynamically explore one or more variant mutation profiles provided as input. The focus on interactive visualization with biologic and medical annotation significantly lowers the barriers between complex genomics data and biomedical investigators. We describe how D3Oncoprint helps researchers explore their own data without the need for an extensive computational background. CONCLUSION: D3Oncoprint is free software for noncommercial use. It is available for download from the Web site of the Biometric Research Program of the Division of Cancer Treatment and Diagnosis at the National Cancer Institute ( https://brb.nci.nih.gov/d3oncoprint ). We believe that this tool provides an important means of empowering researchers to translate information from collected data sets to biologic insights and clinical development.
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Authors: Kristian Cibulskis; Michael S Lawrence; Scott L Carter; Andrey Sivachenko; David Jaffe; Carrie Sougnez; Stacey Gabriel; Matthew Meyerson; Eric S Lander; Gad Getz Journal: Nat Biotechnol Date: 2013-02-10 Impact factor: 54.908
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