Evidence map›Paper›PMID 34252935›Full record

ArticleBioinformatics (Oxford, England)2021

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

Theresa A Harbig, Sabrina Nusrat, Tali Mazor, Qianwen Wang, Alexander Thomson, Hans Bitter, Ethan Cerami, Nils Gehlenborg

Erratum issuedOpen access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.2field-weighted citation impact, top 51% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. ThreadStates: State-based Visual Analysis of Disease Progression.IEEE transactions on visualization and computer graphics · 2022
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors at 2 institutions in 1 country.

Theresa A HarbigDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Sabrina NusratDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Tali MazorDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Qianwen WangDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Alexander ThomsonOncology Bioinformatics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
Hans BitterOncology Bioinformatics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
Ethan CeramiDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Nils GehlenborgDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Harvard University · USDana-Farber Cancer Institute · US

Funding

Visualization of (Epi)Genomic Data for Discovery of Disease-Associated VariantsR00HG007583 · NHGRI · HARVARD MEDICAL SCHOOL · PI GEHLENBORG, NILS · 2015 to 2017
$727k
Drug Discovery & Translational Research ProgramNHGRI NIH HHS R00 HG007583NIH HHS R00 HG007583Novartis to the Dana-Farber Cancer Institute
6 · The paper itself

Abstract

motivationMolecular 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.

resultsTo 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.

Indexed as

Biochemical PhenomenaNeoplasmsGenomicsHigh-Throughput Nucleotide SequencingHumansSoftware

Identifiers

PMID34252935
PMCPMC8275328
OpenAlexW3180025521

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.