4.10. Analysis of Copy Number Variation from WES
BAM files were pre-processed to remove duplicates and PCR artifacts using the Picard Tool function MarkDuplicates before being imported into Nexus Copy NumberTM software (version 8.0, BioDiscovery, El Segundo, CA, USA) for CNA analysis. For each sample analyzed, the matched normal DNA from blood samples derived from the same patients was used in the ngCGH (matched) processing according to the software instructions. Systematic GC wave correction was applied using Quadratic Correction. The robust variance sample quality score threshold was ≤0.2. Numerical CNAs (involving the whole chromosome arm) were manually assessed, while focal CNAs were identified by the GISTIC test (see 