Somatic mutational profiling identifies aggressive and indolent disease phenotypes in well-differentiated pancreatic neuroendocrine tumors

Data Availability

Below is a breakdown of the data that this project relies upon, specifically what it represents and whether it is publicly available.

• 450-panel.txt: The gene panel used by PanOrigiMed -- 450 genes, see Table S1 of https://doi.org/10.1634/theoncologist.2019-0236
• gene_panels/: The gene panels used across cBioPortal, available through https://github.com/cBioPortal/datahub
• regional LN.csv: Supplemental data from MSK-MET, https://doi.org/10.1016/j.cell.2022.01.003
• Updated PNET case list.csv: Manually curated data regarding PNET cases gathered from individual reports

All other data is available via download from cBioPortal using the following study IDs:

• PANET ARCNET 2017: panet_arcnet_2017
• PANET JHU 2011: panet_jhu_2011
• MSK-IMPACT: msk_impact_2017
• MSK-MET: ms_met_2021
• PANET MSK ERC 2023: panet_msk_erc_2023
• PANET Shanghai: panet_shanghai_2013
• PCAWG: pancan_pcawg_2020
• MET500: metastatic_solid_tumors_mich_2017
• OrigiMed: pan_origimed_2020

System Requirements

Software Dependencies

This project uses renv for dependency management. It should be sufficient to first install renv from within an R console:

install.packages("renv")

Then to install all dependencies, from an R console in the root of this project:

renv::restore()

This will install the specified versions of dependencies as listed in the renv.lock file, placing them in a directory under renv/library/ -- which will often be loaded by default upon opening the RProject, but can be forced via source("renv/activate.R") from within an R console. The dependency installation process can take up to an hour if compiling all dependencies from source, but typically takes less than 30 minutes.

Operating Systems

This project has been successfully run on Windows, Linux (Ubuntu family), and MacOS (Intel based) distributions.

Hardware

No non-standard hardware is required to run this project.

Running the Project

If you have RStudio installed, you can double-click the PNET_somatic_mutations.Rproj file to open the project from your file manager. Once the project is open in RStudio, open the wgd_disparities.Rmd file. Just above where the file opens there will be a button labeled Knit -- clicking this button will run the code and produce an HTML report called wgd_disparities.html. Open this report in your preferred web browser to read the report. Running the project can take 20-40 minutes on a normal desktop computer.