Bioinformatic analyses
tumor, TCGA
TUMOR, POINT MUTATION
Point mutations, small indels and CNAs were detected using an end-to-end pipeline described previouslyCNAs, tumor purity and average tumor ploidy were identified with the FACETS R package version 0.5.14 (ref. Patient and sample attributes for the TCGA cohort were downloaded from the GDC data portal (gdc-tcga-phs000178-controlled) using the R package GenomicDataCommons version 1.18.0 and from the supplementary tables publicly available on the PanCanAtlas page (