rootchang / Aneuploidy-FGA-ICB

Aneuploidy-FGA-ICB

Test predictive power of tumor aneuploidy and fraction of copy-number alterations in prediction of patient overall survival after immunotherapy in different cancer types.

Usage

1. Download data (folder "tmb_mskcc_2018") for the Samstein et al. cohort at https://www.cbioportal.org/study/summary?id=tmb_mskcc_2018.
2. Download the GENIE v.7.1 release ("genie_data_cna_hg19.seg") at https://www.synapse.org/#!Synapse:syn7222066/wiki/405659.
3. Download data ("41587_2021_1070_MOESM3_ESM.xlsx") for the Chowell et al. cohort at https://static-content.springer.com/esm/art%3A10.1038%2Fs41587-021-01070-8/MediaObjects/41587_2021_1070_MOESM3_ESM.xlsx.
4. Download this GitHub project and run the R Markdown pipeline (and the python code for elbow method analysis).

Support or Contact

[e-mail]