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OncoThreads: visualization of large-scale longitudinal cancer molecular data.

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Title: OncoThreads: visualization of large-scale longitudinal cancer molecular data.
Authors: Harbig, Theresa A, Nusrat, Sabrina, Mazor, Tali, Wang, Qianwen, Thomson, Alexander, Bitter, Hans, Cerami, Ethan, Gehlenborg, Nils
Source: Bioinformatics; 2021 Supplement, Vol. 37, pi59-i66, 8p
Subject Terms: VISUALIZATION, MEDICAL research, NUCLEOTIDE sequencing, BASIC needs, FRACTIONS, GLIOMAS, GENOMICS
Abstract: Motivation Molecular profiling of patient tumors and liquid biopsies over time with next-generation sequencing technologies and new immuno-profile assays are becoming part of standard research and clinical practice. With the wealth of new longitudinal data, there is a critical need for visualizations for cancer researchers to explore and interpret temporal patterns not just in a single patient but across cohorts. Results To address this need we developed OncoThreads , a tool for the visualization of longitudinal clinical and cancer genomics and other molecular data in patient cohorts. The tool visualizes patient cohorts as temporal heatmaps and Sankey diagrams that support the interactive exploration and ranking of a wide range of clinical and molecular features. This allows analysts to discover temporal patterns in longitudinal data, such as the impact of mutations on response to a treatment, for example, emergence of resistant clones. We demonstrate the functionality of OncoThreads using a cohort of 23 glioma patients sampled at 2–4 timepoints. Availability and implementation Freely available at http://oncothreads.gehlenborglab.org. Implemented in Java Script using the cBioPortal web API as a backend. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
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Database: Complementary Index
Description
Abstract:Motivation Molecular profiling of patient tumors and liquid biopsies over time with next-generation sequencing technologies and new immuno-profile assays are becoming part of standard research and clinical practice. With the wealth of new longitudinal data, there is a critical need for visualizations for cancer researchers to explore and interpret temporal patterns not just in a single patient but across cohorts. Results To address this need we developed OncoThreads , a tool for the visualization of longitudinal clinical and cancer genomics and other molecular data in patient cohorts. The tool visualizes patient cohorts as temporal heatmaps and Sankey diagrams that support the interactive exploration and ranking of a wide range of clinical and molecular features. This allows analysts to discover temporal patterns in longitudinal data, such as the impact of mutations on response to a treatment, for example, emergence of resistant clones. We demonstrate the functionality of OncoThreads using a cohort of 23 glioma patients sampled at 2–4 timepoints. Availability and implementation Freely available at http://oncothreads.gehlenborglab.org. Implemented in Java Script using the cBioPortal web API as a backend. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]
ISSN:13674803
DOI:10.1093/bioinformatics/btab289