Molecular Tumor Board Report

- Tool to browse clinically actionable variants of cancer patients -

developed by Nadine S. Kurz, Júlia Perera-Bel, Charlotte Höltermann, Tim Tucholski, Jingyu Yang, Tim Beißbarth and Jürgen Dönitz



1. Upload of the patient's somatic variants (SNVs , CNVs, fusions)



2. Public databases are browsed for clinically actionable somatic variants by the tool



3. The patient-specific results are shown in the web interface for further processing.

Additionally, pdf reports and other formats can be downloaded

MTB Report information

The Molecular Tumor Board Report (MTB Report) is a tool designed to bring together all efforts and knowledge on predictive biomarkers. The tool is oriented at identifying actionable somatic variants of a patient's genomic profile.
More detailed information about the method can be found in our publication (Perera-Bel et al., 2018).

Supplementary Information

Additional information and example data files can be found in the download section. Download MTB Report Docker image here.

Current databases supported:

Loaded Databases:
  • CIViC: date: Griffith et al. Nat Genet (2017), version: 10.1038/ng.3774
  • GDKD: date: Dienstmann et al. Cancer discovery 5.2 (2015) v20.0, version: 10.1158/2159-8290.CD-14-1118
  • OncoKB date: Chakravarty et al. JCO Precis Oncol. (2017), version: 10.1200/PO.17.00011

Generate MTB-Report of user defined data

Upload file with Single Nucleotide Variants (SNVs). Check CSV format here
For SNVs, MAF (Mutation Annotation Format) and VCF (Variant Call Format) files are also accepted.

This tool does not check the quality of the variants, so please make sure they are validated and fullfilling your own requirements
File extensions accepted are: .xls, .xlsx, .csv, .dat, .tsv, .maf, .vcf
Upload file with Copy Number Variations (CNVs). Check CSV format here

This tool does not check the quality of the variants, so please make sure they are validated and fullfilling your own requirements
File extensions accepted are: .xls, .xlsx, .csv, .dat, .tsv
Mandatory columns: Gene Symbol, variant type
Upload file with fusions. Check CSV format here

This tool does not check the quality of the variants, so please make sure they are validated and fullfilling your own requirements
File extensions accepted are: .xls, .xlsx, .csv, .dat, .tsv
Single nucleotide variants of the patient's tumor:

Copy number variants of the patient's tumor:

Gene fusions of the patient's tumor:

2. If the genomic data looks correct, launch the MTB report by clicking the button:

Browse clinically relevant genomic data of the selected patient:

You can now explore the filtered variants divided into 6 levels of evidence, which determine the actionability of the variant.
You can also download a .pdf or .csv report with the results. For more information on the method we forward you to our publication.

Summary of Actionable Variants: Filter & Selection

Select Actionable Variants


Select Levels of Evidence

Evidence on SAME cancer type
Evidence on OTHER cancer types


Download results
Download report (.pdf)
Download report (.csv)
Download metadata (.yml)

Details of Actionable Variants


Explore the Cancer Genome Atlas Dataset


1. You can browse up to 34 cancer cohorts. Data is dowloaded using the FirebrowseR package (R client for Broad Firehose Web API)

  • TCGA
  • Select Patient
Please select one cohort from the list below:
Please select one row from the table to explore its clinically relevant data:
Single nucleotide variants of the patient's tumor:
Copy number variants of the patient's tumor:
Main clinical features of the patient's tumor:

2. The tool will search in public databases for clinically relevant information. To see the results, launch the MTB report by pressing the button below.
After selecting another patient, please remember to refresh the results by pressing the button again.





Browse clinically relevant genomic data of the selected patient:

You can now explore the filtered variants divided into 6 levels of evidence, which determine the actionability of the variant.
You can also download a .pdf or .csv report with the results. For more information on the method we forward you to our publication.



Imprint

Provider Information
Department of Medical Bioinformatics, University Medical Center Göttingen
Goldschmidtstraße 1
37077 Göttingen
Germany

Website: https://bioinformatics.umg.eu

Responsible for Content (as per § 18 Abs. 2 MStV)
Prof. Tim Beißbarth
Goldschmidtstraße 1
37077 Göttingen
Germany

Phone: +49 551 3961782

Data Privacy

1. General Information
We take the protection of your personal data very seriously. This data privacy statement explains how we collect, process, and use your data when you use our website and web application. All data processing activities are carried out in compliance with the General Data Protection Regulation (GDPR) and other applicable laws.

2. Data protection officer
The legal bases for the data protection are the General Data Protection Regulation (GDPR), the Federal Data Protection Act (BDSG), the Lower Saxony Data Protection Act (NdsDSG) and the Telemedia Act (TMG). The UMG declares that it complies with the applicable laws, in particular when processing personal data.

The UMG Data Protection Officer can be contacted at:
Universitätsmedizin Göttingen
- Datenschutzbeauftragter -
37099 Göttingen
Germany
Email:
Phone: +49 (0)551 3922762

3. Data We Collect
When you use our web application, the following types of data may be collected:
  • Uploaded data: Data files you upload within the application.
  • Technically required data.
  • Cookies: Small files stored on your device to enhance the functionality and usability of the website. See section 9 for more information on cookies.
4. Purpose of Data Processing
We collect and process your data for the following purposes: To provide and operate the web application. To enable data uploads and ensure secure storage. To respond to user inquiries and provide customer support. To analyze usage trends and improve the website’s functionality. To comply with legal obligations, including data retention requirements.

5. Legal Basis for Processing
The legal basis for processing your data depends on the purpose:
  • Consent (Article 6(1)(a) GDPR): For processing activities where you explicitly grant permission.
  • Performance of a Contract (Article 6(1)(b) GDPR): For providing the requested services.
  • Legitimate Interests (Article 6(1)(f) GDPR): For analytics and improving our services.
  • Legal Obligation (Article 6(1)(c) GDPR): To comply with applicable laws and regulations.
6. Technically required data
When you visit our website, we collect the following data, which is technically necessary for us to ensure the functionality of the website, as well as the stability and security of our information technology systems and to enable optimization of the website:

  • IP address
  • Date and time of access to this website
  • Time zone difference to Greenwich Mean Time(GMT)
  • Access status/HTTP status code
  • Amount of data transferred in each case
  • Browser type
  • Operating system
  • Language and version of the browser software
7. Recipients of personal data
MTB-Report is hosted on our own servers. All data collected is processed locally on our servers within the Department of Medical Bioinformatics, UMG.
Uploaded files are processed securely and are accessible only to authorized personnel. We will not access or use your uploaded data for purposes other than providing the service unless required by law. Please ensure that you do not upload sensitive data.

8. Data Sharing
We will not share your personal data with third parties.

9. Cookies and Analytics
We use the web analysis tool Matomo to enhance the functionality and usability of our website. You can configure your browser to reject cookies or notify you when cookies are being set. We may also use analytics tools to understand user behavior and improve the website. These tools anonymize data where possible.

10. Your Rights
You have the following rights regarding the processing of your personal data:
  • Right to access (Article 15 GDPR).
  • Right to rectification (Article 16 GDPR).
  • Right to erasure ("right to be forgotten") (Article 17 GDPR).
  • Right to restriction of processing (Article 18 GDPR).
  • Right to data portability (Article 20 GDPR).
  • Right to object to processing (Article 21 GDPR).
  • Right to withdraw consent (Article 7(3) GDPR).
To exercise these rights, please contact the UMG data protection officer. You also have the right to lodge a complaint with a supervisory authority.

11. Data Retentions and Data Security
Uploaded data will be stored for the duration of your use of the application unless otherwise specified. Uploaded files are automatically deleted after 72 hours. We implement technical and organizational measures to ensure the security of your data and protect it against unauthorized access, alteration, disclosure, or destruction.

12. Changes to This Privacy Policy
We may update this privacy policy from time to time. The latest version will always be available on our website.

Disclaimer

Disclaimer: This resource is intended for research use only. It should not be used for medical or professional advice. We make no guarantee regarding comprehensiveness, accuracy or reliability of the content on this site. By using this site, you assume full responsibility for all risks associated with this.

1. General Information
The information provided on this web application is for general informational purposes only. While we strive to ensure that all content is accurate and up-to-date, we make no representations or warranties of any kind, express or implied, about the completeness, accuracy, reliability, suitability, or availability with respect to the website or the information, services, or related graphics contained on the website for any purpose. Any reliance you place on such information is strictly at your own risk.

2. Limitation of Liability
We make every effort to keep the information on our website up to date. However, we do not accept liability for the content provided. According to § 7 Abs. 1 TMG, we are responsible for our own content on these pages under general law. According to §§ 8 to 10 TMG, we are not obligated to monitor third-party information provided or stored on our website or to investigate circumstances indicating illegal activity. Obligations to remove or block the use of information under general law remain unaffected.
We are not liable for any loss or damage, including but not limited to direct, indirect, incidental, consequential, or punitive damages, arising from the use of this web application or the inability to use it, even if advised of the possibility of such damages. This includes, without limitation, damages resulting from:

Errors, omissions, or inaccuracies in the content. Downtime or interruptions of service. Loss of data due to uploads, misuse, or errors. Unauthorized access to or alteration of your data.

3. Uploaded Data
By using the upload feature in this web application, you confirm that you have the legal right to use and upload the data. We are not responsible for the content you upload or any legal consequences that arise from the upload or use of such data. Users are solely responsible for ensuring that their data complies with applicable laws and does not infringe on the rights of third parties.

4. External Links
MTB-Report may contain links to external websites that are not controlled or operated by us. We have no control over the content or practices of these external websites and accept no responsibility or liability for them. The inclusion of any links does not necessarily imply a recommendation or endorse the views expressed within them.

5. No Guarantee of Availability
We do not guarantee that the web application will always be available, uninterrupted, or free of errors. Maintenance, updates, or technical issues may temporarily affect availability, and we reserve the right to modify, suspend, or discontinue the web application at any time without notice.

6. Intellectual Property
All intellectual property rights related to this web application, including text, images, logos, and software, remain the property of their respective owners. Unauthorized use, reproduction, or distribution of any content from this application is prohibited and may result in legal action.

7. Changes to the Disclaimer
We reserve the right to update this disclaimer at any time. Users are encouraged to review the disclaimer periodically to stay informed of any changes.

License

This web application and its content are licensed under the Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0).

1) You are free to:

  • Share: Copy and redistribute the material in any medium or format.
  • Adapt: Remix, transform, and build upon the material for any purpose, even commercially.
2) Under the following terms:

  • Attribution: You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
  • ShareAlike: If you remix, transform, or build upon the material, you must distribute your contributions under the same license as the original.
No additional restrictions: You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.

Disclaimer:
This license does not apply to:
Third-party content included in the web application, which may be subject to other licenses or permissions.
User-uploaded data, which remains the property of the respective user or third-party owner.

For the full legal text of the Creative Commons Attribution-ShareAlike 4.0 International License .