GSA Illumina SNP arrays (~760 k positions) were used on tumor DNA from 473 patients in order to assess copy number alterations. We previously applied the Infinium OncoArray-500K BeadChipGenotyping arrays for the paired germline samples and used this as reference. LogR Ratio (LRR) and B-allele-fraction (BAF) were corrected and normalized using the Genotyping module from GenomeStudio 2.0 (Illumina) within each array type and all positions uniquely found in both arrays were exported for further analysis (151,291 probes). The R package ASCAT was used for segmentation of the genome and we used the raw-segmented total copy number, the raw-segmented BAF data and various empiric thresholds (gains: > 0.08, high gains: > 0.16, loss: < −0.1, high loss: < −0.2, allelic imbalance (AI): < 0.45) to identify five different types of CNAs: (1) losses associated with AI (i.e., associated with a deviation in BAF), (2) gains associated with AI, (3) high losses without AI, (4) high gains without AI and (5) AI without a change in total copy number. The applied thresholds were validated using histograms of LRR and in all diploid cases (83%), the peak for no change in copy number was within the thresholds defined for the gains/losses without deviation in BAF. Using these thresholds, subclonal events present in a minority of carcinoma cells will either not be called or instead be defined as regions with no copy number changes but with deviation in BAF (due to the higher sensitivity of the BAF measurement). Therefore, defined gains/losses are clonal events or subclonal events present in the majority of carcinoma cells.

The amount of genome in a non-normal state was calculated using the thresholds above (referred to as the CNA burden). Tumors were assigned to three genomic classes (GC1-3) of equal size based on the CNA burden to illustrate low, intermediate, and high chromosomal instability (cut-offs at the 33rd and 67th percentiles). Furthermore, based on LRR and BAF plots, we manually defined tumors as being diploid or not diploid.

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