qanpcrt
Quality Assurance of Nasopharyngeal Cancer Radiation Therapy Targets (CTV's) using a novel web-based quality assurance application
Science Score: 51.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: medrxiv.org -
✓Committers with academic emails
2 of 2 committers (100.0%) from academic institutions -
○Institutional organization owner
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Low similarity (11.6%) to scientific vocabulary
Keywords
Repository
Quality Assurance of Nasopharyngeal Cancer Radiation Therapy Targets (CTV's) using a novel web-based quality assurance application
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- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
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Metadata Files
README.md
Quality Assurance of Nasopharyngeal Cancer Radiation Therapy Targets (CTV's) using a novel web-based quality assurance application
MedRxiv submission "Development of web-based quality-assurance tool for radiotherapy target delineation for head and neck cancer: quality evaluation of nasopharyngeal carcinoma"
Clinical Acceptability Testing Web Application
QUANNOTATE (Web App) (GitHub)
Code Ocean Capsule
This Code Ocean compute capsule will allow you to reproduce the results published by the author on your local machine1. Follow the instructions below, or consult our knowledge base for more information. Don't hesitate to reach out via live chat or email if you have any questions.
1 You may need access to additional hardware and/or software licenses.
Prerequisites
- Docker Community Edition (CE)
- MATLAB/MOSEK/Stata licenses where applicable
Instructions
The computational environment (Docker image)
This capsule is private and its environment cannot be downloaded at this time. You will need to rebuild the environment locally.
If there's any software requiring a license that needs to be run during the build stage, you'll need to make your license available. See our knowledge base for more information.
In your terminal, navigate to the folder where you've extracted the capsule and execute the following command:
shell
cd environment && docker build . --tag 556c150d-cc06-4333-b25f-4ab024bb5ba9; cd ..
This step will recreate the environment (i.e., the Docker image) locally, fetching and installing any required dependencies in the process. If any external resources have become unavailable for any reason, the environment will fail to build.
Running the capsule to reproduce the results
In your terminal, navigate to the folder where you've extracted the capsule and execute the following command, adjusting parameters as needed:
shell
docker run --rm \
--workdir /code \
--volume "$PWD/data":/data \
--volume "$PWD/code":/code \
--volume "$PWD/results":/results \
556c150d-cc06-4333-b25f-4ab024bb5ba9 ./run
Owner
- Name: BHKLAB
- Login: bhklab
- Kind: organization
- Location: Toronto, Ontario, Canada
- Website: http://www.pmgenomics.ca/bhklab/
- Repositories: 168
- Profile: https://github.com/bhklab
The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre
Citation (citation.bib)
@article {Kim2021.02.24.21252123,
author = {Kim, Jun Won and Marsilla, Joseph and Kazmierski, Michal and Tkachuk, Denis and Huang, Shao Hui and Xu, Wei and Cho, John and Ringash, Jolie and Bratman, Scott and Haibe-Kains, Benjamin and Hope, Andrew},
title = {Development of web-based quality-assurance tool for radiotherapy target delineation for head and neck cancer: quality evaluation of nasopharyngeal carcinoma},
elocation-id = {2021.02.24.21252123},
year = {2021},
doi = {10.1101/2021.02.24.21252123},
publisher = {Cold Spring Harbor Laboratory Press},
abstract = {Purpose We developed QUANNOTATE, a new web-application for rapid review of radiotherapy (RT) target volumes, and used it to evaluate the relationship between target delineation compliance with the international guidelines and treatment outcomes in nasopharyngeal carcinoma (NPC) patients undergoing definitive RT.Methods and Materials The dataset used for this study consists of anonymized CT simulation scans, RT structures, and clinical data of 332 pathologically confirmed NPC patients treated with intensity-modulated RT between July 2005 and August 2017. We imported the contours of intermediate risk clinical target volumes of the primary tumor (IR-CTVp) receiving 56 Gy into QUANNOTATE. We determined inclusion of anatomic sites within IR-CTVp in accordance with 2018 International guideline for CTV delineation for NPC and correlated the results with time to local failure (TTLF) using Cox-regression.Results At a median follow-up of 5.6 years, 5-year TTLF and overall survival rates were 93.1\% and 85.9\% respectively. The most frequently non-guideline compliant anatomic sites were sphenoid sinus (n = 69, 20.8\%), followed by cavernous sinus (n = 38, 19.3\%), left and right petrous apices (n = 37 and 32, 11.1\% and 9.6\%), clivus (n = 14, 4.2\%), and right and left foramen rotundum (n = 14 and 12, 4.2\% and 3.6\%). Among 23 patients with a local failure (6.9\%), the number of non-compliant cases were 8 for sphenoid sinus, 7 cavernous sinus, 4 left and 3 right petrous apices, and 2 clivus. Compared to conforming cases, cases which did not contour the cavernous sinus had a higher local failure (LF) rate (89.1\% vs 93.6\%, p= 0.013). Multivariable analysis confirmed that lack of cavernous sinus contouring was prognostic for LF.Conclusions QUANNOTATE allowed rapid review of target volumes in a large patient cohort. Despite an overall high compliance with the international guidelines, undercoverage of the cavernous sinus was correlated with LF.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThis work was supported by Canadian Institutes of Health Research (CIHR) Project $\#$426366 and the National Research Foundation of Korea (NRF) grant funded by the Korean Government Ministry of Science and ICT (NRF-2020R1A2C1102559).Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:This study was approved by the Health Canada and Public Health Agency of Canada (PHAC) Research Ethics Board (REB, approval $\#$17-5871).All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesThe web-based application, QUANNOTAE, is available at https://www.quannotate.com, and all preprocessing scripts used to build the application are available at https://github.com/bhklab/quannotate. https://github.com/bhklab/quannotate https://www.quannotate.com},
URL = {https://www.medrxiv.org/content/early/2021/02/26/2021.02.24.21252123},
eprint = {https://www.medrxiv.org/content/early/2021/02/26/2021.02.24.21252123.full.pdf},
journal = {medRxiv}
}
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Top Committers
| Name | Commits | |
|---|---|---|
| jmarsill | j****a@m****a | 2 |
| Benjamin Haibe-Kains | b****s@u****a | 1 |
Committer Domains (Top 20 + Academic)
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