A total of 31 kidney cancer samples (KIRC) from the Firehose database on GDC’s TCGA were selected based on the status of their VHL-coding region on the short arm of chromosome 3 (3p). All 31 samples were selected to contain deep 3p deletions associated with clear cell renal cell carcinomas. The corresponding Illumina 450k BeadChip IDAT files were downloaded from TCGA. A further 50 low-grade glioma (LGG), subtype oligodendroglioma, samples were also downloaded from the Firehose database. Twenty-five samples are histologically defined oligodendrogliomas and contained codeletion of the short arm of chromosome 1 and the long arm of chromosome 19 (1p/19q), and the other twenty-five samples were astrocyte-like oligodendrogliomas that were copy-number neutral in these regions (Li et al., 2016 (link)). The Affymetrix SNP Array 6.0 (“gold standard”) copy number segmentation data corresponding to the above data was also downloaded from TCGA.
All testing was performed on a Dell Precision 5,820 Tower X-series workstation running Windows 10 Pro 64bit and R 4.1.2. 128 GB of useable RAM and an Intel(R) Core(TM) i9-10900X CPU x64 processor @ 3.70 GHz. All analyses were performed only using a single core as some packages set multiple cores for the analysis; we wanted to ensure equal computational resources were allocated for each routine.
All testing was performed on a Dell Precision 5,820 Tower X-series workstation running Windows 10 Pro 64bit and R 4.1.2. 128 GB of useable RAM and an Intel(R) Core(TM) i9-10900X CPU x64 processor @ 3.70 GHz. All analyses were performed only using a single core as some packages set multiple cores for the analysis; we wanted to ensure equal computational resources were allocated for each routine.
