2.5. Copy Number Variation (CNV) Analysis

The masked copy number segment file is a table that associates continuous chromosome fragments with the genome coordinates, the mean array intensity, and the number of probes bound to each fragment after removing the Y chromosome and the probes containing germline mutations (42). The heterozygosity and homozygosity of the amplification and deletion were included to evaluate the copy number alteration of each gene, of which over five percent were regarded as “high-frequency” CNVs. GISTIC2 and the R package, “maftools”, were used to identify the CNV regions and annotate the genes.