The user can generate Molecular Tumor Board (MTB) reports for TCGA samples. MTB reports include a filtered list of actionable variants. To do so, it follows the following steps:
- Input SNVs, CNVs and fusions are queried against databases of actionable variants:
- Gene Drug Knowledge Database: Dienstmann et al., Cancer discovery 5.2 (2015), v20.0
- CIViC: Griffith et al., Nat Genet (2017), release 01-Mar-2020
- TARGET: Van Allen et al., Nat Med (2014), v3
- Meric-Bernstam et al., J Natl Cancer Inst. (2015)
- Matching variants are then classified into levels of evidence
- Finally, a pdf report is generated
If you use MTB report, please cite this pulication:
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. 2008 15;10(1):18. doi: 10.1186/s13073-018-0529-2.
install.packages("knitr")
install.packages("stringr")
install.packages("xtable")
install.packages("ggplot2")
install.packages("pander")
install.packages("timeSeries")
devtools::install_github("mariodeng/FirebrowseR")Requires LaTeX an Texinfo. In Linux, install them with:
sudo apt-get install texlive-full
sudo apt-get install texinfo
Open the main R script (script.r) in R or RStudio. The user can change the default patient ID (TCGA ID) to any TCGA sample which is available through Firebrowse.
This script can also be used to analyze user-defined data as long as it follows the same data structure:
| Hugo_Symbol | Variant_Classification | Protein_Change |
|---|---|---|
| EGFR | missense mutation | T790M |
| APC | nonsense mutation | K670* |
| Hugo_Symbol | CN alteration |
|---|---|
| HER2 | amplification |
| FBN3 | deletion |
Gene names must be Hugo Symbols.
Variant Classification comprises the following levels: {Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins, Missense_Mutation, Nonsense_Mutation, Silent, Splice_Site, Translation_Start_Site, Nonstop_Mutation, RNA, Targeted_Region}.
Protein Chanage must be e.g. T790M
CN alteration must be one of the foollowing levels: {amplification, deletion}_
Main script. Allows the user to filter SNVs and CNVs using gene-drug public databases. Then classifies the variants into levels of evidence and finally generates report in pdf format.
Contains the databases used to filter for actionable variants and an in-house file with cancer type equivalences between the databases
Contains four files with the helper functions used by script.r