An elevated rate of whole-genome duplications in cancers from Black patients

This repository represents the computational analysis for the investigation of WGD racial disparities as conducted in the Sheltzer Lab. This work was published as:

Brown, L.M., Hagenson, R.A., Koklič, T. et al. An elevated rate of whole-genome duplications in cancers from Black patients. Nat Commun 15, 8218 (2024). https://doi.org/10.1038/s41467-024-52554-5

Data Availability

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

• impact-505.csv: Contains the HUGO symbols for the IMPACT-505 geneset, publicly available
• MSK-WGD.csv: WGD data from the original cohort study, publicly available
• msk-met-cell2022-ancestry.tsv: Ancestry determinations for MSK-MET patients following the method of Arora, et al. (2022), data provided by Kanika Arora
• regionalLN.csv: Metastasis data from Nguyen, et al. (2022), publicly available
• cBioPortal data for MSK-MET: mutational, copy number, sample, and patient data that is publicly available from cBioPortal under project msk_met_2021
• pancan_pcawg_2020_clinical_data.csv: Clinical data for PCAWG, publicly available
• TCGA_Demographics.csv and TCGA_arm_scores.csv: Clinical and aneuploidy data for TCGA, publicly available

Copies of these data are available in the data.zip file in this repository.

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 wgd_disparities.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.