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. Author manuscript; available in PMC: 2023 Feb 3.
Published in final edited form as: Cell. 2022 Feb 3;185(3):563–575.e11. doi: 10.1016/j.cell.2022.01.003

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Biological Samples
Human tumor and matched normal samples (blood) This paper N/A
Deposited Data
Clinical data, including metastatic events at the patient level is deposited for visualization, and download in the cBioPortal for Cancer Genomics. This paper https://www.cbioportal.org/study?id=msk_met_2021 https://doi.org/10.5281/zenodo.5801902
Targeted DNA sequencing This paper https://doi.org/10.5281/zenodo.5801902
Software and Algorithms
ASCETS Spurr et al., 2020 https://github.com/beroukhim-lab/ascets
BradleyTerryScalable Kaye and Firt, 2020 https://github.com/EllaKaye/BradleyTerryScalable
brglm Kosmidis and Firth, 2020 https://cran.r-project.org/web/packages/brglm/index.html
cBioPortal Cerami et al., 2012 https://www.cbioportal.org/
CNtools Jianhua Zhang, 2018 https://bioconductor.org/packages/release/bioc/html/CNTools.html
FACETS Shen and Seshan, 2016 https://github.com/mskcc/facets-suite
MSIsensor Niu et al., 2014 https://github.com/ding-lab/msisensor
MutSigCV Lawrence et al. 2014 https://github.com/genepattern/MutSigCV
OncoKB Chakravarty et al., 2017 https://github.com/oncokb/oncokb
organ-site-mapping This paper https://github.com/clinical-data-mining/organ-site-mapping https://doi.org/10.6084/m9.figshare.17118848.v1
R (v3.5.2) R CRAN https://cran.r-project.org/
survival The R Foundation https://cran.r-project.org/web/%20packages/survival/index.html