MTB-Report


An automated data integration platform for interpreting genomic data and reporting treatment options in molecular tumor boards

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Aims of this collaborative project

With growing knowledge of biomarkers and resent developments in sequencing techniques, nowaday genomic data is considered as extremely valuable and indispensable for the diagnosis and therapy recommendation particularly of tumor patients. The complexity of interpreting genomic data is hindering its application in the routine clinical context.
In the MTB-Report project the consortium aims to develop a tool to support the decision finding in a molecular tumor board (MTB). Biomarkers and other omics data from the patient will be compared to a multitude of available data bases in order to find case studies with a  parameter set equivalent to the patient’s one. Based on tumor type and certainty of the study an evidence level is assigned and used to propose the most relevant to the MTB in form a short report.

For access to the clinical data and to ensure data privacy the tool will be embedded in the IT-infrastructure. Clinical experts will define use cases for an optimal usage of the reporting tool and will validate the results.

Project partners

Department of Medical Bioinformatics (UMG)

Prof. Tim Beißbart
Dr. Jürgen Dönitz

Department of Medical Informatics

Prof Ulrich Sax

Department of Hematology and Medical Oncology

Prof. Annalen Bleckmann (now Münster University Hospital, UKM)
Dr. Raphael Koch

MTB-Report Seminar

The MTB-Report Seminar Series is a joint event of all partners and members of the MTB-Report project. Monthly, members of the different groups as well as invited speakers present their projects.

Unless announced otherwise, the seminar takes place monthly on the fourth Wednesday at 10.30am . Due to the SARS-CoV-2 related measures, the seminar takes place via video conference .

Coordination/Contact: Dr. Jürgen Dönitz 

Date: 28th of July 10.30 am

Speaker: Jingyu Yang

Topic:  DNA-seq-pipeline for molecular tumor board platform (Onkopus)

Abstract: Next-generation sequencing is empowering precision medical oncology research. Formerly, Our MTB platform (Onkopus) can only accept well-defined CSV format (CNV, SNV, Structural variants) as input. To fill the gap between raw genome sequencing data to annotated variants information. We developed a DNA sequencing analysis pipeline, It covers essential phases for full DNA-seq analyzing procedure, including quality control, alignment, raw bam preprocessing and variant discovery sessions such as SNV calling, CNV calling, and Structural variants detecting. The pipeline holds a dockerized version and can be easily customized and deployed on different systems.

Location: meet.gwdg.de/b/jue-ywf-v93

Former and upcoming Talks

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Publications

Borchert, F., Mock A., ...., Hügel J., et al.
Knowledge bases and software support for variant interpretation in precision oncology
Briefings in Bioinformatics, bbab134, 2021, 1–17
doi: https://doi.org/10.1093/bib/bbab134

Publications from preliminary work

Perera-Bel J., Leha A., Beißbarth T.
Bioinformatic Methods and  Resources for Biomarker Discovery, Validation, Development, and  Integration.
In: Badve S., Kumar G. (eds) Predictive Biomarkers in  Oncology. Springer, Cham. (2019)

Perera-Bel J, Hutter B, Heining C, Bleckmann A, Fröhlich M, Fröhling S, Glimm H, Brors B, Beißbarth T.
From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards.
Genome  Med. 2018 Mar 15;10(1):18. 
doi:10.1186/s13073-018-0529-2.

Contact data of the coordinator

Director

Prof. Dr. Tim Beißbarth

contact information

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