ArticleJCO clinical cancer informatics2018
D3Oncoprint: Stand-Alone Software to Visualize and Dynamically Explore Annotated Genomic Mutation Files.
Article in JCO clinical cancer informatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed, 3 citations in OpenAlex.
- Molecular genomic features associated with in vitro response of the NCI-60 cancer cell line panel to natural products.Molecular oncology · 2021Article
- D3Oncoprint: Stand-Alone Software to Visualize and Dynamically Explore Annotated Genomic Mutation Files.JCO clinical cancer informatics · 2018Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
purposeAdvances 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.
methodsTo 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.
resultsThis 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.
conclusionD3Oncoprint 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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