Cargando…
OncoThreads: visualization of large-scale longitudinal cancer molecular data
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 visualizatio...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275328/ https://www.ncbi.nlm.nih.gov/pubmed/34252935 http://dx.doi.org/10.1093/bioinformatics/btab289 |
_version_ | 1783721690779353088 |
---|---|
author | Harbig, Theresa A Nusrat, Sabrina Mazor, Tali Wang, Qianwen Thomson, Alexander Bitter, Hans Cerami, Ethan Gehlenborg, Nils |
author_facet | Harbig, Theresa A Nusrat, Sabrina Mazor, Tali Wang, Qianwen Thomson, Alexander Bitter, Hans Cerami, Ethan Gehlenborg, Nils |
author_sort | Harbig, Theresa A |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8275328 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-82753282021-07-13 OncoThreads: visualization of large-scale longitudinal cancer molecular data Harbig, Theresa A Nusrat, Sabrina Mazor, Tali Wang, Qianwen Thomson, Alexander Bitter, Hans Cerami, Ethan Gehlenborg, Nils Bioinformatics Biomedical Informatics 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. Oxford University Press 2021-07-12 /pmc/articles/PMC8275328/ /pubmed/34252935 http://dx.doi.org/10.1093/bioinformatics/btab289 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Biomedical Informatics Harbig, Theresa A Nusrat, Sabrina Mazor, Tali Wang, Qianwen Thomson, Alexander Bitter, Hans Cerami, Ethan Gehlenborg, Nils OncoThreads: visualization of large-scale longitudinal cancer molecular data |
title | OncoThreads: visualization of large-scale longitudinal cancer molecular data |
title_full | OncoThreads: visualization of large-scale longitudinal cancer molecular data |
title_fullStr | OncoThreads: visualization of large-scale longitudinal cancer molecular data |
title_full_unstemmed | OncoThreads: visualization of large-scale longitudinal cancer molecular data |
title_short | OncoThreads: visualization of large-scale longitudinal cancer molecular data |
title_sort | oncothreads: visualization of large-scale longitudinal cancer molecular data |
topic | Biomedical Informatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275328/ https://www.ncbi.nlm.nih.gov/pubmed/34252935 http://dx.doi.org/10.1093/bioinformatics/btab289 |
work_keys_str_mv | AT harbigtheresaa oncothreadsvisualizationoflargescalelongitudinalcancermoleculardata AT nusratsabrina oncothreadsvisualizationoflargescalelongitudinalcancermoleculardata AT mazortali oncothreadsvisualizationoflargescalelongitudinalcancermoleculardata AT wangqianwen oncothreadsvisualizationoflargescalelongitudinalcancermoleculardata AT thomsonalexander oncothreadsvisualizationoflargescalelongitudinalcancermoleculardata AT bitterhans oncothreadsvisualizationoflargescalelongitudinalcancermoleculardata AT ceramiethan oncothreadsvisualizationoflargescalelongitudinalcancermoleculardata AT gehlenborgnils oncothreadsvisualizationoflargescalelongitudinalcancermoleculardata |